PDB-8tlh: CDCA7 (Mouse) Binds Non-B-form 32-mer DNA oligo

ID or keywords:

Entry

Database: PDB / ID: 8tlh

Title

CDCA7 (Mouse) Binds Non-B-form 32-mer DNA oligo

Components

Cell division cycle-associated protein 7
DNA (32-MER)

Keywords

DNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN / zinc fingers / chromatin architecture / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

regulation of cell population proliferation / regulation of DNA-templated transcription / apoptotic process / nucleoplasm / nucleus / cytosol
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.94 Å

Authors

Horton, J.R. / Ren, R. / Cheng, X.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM049245-23	United States
Cancer Prevention and Research Institute of Texas (CPRIT)	RR160029	United States

Citation

Journal: Biorxiv / Year: 2023
Title: The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA.
Authors: Hardikar, S. / Ren, R. / Ying, Z. / Horton, J.R. / Bramble, M.D. / Liu, B. / Lu, Y. / Liu, B. / Dan, J. / Zhang, X. / Cheng, X. / Chen, T.

History

Deposition	Jul 26, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tlh.cif.gz	211.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8tlh.ent.gz	135.4 KB	Display	PDB format
PDBx/mmJSON format	8tlh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tlh_validation.pdf.gz	474.2 KB	Display	wwPDB validaton report
Full document	8tlh_full_validation.pdf.gz	476.8 KB	Display
Data in XML	8tlh_validation.xml.gz	13.6 KB	Display
Data in CIF	8tlh_validation.cif.gz	18.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tl/8tlh ftp://data.pdbj.org/pub/pdb/validation_reports/tl/8tlh	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Cell division cycle-associated protein 7

X: DNA (32-MER)

B: Cell division cycle-associated protein 7

C: DNA (32-MER)

hetero molecules

53.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cell division cycle-associated protein 7

X: DNA (32-MER)

hetero molecules

A: Cell division cycle-associated protein 7

X: DNA (32-MER)

hetero molecules

defined by author&software
53.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cell division cycle-associated protein 7

C: DNA (32-MER)

hetero molecules

B: Cell division cycle-associated protein 7

C: DNA (32-MER)

hetero molecules

defined by author&software
53.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	169.679, 31.523, 91.634
Angle α, β, γ (deg.)	90.000, 110.590, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	X-103- MG

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Protein / DNA chain , 2 types, 4 molecules ABXC

#1: Protein	Cell division cycle-associated protein 7 Mass: 16452.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdca7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codon-plus (DE3)-RIL / References: UniProt: Q9D0M2
#2: DNA chain	DNA (32-MER) Mass: 9850.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: n vitro SELEX screening / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 5 types, 138 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.59 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M MgCl2, 0.1 M Tris pH8.5 and 25 % PEG3350.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.94→39.71 Å / Num. obs: 29047 / % possible obs: 84.8 % / Redundancy: 5.2 % / B_iso Wilson estimate: 41.67 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.08 / R_pim(I) all: 0.035 / Net I/σ(I): 17.8
Reflection shell	Resolution: 1.94→2.02 Å / R_merge(I) obs: 0.678 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1162 / CC_1/2: 0.723 / R_pim(I) all: 0.464

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Processing

Software

Name	Version	Classification
SERGUI		data collection
PHENIX	1.20.1_4487	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.94→39.71 Å / SU ML: 0.221 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2266	1454	5.01 %
R_work	0.1991	27593	-
obs	0.2005	29047	84.18 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 66.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.94→39.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1622	1306	44	122	3094

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	3155
X-RAY DIFFRACTION	f_angle_d	0.5364	4531
X-RAY DIFFRACTION	f_chiral_restr	0.0361	495
X-RAY DIFFRACTION	f_plane_restr	0.005	366
X-RAY DIFFRACTION	f_dihedral_angle_d	23.0275	1281

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.94-2.01	0.3133	54	0.3447	1044	X-RAY DIFFRACTION	32.42
2.01-2.09	0.32	93	0.313	1763	X-RAY DIFFRACTION	53.94
2.09-2.18	0.3009	130	0.2892	2433	X-RAY DIFFRACTION	76.1
2.18-2.3	0.2844	154	0.2817	2942	X-RAY DIFFRACTION	90.79
2.3-2.44	0.2876	166	0.2438	3118	X-RAY DIFFRACTION	95.41
2.44-2.63	0.2278	171	0.2253	3256	X-RAY DIFFRACTION	98.96
2.63-2.9	0.2486	169	0.247	3214	X-RAY DIFFRACTION	98.77
2.9-3.31	0.2559	169	0.2251	3219	X-RAY DIFFRACTION	98.4
3.31-4.17	0.2251	171	0.1699	3232	X-RAY DIFFRACTION	98.07
4.18-39.71	0.187	177	0.162	3372	X-RAY DIFFRACTION	97.34

