3PDR - JenaLib

Title :   CRYSTAL STRUCTURE OF MANGANESE BOUND M-BOX RNA

Authors :   A Ramesh, W. C. Winkler

Date :   23 Oct 10 (Deposition) - 23 Feb 11 (Release) - 23 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,X
Biol. Unit 1: X  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: A,X  (1x)

Keywords :   Manganese-Rna Complex, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ramesh, C. A. Wakeman, W. C. Winkler
Insights Into Metalloregulation By M-Box Riboswitch Rnas Vi Structural Analysis Of Manganese-Bound Complexes.
J. Mol. Biol. V. 407 556 2011
PubMed-ID: 21315082 | Reference-DOI: 10.1016/J.JMB.2011.01.049

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 31)

Sites (30, 30)

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G X:27 , U X:28 , A X:155 , G X:157 , C X:158 , HOH X:212 , HOH X:342	BINDING SITE FOR RESIDUE K X 1
02	AC2	SOFTWARE	U X:67 , C X:75 , A X:106	BINDING SITE FOR RESIDUE K X 2
03	AC3	SOFTWARE	G X:73	BINDING SITE FOR RESIDUE K X 3
04	AC4	SOFTWARE	G X:100 , C X:102 , A X:103 , U X:104 , HOH X:187 , HOH X:497	BINDING SITE FOR RESIDUE MN X 176
05	AC5	SOFTWARE	U X:23 , C X:99 , G X:100 , HOH X:203 , HOH X:209 , HOH X:316 , HOH X:327	BINDING SITE FOR RESIDUE MN X 177
06	AC6	SOFTWARE	U X:24 , A X:25 , HOH X:247 , HOH X:272 , HOH X:279 , HOH X:498	BINDING SITE FOR RESIDUE MN X 178
07	AC7	SOFTWARE	A X:72 , HOH X:288 , HOH X:299 , HOH X:471	BINDING SITE FOR RESIDUE MN X 4
08	AC8	SOFTWARE	A X:117 , A X:118 , U X:119 , HOH X:547	BINDING SITE FOR RESIDUE MN X 7
09	AC9	SOFTWARE	C X:35 , C X:36 , HOH X:504 , HOH X:522 , HOH X:523 , HOH X:524	BINDING SITE FOR RESIDUE MN X 9
10	BC1	SOFTWARE	A X:106 , G X:107 , HOH X:500 , HOH X:501 , HOH X:502 , HOH X:503	BINDING SITE FOR RESIDUE MN X 10
11	BC2	SOFTWARE	G X:45 , HOH X:525 , HOH X:526 , HOH X:551	BINDING SITE FOR RESIDUE MN X 12
12	BC3	SOFTWARE	G X:127 , A X:128 , U X:129 , HOH X:505 , HOH X:506	BINDING SITE FOR RESIDUE MN X 13
13	BC4	SOFTWARE	A X:30 , G X:31 , HOH X:507 , HOH X:508 , HOH X:509 , HOH X:510	BINDING SITE FOR RESIDUE MN X 14
14	BC5	SOFTWARE	G X:15 , HOH X:527	BINDING SITE FOR RESIDUE MN X 179
15	BC6	SOFTWARE	A X:46 , G X:126 , HOH X:542 , HOH X:543 , HOH X:544 , HOH X:545	BINDING SITE FOR RESIDUE MN X 180
16	BC7	SOFTWARE	G A:27 , U A:28 , G A:29 , A A:155 , G A:157 , C A:158 , HOH A:181 , HOH A:225	BINDING SITE FOR RESIDUE K A 1
17	BC8	SOFTWARE	U A:67 , C A:75 , A A:106	BINDING SITE FOR RESIDUE K A 2
18	BC9	SOFTWARE	G A:100 , C A:102 , A A:103 , U A:104 , HOH A:195 , HOH A:198	BINDING SITE FOR RESIDUE MN A 176
19	CC1	SOFTWARE	U A:23 , C A:99 , G A:100 , HOH A:217 , HOH A:220 , HOH A:230 , HOH A:472 , HOH A:546	BINDING SITE FOR RESIDUE MN A 177
20	CC2	SOFTWARE	U A:24 , A A:25 , HOH A:222 , HOH A:244 , HOH A:255 , HOH A:258	BINDING SITE FOR RESIDUE MN A 178
21	CC3	SOFTWARE	A A:72 , HOH A:320 , HOH A:332 , HOH A:490 , HOH A:491	BINDING SITE FOR RESIDUE MN A 4
22	CC4	SOFTWARE	A A:63 , HOH A:263 , HOH A:473 , HOH A:474 , HOH A:475 , HOH A:492	BINDING SITE FOR RESIDUE MN A 5
23	CC5	SOFTWARE	A A:80 , U A:81 , HOH A:247 , HOH A:476 , HOH A:477 , HOH A:487	BINDING SITE FOR RESIDUE MN A 6
24	CC6	SOFTWARE	A A:117 , A A:118 , U A:119 , HOH A:478 , HOH A:548 , HOH A:550	BINDING SITE FOR RESIDUE MN A 7
25	CC7	SOFTWARE	C A:35 , C A:36 , HOH A:310 , HOH A:481 , HOH A:482 , HOH A:549	BINDING SITE FOR RESIDUE MN A 9
26	CC8	SOFTWARE	A A:106 , G A:107 , HOH A:483 , HOH A:484 , HOH A:485 , HOH A:486	BINDING SITE FOR RESIDUE MN A 10
27	CC9	SOFTWARE	A A:60 , HOH A:187 , HOH A:231 , HOH A:306 , HOH A:488 , HOH A:489	BINDING SITE FOR RESIDUE MN A 11
28	DC1	SOFTWARE	G A:45 , HOH A:324 , HOH A:495 , HOH A:519 , HOH A:520	BINDING SITE FOR RESIDUE MN A 12
29	DC2	SOFTWARE	G A:127 , A A:128 , U A:129 , HOH A:496 , HOH A:515 , HOH X:322	BINDING SITE FOR RESIDUE MN A 13
30	DC3	SOFTWARE	G A:15	BINDING SITE FOR RESIDUE MN A 179

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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Chain A from PDB  Type:RNA  Length:161
                                                                                                                                                                                                 
                 3pdr A  15 GGGCUUCGUUAGGUGAGGCUCCUGUAUGGAGAUACGCUGCUGCCCAAAAAUGUCCAAAGACGCCAAUGGGUCAACAGAAAUCAUCGACAUAAGGUGAUUUUUAAUGCAGCUGGAUGCUUGUCCUAUGCCAUACAGUGCUAAAGCUCUACGAUUGAAGCCCA 175
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain X from PDB  Type:RNA  Length:161
                                                                                                                                                                                                 
                 3pdr X  15 GGGCUUCGUUAGGUGAGGCUCCUGUAUGGAGAUACGCUGCUGCCCAAAAAUGUCCAAAGACGCCAAUGGGUCAACAGAAAUCAUCGACAUAAGGUGAUUUUUAAUGCAGCUGGAUGCUUGUCCUAUGCCAUACAGUGCUAAAGCUCUACGAUUGAAGCCCA 175
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

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