Magnesium in PDB 9lcr: Clostridium Botulinum Ole Rna Dimer

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Magnesium atom in the Clostridium Botulinum Ole Rna Dimer (pdb code 9lcr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 28 binding sites of Magnesium where determined in the Clostridium Botulinum Ole Rna Dimer, PDB code: 9lcr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:9.7 occ:1.00 N7 A:G39 3.3 3.7 1.0 C5 A:C38 4.0 2.5 1.0 O6 A:G39 4.0 1.2 1.0 C5 A:G39 4.1 0.0 1.0 N4 A:C38 4.2 3.5 1.0 C4 A:C38 4.2 0.2 1.0 C8 A:G39 4.2 0.5 1.0 C6 A:G39 4.4 0.0 1.0 N7 A:G40 4.6 0.0 1.0 C6 A:C38 4.6 5.3 1.0 O6 A:G40 4.8 0.0 1.0 N3 A:C38 5.0 2.3 1.0

Magnesium binding site 2 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:0.7 occ:1.00 OP1 A:A49 2.0 2.7 1.0 OP1 A:G36 2.1 1.2 1.0 OP2 A:G37 2.3 10.4 1.0 P A:A49 3.4 0.0 1.0 P A:G37 3.5 0.0 1.0 P A:G36 3.5 0.0 1.0 O3' A:A48 4.0 6.6 1.0 OP1 A:G37 4.0 7.8 1.0 OP2 A:A49 4.1 2.4 1.0 OP2 A:G36 4.2 5.3 1.0 O3' A:G36 4.3 6.0 1.0 O5' A:G36 4.4 0.0 1.0 O5' A:A49 4.5 3.6 1.0 O3' A:A35 4.5 15.3 1.0 C3' A:G36 4.6 4.2 1.0 C5' A:G36 4.7 4.4 1.0 O5' A:G37 4.7 7.0 1.0 C5' A:A49 4.8 0.0 1.0

Magnesium binding site 3 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:17.7 occ:1.00 O6 A:G37 3.9 0.4 1.0 O6 A:G36 4.4 0.7 1.0 N4 A:C54 4.6 3.6 1.0 O6 A:G53 4.7 0.0 1.0 N4 A:C52 5.0 0.0 1.0

Magnesium binding site 4 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:1.7 occ:1.00 OP2 A:A48 2.6 6.0 1.0 O6 A:G42 3.4 0.0 1.0 P A:A48 3.9 0.0 1.0 O4 A:U50 4.0 0.0 1.0 N7 A:G42 4.1 0.0 1.0 O6 A:G41 4.2 0.0 1.0 C6 A:G42 4.3 0.0 1.0 O5' A:A48 4.4 4.8 1.0 OP1 A:A48 4.5 3.6 1.0 N7 A:A49 4.6 0.0 1.0 C5 A:G42 4.6 0.0 1.0 N3 A:C43 4.7 0.0 1.0 N6 A:A49 4.8 0.0 1.0 C4 A:U50 5.0 0.0 1.0 C6 A:G41 5.0 0.0 1.0

Magnesium binding site 5 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:0.0 occ:1.00 OP1 A:C229 2.6 4.9 1.0 OP1 A:G252 2.9 9.0 1.0 P A:C229 3.9 1.1 1.0 OP1 A:G117 3.9 4.3 1.0 P A:G252 4.0 0.0 1.0 O3' A:U116 4.0 11.9 1.0 OP2 A:C230 4.1 5.3 1.0 OP2 A:G252 4.1 4.3 1.0 C5' A:C229 4.3 6.9 1.0 O5' A:C229 4.3 15.3 1.0 P A:G117 4.7 0.0 1.0 OP2 A:C229 4.7 13.6 1.0 O3' A:U251 4.9 7.8 1.0 C4' A:U116 5.0 0.0 1.0 P A:C230 5.0 0.0 1.0

Magnesium binding site 6 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:6.9 occ:1.00 O6 A:G86 2.7 0.9 1.0 O6 A:G111 3.2 10.1 1.0 O4 A:U110 3.3 5.0 1.0 O4 A:U85 3.5 1.8 1.0 C6 A:G86 3.8 1.7 1.0 N3 A:U110 4.0 0.0 1.0 N7 A:G86 4.0 3.3 1.0 C4 A:U110 4.1 1.7 1.0 C6 A:G111 4.1 5.5 1.0 C5 A:G86 4.3 6.9 1.0 C4 A:U85 4.3 4.1 1.0 N3 A:U85 4.3 6.5 1.0 O6 A:G87 4.5 0.4 1.0 N7 A:G111 4.7 4.9 1.0 C5 A:G111 4.8 6.3 1.0 N1 A:G86 5.0 5.3 1.0

