9Q87

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	30S	polymer	1554	503775.9	1	GenBank (991965528)	Escherichia coli B
2	B (B)	Small ribosomal subunit protein uS2	polymer	233	25872.7	1	UniProt (P0A7V0) Pfam (PF00318)	Escherichia coli B	30S ribosomal protein S2
3	C (C)	Small ribosomal subunit protein uS3	polymer	233	26031.3	1	UniProt (P0A7V3) Pfam (PF07650) Pfam (PF00189)	Escherichia coli B	30S ribosomal protein S3
4	D (D)	Small ribosomal subunit protein uS4	polymer	206	23514.2	1	UniProt (P0A7V8) Pfam (PF00163) Pfam (PF01479)	Escherichia coli B	30S ribosomal protein S4
5	E (E)	Small ribosomal subunit protein uS5	polymer	167	17629.4	1	UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719)	Escherichia coli B	30S ribosomal protein S5
6	F (F)	Small ribosomal subunit protein bS6, fully modified isoform	polymer	135	15727.5	1	UniProt (P02358) Pfam (PF01250)	Escherichia coli B
7	G (G)	Small ribosomal subunit protein uS7	polymer	179	20055.2	1	UniProt (P02359) Pfam (PF00177)	Escherichia coli B	30S ribosomal protein S7
8	H (H)	Small ribosomal subunit protein uS8	polymer	130	14146.6	1	UniProt (P0A7W7) Pfam (PF00410)	Escherichia coli B	30S ribosomal protein S8
9	I (I)	Small ribosomal subunit protein uS9	polymer	130	14886.3	1	UniProt (P0A7X3) Pfam (PF00380)	Escherichia coli B	30S ribosomal protein S9
10	J (J)	Small ribosomal subunit protein uS10	polymer	103	11755.6	1	UniProt (P0A7R5) Pfam (PF00338)	Escherichia coli B	30S ribosomal protein S10,Transcription termination/antitermination protein NusE
11	K (K)	Small ribosomal subunit protein uS11	polymer	129	13872.0	1	UniProt (P0A7R9) Pfam (PF00411)	Escherichia coli B	30S ribosomal protein S11
12	L (L)	Small ribosomal subunit protein uS12	polymer	124	13814.2	1	UniProt (P0A7S3) Pfam (PF00164)	Escherichia coli B	30S ribosomal protein S12
13	M (M)	Small ribosomal subunit protein uS13	polymer	118	13128.5	1	UniProt (P0A7S9) Pfam (PF00416)	Escherichia coli B	30S ribosomal protein S13
14	N (N)	Small ribosomal subunit protein uS14	polymer	101	11606.6	1	UniProt (P0AG59) Pfam (PF00253)	Escherichia coli B	30S ribosomal protein S14
15	O (O)	Small ribosomal subunit protein uS15	polymer	89	10290.8	1	UniProt (P0ADZ4) Pfam (PF00312)	Escherichia coli B	30S ribosomal protein S15
16	P (P)	Small ribosomal subunit protein bS16	polymer	82	9207.6	1	UniProt (P0A7T3) Pfam (PF00886)	Escherichia coli B	30S ribosomal protein S16
17	Q (Q)	Small ribosomal subunit protein uS17	polymer	84	9724.5	1	UniProt (P0AG63) Pfam (PF00366)	Escherichia coli B	30S ribosomal protein S17
18	R (R)	Small ribosomal subunit protein bS18	polymer	75	9005.5	1	UniProt (P0A7T7) Pfam (PF01084)	Escherichia coli B	30S ribosomal protein S18
19	S (S)	Small ribosomal subunit protein uS19	polymer	92	10455.4	1	UniProt (P0A7U3) Pfam (PF00203)	Escherichia coli B	30S ribosomal protein S19
20	T (T)	Small ribosomal subunit protein bS20	polymer	87	9708.5	1	UniProt (P0A7U7) Pfam (PF01649)	Escherichia coli B	30S ribosomal protein S20