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.80315733777	0.0353429137595	-1.17813185061	4.86203108232	1.65802482156	2.05058930698	0.221537584055	0.17324351749	0.43989218375	-0.520976359145	0.0423185623651	0.130532764352	-0.862577171454	-0.125348017296	-0.28850770645	0.640303553025	0.0336708748795	0.0337856346746	0.441578105623	0.0837760862937	0.444911890198	-8.77215091892	9.4565747078	30.8877044861
2	6.68449624751	-2.41903912769	4.63536171458	2.24878521331	-0.234642315161	6.10007948637	-0.896147436953	0.529296438641	1.16531148982	-0.683215182984	-0.0315699911267	-1.0579982393	-1.32351805275	0.208063226909	0.370795949618	0.906027815917	-0.026749575405	0.325986765612	0.655663524728	0.146087117386	0.35463319065	5.67864753176	7.44201704072	20.446885199
3	7.50834601947	1.56467715296	0.749940793029	8.13310450629	1.02743758466	4.77623535284	-0.0172912004416	-0.278686503957	-0.306528051869	-0.46368116526	0.00210639346805	-2.60400554094	0.194536268964	1.00624761273	0.0717175705128	0.391122663385	0.0211059978768	0.119926211776	0.491462635227	-0.0283163089356	0.824429495221	13.9840862586	1.70730829748	34.5655048526
4	1.5380603386	-0.535618939712	0.781000048833	3.83283433011	-0.638510691447	1.16647817843	0.0103767125208	-0.0491392105871	0.361420856713	-0.415691714062	-0.100184892051	-1.06940192414	-0.205965973472	0.0918339342058	0.102024662019	0.317279539553	-0.00602498135679	0.00413890568605	0.272685469799	-0.0407581922119	0.485519185373	6.20137770991	12.1315051875	38.6001732581
5	2.67058649237	-0.168356498592	-0.299596586755	3.54435237569	-1.25311578007	2.18909028355	-0.0524637293639	0.502335819285	-0.030422439026	-0.616316127606	0.0633224301044	-0.33398679081	0.140111396593	-0.0977657916611	-0.0211781080232	0.38354505156	-0.0125327972503	0.06045940375	0.306644450998	-0.0149317354024	0.241656575144	-0.940075913915	-0.825021619314	31.0446681203
6	1.37948157388	1.40367541676	3.52593665562	5.03245350878	4.19487997597	9.11093575054	-0.0208846018398	-0.610766815156	-0.510235106525	0.328916765489	-0.262100916318	0.176448018153	0.427387518266	-1.17622530647	0.176565665916	0.41767882109	-0.0525292762204	0.0748377048799	0.402058531517	0.0691859092655	0.401701870698	-5.10536873437	-7.59853225622	42.2034149659
7	4.11245227754	0.832431416683	0.123702431688	2.22589928999	0.680003547155	2.78394661363	-0.205180743884	1.008822469	-0.116727004635	-0.897668162402	0.276111913183	1.11763208024	0.0241992203382	-1.52905105585	-0.0992373834545	0.699118028009	-0.149512785154	-0.117546441792	0.924599889482	0.00197070574845	0.919075517281	-52.7443615474	-8.76093284365	39.5180034234
8	3.2135384207	0.365175100775	-1.31130176581	1.96662817498	0.00241810879091	0.436405123693	0.0103927004321	-0.332482466584	0.223306231048	0.197256876285	-0.0413305686652	-0.36731258187	0.203480369577	0.19817144249	0.0140251054351	0.3767323986	0.0502936961736	-0.0198111982792	0.403731436799	-0.0368267871312	0.186126245099	-4.23589825086	-0.858474748729	44.3564812765
9	1.97043775656	0.528656754879	1.72428318988	5.92424598348	-1.65647498794	6.66924902641	-0.564237770754	0.266472954391	0.19865879152	-0.224129359322	0.443896561043	-0.558727862616	-0.360885858062	-0.632880404494	0.00813242196049	0.99251233496	-0.125601722465	-0.000669473299473	0.639713591188	-0.0803809418266	0.519340257564	-9.67384841157	-4.28404122218	11.3390946163
10	2.08474966901	0.145382011584	0.545954662794	1.66230316069	0.419124635407	1.25032482187	0.17584278806	-0.863182990204	1.25024901846	0.633745403728	-0.218789395697	0.325596987128	-0.279262772881	0.129505484409	-0.24730545414	0.9672502072	-0.201948570208	0.177033051833	0.881092026611	-0.210190788968	0.776826545139	-25.9349596186	-6.35386941973	18.7492795913
11	6.06418074511	-0.466618462499	2.72674937796	3.40757790342	-3.01221291808	4.25801052197	0.611250223728	0.33883172865	0.383187298531	-0.283669591266	-0.177902874189	1.32420284707	0.698456367664	-0.323478626915	-0.533015116033	0.654714862492	-0.102493598995	0.013025146961	0.67049535715	-0.12610241725	0.706530758771	-31.1280164156	-12.1873618556	3.50033604555
12	2.93120887183	-0.779273278176	-0.0951273456695	3.17531964305	0.572254206509	1.54065995094	0.104179923472	-0.076385995871	0.699700079423	0.232056966523	-0.33468703822	0.116905563348	-0.217373054519	-0.223274509111	0.19551256554	0.525075655985	-0.0531967521108	-0.02959611457	0.423404520323	-0.045884103934	0.606741401492	-21.1806288293	-6.86573463295	3.55695384661