Magnesium binding site 7 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:7.2 occ:1.00 O6 A:G80 2.7 0.0 1.0 O4 A:U116 2.9 0.0 1.0 O6 A:G117 3.4 0.0 1.0 O4 A:U79 3.7 2.5 1.0 C4 A:U116 3.7 0.0 1.0 N3 A:U116 3.8 0.0 1.0 C6 A:G80 3.8 0.0 1.0 O6 A:G81 4.1 0.0 1.0 N3 A:U79 4.4 0.0 1.0 C6 A:G117 4.4 0.0 1.0 C4 A:U79 4.4 0.0 1.0 N7 A:G80 4.5 0.0 1.0 C5 A:G80 4.5 0.0 1.0 N4 A:C115 4.6 0.0 1.0 N7 A:G117 4.7 0.0 1.0 C5 A:G117 4.9 0.0 1.0 N1 A:G80 4.9 0.0 1.0

Magnesium binding site 8 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:6.4 occ:1.00 OP1 A:A250 2.8 7.5 1.0 O2' A:G81 3.1 0.0 1.0 O2' A:C263 3.3 0.3 1.0 O3' A:G81 3.6 0.8 1.0 O3' A:U249 3.6 5.9 1.0 O3' A:C263 3.7 6.3 1.0 P A:A250 3.8 3.1 1.0 C5' A:C264 3.8 0.5 1.0 C5' A:U82 3.8 2.5 1.0 OP1 A:U82 4.2 7.9 1.0 OP1 A:C264 4.2 2.6 1.0 C2' A:G81 4.2 3.8 1.0 C5' A:A250 4.3 1.7 1.0 C3' A:G81 4.3 0.0 1.0 P A:U82 4.4 0.0 1.0 C2' A:C263 4.4 9.7 1.0 C3' A:C263 4.4 2.9 1.0 P A:C264 4.5 0.0 1.0 O5' A:U82 4.6 8.5 1.0 O5' A:A250 4.6 10.6 1.0 O5' A:C264 4.6 0.1 1.0 C4' A:G81 4.7 0.0 1.0 C4' A:C263 4.7 5.1 1.0 C3' A:U249 4.8 2.8 1.0 C4' A:U82 4.9 2.6 1.0 C4' A:C264 4.9 0.0 1.0

Magnesium binding site 9 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg609 b:10.0 occ:1.00 O6 A:G350 2.9 0.0 1.0 O6 A:G275 2.9 9.3 1.0 O4 A:U274 3.3 0.9 1.0 O4 A:U349 3.3 14.0 1.0 N3 A:U349 3.8 8.6 1.0 C4 A:U349 3.8 9.8 1.0 C6 A:G275 3.9 2.7 1.0 C6 A:G350 3.9 0.0 1.0 N7 A:G350 4.0 4.0 1.0 N4 A:C351 4.0 0.0 1.0 N3 A:U274 4.1 5.0 1.0 C4 A:U274 4.1 4.0 1.0 O6 A:G273 4.3 0.0 1.0 C5 A:G350 4.3 0.0 1.0 C5 A:G275 4.6 1.3 1.0 N7 A:G275 4.6 3.1 1.0 N1 A:G275 4.9 0.0 1.0 MG A:MG610 4.9 18.7 1.0 C2 A:U349 4.9 12.6 1.0 C4 A:C351 4.9 0.0 1.0

Magnesium binding site 10 out of 28 in the Clostridium Botulinum Ole Rna Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Clostridium Botulinum Ole Rna Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:18.7 occ:1.00 N7 A:G273 3.4 0.0 1.0 O4 A:U274 3.9 0.9 1.0 O6 A:G273 4.0 0.0 1.0 C5 A:G273 4.3 0.0 1.0 C8 A:G273 4.4 1.3 1.0 O2' A:G271 4.5 5.9 1.0 C6 A:G273 4.5 0.7 1.0 OP2 A:A272 4.6 4.0 1.0 C4 A:U274 4.7 4.0 1.0 MG A:MG609 4.9 10.0 1.0

L.Wang, J.Xie, T.Gong, H.Wu, Y.Tu, X.Peng, S.Shang, X.Jia, H.Ma, J.Zou, S.Xu, X.Zheng, D.Zhang, Y.Liu, C.Zhang, Y.Luo, Z.Huang, B.Shao, B.Ying, Y.Cheng, Y.Guo, Y.Lai, D.Huang, J.Liu, Y.Wei, S.Sun, X.Zhou, Z.Su. Cryo-Em Reveals Mechanisms of Natural Rna Multivalency Science 2025.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADV3451