21	U (U)	Small ribosomal subunit protein bS21	polymer	71	8524.0	1	UniProt (P68679) Pfam (PF01165)	Escherichia coli B	30S ribosomal protein S21
22	V (X)	mRNA	polymer	6	1923.2	1		Escherichia coli B
23	W (Z)	P-site tRNA	polymer	77	24848.9	1	GenBank (1173003849)	Escherichia coli B
24	X (0)	Large ribosomal subunit protein bL33	polymer	55	6388.6	1	UniProt (P0A7N9) Pfam (PF00471)	Escherichia coli B	50S ribosomal protein L33
25	Y (1)	Large ribosomal subunit protein bL34	polymer	46	5397.5	1	UniProt (P0A7P5) Pfam (PF00468)	Escherichia coli B	50S ribosomal protein L34
26	Z (2)	Large ribosomal subunit protein bL35	polymer	65	7313.0	1	UniProt (C3T7Q2) Pfam (PF01632) UniProt (by SIFTS) (P0A7Q1)	Escherichia coli B
27	AA (3)	Large ribosomal subunit protein bL36	polymer	38	4377.4	1	UniProt (A0A2X1PTA3) Pfam (PF00444) UniProt (by SIFTS) (P0A7Q6)	Escherichia coli B
28	BA (5)	Large ribosomal subunit protein uL11	polymer	141	14763.2	1	UniProt (C3SIC7) Pfam (PF03946) Pfam (PF00298) UniProt (by SIFTS) (P0A7J7)	Escherichia coli B
29	CA (6)	A-site tRNA	polymer	2	589.4	1		Escherichia coli B
30	DA (a)	23S rRNA	polymer	2907	942834.3	1		Escherichia coli B
31	EA (b)	5S rRNA	polymer	120	38790.1	1	GenBank (1815787944)	Escherichia coli B
32	FA (c)	Large ribosomal subunit protein uL2	polymer	273	29923.6	1	UniProt (C3SQV7) Pfam (PF00181) Pfam (PF03947) UniProt (by SIFTS) (P60422)	Escherichia coli B
33	GA (d)	Large ribosomal subunit protein uL3	polymer	209	22291.6	1	UniProt (C3SQU2) Pfam (PF00297) UniProt (by SIFTS) (P60438)	Escherichia coli B
34	HA (e)	Large ribosomal subunit protein uL4	polymer	201	22121.6	1	UniProt (C3SQU7) Pfam (PF00573) UniProt (by SIFTS) (P60723)	Escherichia coli B
35	IA (f)	Large ribosomal subunit protein uL5	polymer	179	20333.6	1	UniProt (C3SR02) Pfam (PF00281) Pfam (PF00673) UniProt (by SIFTS) (P62399)	Escherichia coli B
36	JA (g)	Large ribosomal subunit protein uL6	polymer	177	18932.8	1	UniProt (C3SR17) Pfam (PF00347) UniProt (by SIFTS) (P0AG55)	Escherichia coli B
37	KA (h)	Large ribosomal subunit protein bL9	polymer	149	15789.0	1	UniProt (C3SFP2) Pfam (PF01281) Pfam (PF03948) UniProt (by SIFTS) (P0A7R1)	Escherichia coli B
38	LA (i)	Large ribosomal subunit protein uL13	polymer	142	16050.6	1	UniProt (C3SRX7) Pfam (PF00572) UniProt (by SIFTS) (P0AA10)	Escherichia coli B
39	MA (j)	Large ribosomal subunit protein uL14	polymer	123	13565.1	1	UniProt (C3SQZ2) Pfam (PF00238) UniProt (by SIFTS) (P0ADY3)	Escherichia coli B
40	NA (k)	Large ribosomal subunit protein uL15	polymer	144	15008.5	1	UniProt (A0A037Y8L6) Pfam (PF00828) UniProt (by SIFTS) (P02413)	Escherichia coli B
41	OA (l)	Large ribosomal subunit protein uL16	polymer	135	15196.1	1	UniProt (C3SQX7) Pfam (PF00252) UniProt (by SIFTS) (P0ADY7)	Escherichia coli B
42	PA (m)	Large ribosomal subunit protein bL17	polymer	127	14393.7	1	UniProt (C3SR72) Pfam (PF01196) UniProt (by SIFTS) (P0AG44)	Escherichia coli B
