MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 2qou:A1560, See in JSmolMgRNA representative site for type NB             Click on the image to toggle views

Site type: Nb

Schematic drawing for

MgRNA type NB
List of all 284 Mg2+ binding sites with the site type Nb in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1d4r B302 Nb G:B19(N7) B310, B311, B312, B313 G:B20, G:B18
1jj2 08111 Nb G:02609(N7) 03224, 03248, 05142, 05289, 09825 G:02609 G:02606, U:02610
1jj2 08112 Nb A:0187(N1) 03254, 03295, 08648, 08851, 09088 U:0207, C:0155 G:0206 C:0438, C:0188
1k73 A8111 Nb G:A2609(N7) A3297, A3692, A3716, A5606, A5754 G:A2609 U:A2610, G:A2606
1k8a A8112 Nb A:A187(N1) A3314, A3356, A8727, A8925, A9158 U:A207, C:A155 G:A206 C:A438, C:A188
1k9m A8112 Nb A:A187(N1) A3718, A3760, A9132, A9331, A9564 U:A207, C:A155 G:A206 C:A438, C:A188
1kd1 A8111 Nb G:A2609(N7) A3296, A3693, A3716, A5599, A5747 G:A2609 U:A2610, G:A2606
1kd1 A8112 Nb A:A187(N1) A3723, A3764, A9127, A9328, A9561 U:A207, C:A155 G:A206 C:A438, C:A188
1kqs 08111 Nb G:02609(N7) 03206, 03230, 05101, 05250, 09807 G:02609 G:02606, U:02610
1kqs 08112 Nb A:0187(N1) 03236, 03277, 08647, 08844, 09080 U:0207, C:0155 G:0206 C:0438, C:0188
1m1k A8111 Nb G:A2609(N7) A3292, A3316, A5204, A5350, A9897 G:A2609 G:A2606, U:A2610
1n8r A8113 Nb A:A2112(N7) A4148, A4322, A6517, A6788, A9982 A:A2112
1nji A8112 Nb A:A187(N1) A3718, A3759, A9126, A9325, A9561 U:A207, C:A155 G:A206 C:A438, C:A188
1nji A8111 Nb G:A2609(N7) A3297, A3688, A3712, A5600, A5748 G:A2609 U:A2610, G:A2606
1q7y A8113 Nb A:A2112(N7) A3262, A3433, A5625, A5890 A:A2112, G:A2111
1q81 A8112 Nb A:A187(N1) A3240, A3280, A8652, A8847, A9083 U:A207, C:A155 G:A206 C:A438, C:A188
1q82 A8112 Nb A:A187(N1) A3239, A3278, A8648, A8851, A9082 U:A207, C:A155 G:A206 C:A438, C:A188
1q82 A8113 Nb A:A2112(N7) A3263, A3434, A5615, A5886, A9105 A:A2112, G:A2111
1q86 A8112 Nb A:A187(N1) A3253, A3295, A8650, A8856, A9094 U:A207, C:A155 G:A206 C:A438, C:A188
1s72 08110 Nb G:02609(N7) 03219, 03243, 05128, 05273, 09820 G:02609 G:02606, U:02610
1vq6 08111 Nb G:02609(N7) 03605, 04005, 04029, 06005, B9411 G:02609 U:02610, G:02606
1vq6 08112 Nb A:0187(N1) 04035, 04075, 09452, 09655, 09892 U:0207, C:0155 G:0206 C:0438, C:0188
1vq9 08068 Nb A:02569(N7) 04317, 05367, 07106, E920 A:02568, A:02569 C:02565
1vqk 08068 Nb A:02569(N7) 04355, 05413, 08453, E920, E6236 A:02568, A:02569, G:02567 C:02565 A:02568
1vqm 08068 Nb A:02569(N7) 04348, 05393, 07183, E920 A:02568, A:02569 C:02565 G:02570

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
used for Mg2+
"Site type"
Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen
cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform
Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>