5U2R

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001701	biological_process	in utero embryonic development
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005874	cellular_component	microtubule
A	0005876	cellular_component	spindle microtubule
A	0006259	biological_process	DNA metabolic process
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated DNA replication
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006287	biological_process	base-excision repair, gap-filling
A	0006290	biological_process	pyrimidine dimer repair
A	0006297	biological_process	nucleotide-excision repair, DNA gap filling
A	0006303	biological_process	double-strand break repair via nonhomologous end joining
A	0006915	biological_process	apoptotic process
A	0006954	biological_process	inflammatory response
A	0006974	biological_process	DNA damage response
A	0007435	biological_process	salivary gland morphogenesis
A	0008017	molecular_function	microtubule binding
A	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
A	0010332	biological_process	response to gamma radiation
A	0016445	biological_process	somatic diversification of immunoglobulins
A	0016446	biological_process	somatic hypermutation of immunoglobulin genes
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016829	molecular_function	lyase activity
A	0019899	molecular_function	enzyme binding
A	0032991	cellular_component	protein-containing complex
A	0034061	molecular_function	DNA polymerase activity
A	0045471	biological_process	response to ethanol
A	0046872	molecular_function	metal ion binding
A	0048535	biological_process	lymph node development
A	0048536	biological_process	spleen development
A	0048872	biological_process	homeostasis of number of cells
A	0051402	biological_process	neuron apoptotic process
A	0051575	molecular_function	5'-deoxyribose-5-phosphate lyase activity
A	0055093	biological_process	response to hyperoxia
A	0071707	biological_process	immunoglobulin heavy chain V-D-J recombination
A	0071897	biological_process	DNA biosynthetic process
A	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	24
Details	binding site for residue 1S0 A 401

Chain	Residue
A	ARG149
A	PHE272
A	GLY274
A	ASP276
A	ASN279
A	CA402
A	CA403
A	HOH581
A	HOH590
A	HOH595
A	HOH598
A	GLY179
A	HOH616
A	HOH690
P	DC10
P	HOH106
T	DG6
A	SER180
A	ARG183
A	SER188
A	GLY189
A	ASP190
A	ASP192
A	TYR271

---

site_id	AC2
Number of Residues	7
Details	binding site for residue CA A 402

Chain	Residue
A	ASP190
A	ASP192
A	ASP256
A	1S0401
A	CA403
A	HOH581
P	DC10

---

site_id	AC3
Number of Residues	5
Details	binding site for residue CA A 403

Chain	Residue
A	ASP190
A	ASP192
A	1S0401
A	CA402
A	HOH533

---

site_id	AC4
Number of Residues	6
Details	binding site for residue NA A 404

Chain	Residue
A	THR101
A	VAL103
A	ILE106
A	HOH705
P	DG9
P	HOH105

---

site_id	AC5
Number of Residues	6
Details	binding site for residue NA A 405

Chain	Residue
A	LYS60
A	LEU62
A	VAL65
A	HOH711
D	DC3
D	HOH101

---

site_id	AC6
Number of Residues	3
Details	binding site for residue ACT A 406

Chain	Residue
A	PHE200
A	GLU232
A	HOH536

---

site_id	AC7
Number of Residues	6
Details	binding site for residue ACT A 407

Chain	Residue
A	PHE76
A	LYS81
A	LEU82
A	LEU85
A	GLU86
A	ARG89

---

site_id	AC8
Number of Residues	6
Details	binding site for residue ACT A 408

Chain	Residue
A	ILE174
A	THR196
A	LYS262
A	TYR265
A	HOH524
A	HOH604

---

Functional Information from PROSITE/UniProt

site_id	PS00522
Number of Residues	20
Details	DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP

Chain	Residue	Details
A	GLY179-PRO198

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	ACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863

Chain	Residue	Details
A	LYS72

---

site_id	SWS_FT_FI2
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ

Chain	Residue	Details
A	LYS60
A	LEU62
A	VAL65
A	THR101
A	VAL103
A	ILE106

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY

Chain	Residue	Details
A	ARG149
A	SER180
A	GLY189

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX

Chain	Residue	Details
A	ARG183

---

site_id	SWS_FT_FI5
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY

Chain	Residue	Details
A	ASP190
A	ASP192
A	ASP256

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409

Chain	Residue	Details
A	LYS72

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869

Chain	Residue	Details
A	ARG83
A	ARG152

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556

Chain	Residue	Details
A	LYS41
A	LYS61
A	LYS81

---