43	QA (n)	Large ribosomal subunit protein uL18	polymer	117	12794.7	1	UniProt (C3SR22) Pfam (PF00861) UniProt (by SIFTS) (P0C018)	Escherichia coli B
44	RA (o)	Large ribosomal subunit protein bL19	polymer	115	13159.3	1	UniProt (C3SYQ7) Pfam (PF01245) UniProt (by SIFTS) (P0A7K6)	Escherichia coli B
45	SA (p)	Large ribosomal subunit protein bL20	polymer	118	13528.0	1	UniProt (C3T7Q7) Pfam (PF00453) UniProt (by SIFTS) (P0A7L3)	Escherichia coli B
46	TA (q)	Large ribosomal subunit protein bL21	polymer	103	11586.4	1	UniProt (C3SSG2) Pfam (PF00829) UniProt (by SIFTS) (P0AG48)	Escherichia coli B
47	UA (r)	Large ribosomal subunit protein uL22	polymer	110	12253.4	1	UniProt (C3SQW7) Pfam (PF00237) UniProt (by SIFTS) (P61175)	Escherichia coli B
48	VA (s)	Large ribosomal subunit protein uL23	polymer	100	11222.2	1	UniProt (C3SQV2) Pfam (PF00276) UniProt (by SIFTS) (P0ADZ0)	Escherichia coli B
49	WA (t)	Large ribosomal subunit protein uL24	polymer	104	11339.3	1	UniProt (P60624) Pfam (PF00467) Pfam (PF17136)	Escherichia coli B	50S ribosomal protein L24
50	XA (u)	Large ribosomal subunit protein bL25	polymer	94	10713.5	1	UniProt (P68919) Pfam (PF01386)	Escherichia coli B	50S ribosomal protein L25
51	YA (v)	Large ribosomal subunit protein bL27	polymer	85	9146.5	1	UniProt (P0A7L8) Pfam (PF01016)	Escherichia coli B	50S ribosomal protein L27
52	ZA (w)	Large ribosomal subunit protein bL28	polymer	78	9027.6	1	UniProt (P0A7M2) Pfam (PF00830)	Escherichia coli B	50S ribosomal protein L28
53	AB (x)	Large ribosomal subunit protein uL29	polymer	63	7286.5	1	UniProt (P0A7M6) Pfam (PF00831)	Escherichia coli B	50S ribosomal protein L29
54	BB (y)	Large ribosomal subunit protein uL30	polymer	59	6554.8	1	UniProt (P0AG51) Pfam (PF00327)	Escherichia coli B	50S ribosomal protein L30
55	CB (z)	Large ribosomal subunit protein bL32	polymer	57	6463.4	1	UniProt (P0A7N4) Pfam (PF01783)	Escherichia coli B	50S ribosomal protein L32
56	AAA, AD, AF, AG, AL... (c, A, a, d, e...)	POTASSIUM ION	non-polymer		39.1	235	Chemie (K)
57	AC, AE, AI, AJ, AK... (A, a, d, B, k...)	MAGNESIUM ION	non-polymer		24.3	415	Chemie (MG)
58	AH, IAA, IZ, QX, XY (A, w, a)	COPPER (I) ION	non-polymer		63.5	5	Chemie (CU1)
59	IH (3)	ZINC ION	non-polymer		65.4	1	Chemie (ZN)
60	YY (a)	5-hydroxycytidine 5'-(dihydrogen phosphate)	non-polymer		339.2	1	Chemie (TKW)
61	ABA, ACA, BBA, BCA, CBA... (Q, o, R, p, S...)	water	water		18.0	21388	Chemie (HOH)

Sequence modifications

B: 2 - 234 (UniProt: P0A7V0)

PDB	External Database	Details
-	Asp 228	deletion

K: 1 - 130 (UniProt: P0A7R9)

PDB	External Database	Details
Ias 119	Asn 119	conflict

Z: 1 - 76 (GenBank: 1173003849)

PDB	External Database	Details
U 34	C 2218381	conflict

l: 1 - 136 (UniProt: C3SQX7)

PDB	External Database	Details
-	Arg 81	deletion
4d4 81	Met 82	conflict

Contents of the asymmetric unit

Polymers	Number of chains	55
	Total formula weight	2178639.1
Non-Polymers*	Number of molecules	657
	Total formula weight	19996.9
All*	Total formula weight	2198636.1

*Water molecules are not included.