13	2.16296229448	0.868231385568	-0.518332689108	3.89228000676	-0.434482978649	4.22754434861	0.341105778116	-1.20098276635	0.324250281452	0.703739989464	-0.247987634036	-1.15222759035	0.759018872012	0.433031477192	-0.125433212405	0.835470793639	-0.0638662211121	-0.21670757386	0.652249175318	-0.00317567623467	0.714551952529	-7.84303720608	-12.6302237382	16.1115148775
14	2.64159205176	0.798997304416	0.958285627282	2.21575881157	0.324471967551	1.21144904521	0.50613895518	-0.504998039206	-0.457447268419	0.690767285011	-0.276070375007	-0.466416564876	0.36249001065	-0.221519631726	-0.190031750184	0.67764369488	-0.150342939477	-0.0509625261278	0.416910300803	-0.0474331855859	0.617057621064	-18.1888970733	-15.7328430509	6.5238694262
15	3.92388765508	0.343306650497	0.224381884016	3.45847630831	0.325027207702	4.11547101286	0.140768476009	-0.971580326622	-0.917723145137	0.898053135051	0.0231399450362	0.388508186903	-0.297982217778	-0.472380053868	-0.219265911874	0.920429150856	-0.150838051674	0.0828244785805	0.690286973886	-0.0570253135391	0.56492111723	-23.4366930814	-16.7130540502	16.093351697
16	3.12800815705	-0.0154631264568	0.556409469383	2.67750615218	-0.409080528531	2.09554285607	0.66012158869	-0.831904763941	-0.555495238695	1.0789314954	0.390902366299	-0.37579940372	1.29581636402	-0.304940267053	-0.653318116809	0.915082715138	-0.171987398119	-0.160105504898	0.821433736301	0.0392631966821	0.577382673116	-14.228088188	-16.8783762771	17.8002306167
17	4.83447276975	0.900208604195	2.61860663835	4.8800745982	-1.28578953929	2.78899710375	0.226928080741	0.263378900249	-0.796327377909	-0.550666441641	-0.0485015788347	-0.909120174104	0.691472413089	0.240481520923	-0.25900036129	0.651113333471	0.00768254858713	-0.103761869111	0.417391380071	-0.0663431836443	0.623410781679	-11.4474340812	-21.0399892747	2.35582106822
18	0.918937288704	-0.726553322144	0.18531101704	1.65690275591	0.663770275604	0.999023710773	0.390210120468	-0.1661274505	1.00353424071	-0.122506535145	0.320135184891	-0.624353654149	-0.754568155127	-0.639766254359	-0.290232674211	1.44715815473	0.127832176951	-0.223020562303	2.33827072505	-0.450306390404	1.19785813217	36.0487246879	-21.6807766725	16.4512118744
19	5.02464834609	-1.70403708395	-0.376364338734	3.9056236426	0.448962407331	3.57367751616	-0.358834651261	-1.28311709567	0.340246187028	0.264400066091	0.491577213792	-0.784750032244	0.757724666349	0.798588138964	-0.18068785238	0.574609257513	0.123256885653	-0.0415598064274	0.717316878231	0.0428880440218	0.680775775222	25.8743152412	-19.3163133584	5.25966541189
20	3.85366217186	-0.971694127776	2.64317108765	0.645112209154	-1.15481778436	2.27734788241	0.278149411336	-0.480175408523	-0.0439740058563	0.169748745318	1.12868447574	-0.170627731596	0.194468662419	0.682627771897	-1.36498159202	0.524121922711	0.0128095477404	-0.00282277612933	0.943923198418	-0.199971084234	1.06127376308	-1.64101385463	-7.37331612666	4.23889671177
21	2.7775783405	-0.103432226046	-0.214413230709	2.6168262341	0.562031733142	3.37387839826	-0.113663731823	0.646656754289	0.479425309986	-0.486880986678	0.0494053197502	0.0648614294785	-0.825665184788	-0.0905831946143	-0.00198913311689	0.516259374675	-0.0920104003432	-0.0621562690941	0.567933740008	0.177045743196	0.575941321077	-20.504737975	-8.64177293275	-8.57839522658
22	0.786470727486	0.693137785694	-0.244248403161	4.51733159914	0.517851674489	0.358065722926	0.181188056503	1.00319532329	-1.21345688539	-1.05420008755	-0.040760404996	-0.125687803447	1.09538197544	-0.914417755571	-0.298915733395	0.993299514153	-0.190031687069	-0.131511562773	0.873331024918	-0.261878769509	0.927395370305	-30.9458542781	-26.6888042322	-8.69312556732
23	2.61417398927	0.150331573138	1.84931911316	0.874239235751	0.879479640489	2.04363113057	0.401810397042	0.747284740633	-0.606213771169	-0.507387024129	0.256142925552	0.443158554512	0.426150513106	-0.283375495225	-0.400107546489	1.38925280387	-0.248610232382	-0.368628909452	2.31580150157	-0.438938762859	1.25753804899	-36.5337862548	-31.4212509643	-16.9513477679
24	3.93436177644	1.96236545857	0.0860821838793	0.976871876959	0.0424052385704	0.00247299403088	0.279615008318	-0.0161308171655	-0.334346403755	-0.300458150138	-0.00132812078591	0.323011052641	0.201482724756	-0.147980770597	-0.204666547237	1.45715312961	-0.175372180346	-0.45571040148	3.1563690327	-0.229171349836	1.28807038548	-38.9993162106	-28.3015073307	-23.2796577682

