Magnesium in PDB 9h9m: Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)

The structure of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Magnesium atom in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) (pdb code 9h9m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 42 binding sites of Magnesium where determined in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna), PDB code: 9h9m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1601 b:43.6 occ:1.00 O6 1:G1361 4.1 46.6 1.0 O N:SER58 4.2 48.6 1.0 N3 1:C980 4.3 45.4 1.0 O2 1:C980 4.4 45.4 1.0 O N:GLN60 4.5 49.1 1.0 N4 1:C979 4.6 45.1 1.0 OP1 1:A1360 4.7 47.8 1.0 N7 1:A1360 4.7 47.8 1.0 CD N:ARG61 4.7 47.4 1.0 C2 1:C980 4.8 45.4 1.0 O3' 1:C1359 4.9 48.1 1.0

Magnesium binding site 2 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1602 b:47.8 occ:1.00 O6 1:G1050 2.3 60.1 1.0 N7 1:G1050 2.6 60.1 1.0 C6 1:G1050 2.9 60.1 1.0 C5 1:G1050 3.1 60.1 1.0 C6 1:G1048 3.6 58.9 1.0 C5 1:G1048 3.6 58.9 1.0 C8 1:G1050 3.9 60.1 1.0 O6 1:G1048 3.9 58.9 1.0 N7 1:G1048 4.0 58.9 1.0 N1 1:G1048 4.1 58.9 1.0 C4 1:G1048 4.1 58.9 1.0 N1 1:G1050 4.3 60.1 1.0 C4 1:G1050 4.4 60.1 1.0 C2 1:G1048 4.5 58.9 1.0 C8 1:G1048 4.5 58.9 1.0 N3 1:G1048 4.5 58.9 1.0 N4 1:C1051 4.6 61.2 1.0 N9 1:G1048 4.6 58.9 1.0 N4 1:C1208 4.7 65.3 1.0 N9 1:G1050 4.8 60.1 1.0

Magnesium binding site 3 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1603 b:53.4 occ:1.00 OP2 1:A1110 2.6 58.1 1.0 O2 1:U1189 3.2 55.1 1.0 P 1:A1110 3.8 58.1 1.0 C2 1:U1189 4.2 55.1 1.0 OP1 1:A1110 4.2 58.1 1.0 O5' 1:A1110 4.3 58.1 1.0 N3 1:U1189 4.6 55.1 1.0 OP1 1:C1109 4.6 57.3 1.0 OP2 1:C1109 4.7 57.3 1.0 N6 1:A1188 4.7 54.5 1.0 OP2 1:A1111 4.8 61.9 1.0 N7 1:A1111 4.8 61.9 1.0 CD2 C:HIS176 4.9 55.3 1.0

Magnesium binding site 4 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1604 b:46.2 occ:1.00 O6 1:G1370 2.5 53.0 1.0 C6 1:G1370 3.3 53.0 1.0 N7 1:G1370 3.6 53.0 1.0 C5 1:G1370 3.7 53.0 1.0 O6 1:G1371 4.1 54.0 1.0 N4 1:C1352 4.2 54.4 1.0 O4 1:U1351 4.4 55.4 1.0 N1 1:G1370 4.4 53.0 1.0 N7 1:G1371 4.5 54.0 1.0 C8 1:G1370 4.8 53.0 1.0 N4 1:C1369 4.9 51.9 1.0 CG2 I:VAL111 4.9 54.9 1.0 C6 1:G1371 5.0 54.0 1.0 C4 1:G1370 5.0 53.0 1.0

Magnesium binding site 5 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1605 b:57.3 occ:1.00 O6 1:G1177 3.7 67.6 1.0 N7 1:A1176 4.0 70.4 1.0 N7 1:G1175 4.2 74.3 1.0 O2' 1:G1181 4.3 65.6 1.0 N6 1:A1176 4.5 70.4 1.0 O6 1:G1182 4.6 67.4 1.0 C5 1:G1175 4.7 74.3 1.0 C6 1:G1177 4.7 67.6 1.0 C8 1:G1175 4.7 74.3 1.0 OP2 1:A1176 4.8 70.4 1.0 C8 1:A1176 4.9 70.4 1.0 C5 1:A1176 4.9 70.4 1.0 O6 1:G1175 5.0 74.3 1.0 C6 1:G1175 5.0 74.3 1.0

Magnesium binding site 6 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1606 b:55.1 occ:1.00 OP2 1:A1287 3.3 61.4 1.0 P 1:A1287 4.5 61.4 1.0 O3' 1:U1286 4.5 76.6 1.0

Magnesium binding site 7 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1607 b:56.3 occ:1.00 OP1 1:C1200 3.8 55.1 1.0 OP2 1:C1051 4.4 61.2 1.0 OP2 1:U1052 4.5 61.0 1.0 OP1 1:C1051 4.5 61.2 1.0 P 1:C1200 4.8 55.1 1.0 O2' 1:C962 4.8 49.7 1.0 P 1:C1051 5.0 61.2 1.0 OP1 1:A1201 5.0 53.1 1.0

Magnesium binding site 8 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1608 b:53.9 occ:1.00 OP1 1:G944 2.3 60.3 1.0 OP2 1:G945 2.6 59.4 1.0 P 1:G944 3.4 60.3 1.0 O5' 1:G944 3.8 60.3 1.0 P 1:G945 3.9 59.4 1.0 OP2 1:G944 4.0 60.3 1.0 C5' 1:G944 4.1 60.3 1.0 OP1 1:G945 4.4 59.4 1.0 OP2 1:A946 4.5 55.9 1.0 O5' 1:G945 4.7 59.4 1.0 O3' 1:U943 4.7 57.9 1.0 N7 1:A946 4.9 55.9 1.0 O3' 1:G944 5.0 60.3 1.0

Magnesium binding site 9 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1609 b:58.4 occ:1.00 O6 1:G1178 2.6 63.9 1.0 C6 1:G1178 3.8 63.9 1.0 OP2 1:A1176 4.0 70.4 1.0 OP1 1:A1176 4.7 70.4 1.0 N7 1:G1177 4.7 67.6 1.0 N1 1:G1178 4.7 63.9 1.0 C5 1:G1178 4.7 63.9 1.0 OP2 1:G1177 4.8 67.6 1.0 N7 1:G1178 4.9 63.9 1.0 P 1:A1176 4.9 70.4 1.0

Magnesium binding site 10 out of 42 in the Complex 4 (Head) 30S-GE81112 (Weak Residual Trna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Complex 4 (Head) 30S-GE81112 (Weak Residual Trna) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1610 b:56.8 occ:1.00 OP1 1:G1094 3.0 63.2 1.0 OP1 1:G1068 3.0 57.3 1.0 P 1:G1068 4.2 57.3 1.0 P 1:G1094 4.3 63.2 1.0 OP2 1:G1068 4.4 57.3 1.0 OP2 1:G1094 4.8 63.2 1.0

A.Schedlbauer, X.Han, W.Van Bakel, T.Kaminishi, B.Ochoa-Lizarralde, I.Iturrioz, R.Capuni, R.Parry, R.Zegarra, D.Gil-Carton, J.P.Lopez-Alonso, K.Barragan Sanz, L.Brandi, C.O.Gualerzi, P.Fucini, S.R.Connell. A Binding Site For the Antibiotic GE81112 in the Ribosomal Mrna Channel. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39386670
DOI: 10.1101/2024.09.26.614503