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 243 through 252 )	A	A	243 - 252	1 - 10
2	2	chain 'A' and (resid 253 through 263 )	A	A	253 - 263	11 - 21
3	3	chain 'A' and (resid 264 through 270 )	A	A	264 - 270	22 - 28
4	4	chain 'A' and (resid 271 through 280 )	A	A	271 - 280	29 - 38
5	5	chain 'A' and (resid 281 through 335 )	A	A	281 - 335	39 - 93
6	6	chain 'A' and (resid 336 through 346 )	A	A	336 - 346	94 - 104
7	7	chain 'X' and (resid 3 through 12 )	X	E	3 - 12
8	8	chain 'X' and (resid 13 through 34 )	X	E	13 - 34
9	9	chain 'B' and (resid 243 through 252 )	B	H	243 - 252	1 - 10
10	10	chain 'B' and (resid 253 through 263 )	B	H	253 - 263	11 - 21
11	11	chain 'B' and (resid 264 through 270 )	B	H	264 - 270	22 - 28
12	12	chain 'B' and (resid 271 through 295 )	B	H	271 - 295	29 - 53
13	13	chain 'B' and (resid 296 through 300 )	B	H	296 - 300	54 - 58
14	14	chain 'B' and (resid 301 through 316 )	B	H	301 - 316	59 - 74
15	15	chain 'B' and (resid 317 through 325 )	B	H	317 - 325	75 - 83
16	16	chain 'B' and (resid 326 through 331 )	B	H	326 - 331	84 - 89
17	17	chain 'B' and (resid 332 through 346 )	B	H	332 - 346	90 - 104
18	18	chain 'C' and (resid 3 through 7 )	C	I	3 - 7
19	19	chain 'C' and (resid 8 through 17 )	C	I	8 - 17
20	20	chain 'C' and (resid 18 through 22 )	C	I	18 - 22
21	21	chain 'C' and (resid 23 through 28 )	C	I	23 - 28
22	22	chain 'C' and (resid 29 through 31 )	C	I	29 - 31
23	23	chain 'C' and (resid 32 through 33 )	C	I	32 - 33
24	24	chain 'C' and (resid 34 through 34 )	C	I	34

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