Magnesium in PDB 8qrm: Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3

The structure of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 also contains other interesting chemical elements:

Potassium	(K)	17 atoms
Iron	(Fe)	4 atoms
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 - 50; Page 6, Binding sites: 51 - 59;

Binding sites:

The binding sites of Magnesium atom in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 (pdb code 8qrm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 59 binding sites of Magnesium where determined in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3, PDB code: 8qrm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1704 b:104.9 occ:1.00 OP2 A:G791 1.7 96.1 1.0 OP2 A:G719 2.0 103.0 1.0 OP2 A:A718 2.4 92.1 1.0 P A:G791 3.2 98.1 1.0 P A:A718 3.4 95.7 1.0 O5' A:A718 3.4 99.3 1.0 P A:G719 3.5 111.8 1.0 O5' A:A790 3.9 90.8 1.0 O5' A:G791 3.9 85.3 1.0 OP1 A:G791 4.1 89.8 1.0 C3' A:A790 4.1 92.5 1.0 OP1 A:A718 4.1 92.0 1.0 O3' A:A790 4.1 94.9 1.0 OP1 A:G719 4.2 98.0 1.0 OP2 A:A790 4.3 94.2 1.0 O3' A:A718 4.3 97.5 1.0 O5' A:G719 4.4 100.2 1.0 K A:K1761 4.4 132.8 1.0 P A:A790 4.5 98.3 1.0 C3' A:A718 4.6 94.5 1.0 O3' A:G717 4.7 86.9 1.0 C5' A:A718 4.8 95.4 1.0 OP1 A:A790 4.8 92.7 1.0 N7 A:G719 4.8 93.5 1.0 O4 A:U720 4.8 106.5 1.0 C5' A:A790 4.9 87.6 1.0

Magnesium binding site 2 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1705 b:72.8 occ:1.00 OP2 A:A938 2.3 71.7 1.0 OP2 A:A939 2.4 60.0 1.0 OP2 A:A940 2.5 57.7 1.0 P A:A938 3.6 56.7 1.0 P A:A939 3.6 54.0 1.0 OP1 A:A939 3.9 57.7 1.0 P A:A940 3.9 61.1 1.0 OP1 A:U937 4.1 60.6 1.0 OP1 A:A938 4.1 53.3 1.0 C5' A:A938 4.3 60.8 1.0 O5' A:A938 4.3 55.3 1.0 O5' A:U937 4.3 51.9 1.0 C5' A:A940 4.5 65.7 1.0 OP1 A:A940 4.6 59.9 1.0 O3' A:A938 4.6 53.7 1.0 P A:U937 4.7 66.6 1.0 C3' A:A939 4.7 56.0 1.0 O5' A:A940 4.7 57.8 1.0 O5' A:A939 4.7 44.5 1.0 C3' A:A938 4.8 48.1 1.0 O3' A:U937 4.8 58.1 1.0 O3' A:A939 4.8 45.5 1.0 OP2 A:U937 4.9 73.2 1.0 C8 A:A940 5.0 54.3 1.0

Magnesium binding site 3 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1706 b:57.9 occ:1.00 OP2 A:G1028 3.2 60.6 1.0 P A:G1028 4.3 44.3 1.0 OP2 A:A1104 4.4 64.5 1.0 O3' A:C1591 4.5 58.7 1.0 OP2 A:C1106 4.5 88.8 1.0 OP1 A:C1106 4.6 91.1 1.0 N1 A:A1102 4.6 53.5 1.0 OP1 A:G1028 4.6 52.5 1.0 OP1 A:A1027 4.6 52.7 1.0 C5' A:A1027 4.6 52.0 1.0 O2' A:A1104 4.7 57.4 1.0 O2' A:C1591 4.7 69.2 1.0 O3' A:A1027 4.8 46.2 1.0 C4' A:A1104 4.8 61.3 1.0 OP1 A:U1592 4.9 71.6 1.0 C2 A:A1102 4.9 51.9 1.0

Magnesium binding site 4 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1707 b:67.8 occ:1.00 OP2 A:A1054 2.0 65.5 1.0 P A:A1054 3.4 69.5 1.0 N4 A:C1099 3.8 59.5 1.0 O2 A:C1100 3.9 63.1 1.0 OP1 A:A1054 4.0 64.9 1.0 O4 A:U1101 4.1 59.7 1.0 N3 A:C1099 4.1 60.0 1.0 O5' A:A1054 4.3 57.0 1.0 O3' A:A1053 4.4 57.6 1.0 C4 A:C1099 4.4 56.9 1.0 C3' A:A1053 4.4 58.7 1.0 C2 A:C1100 4.6 60.1 1.0 N3 A:C1100 4.6 64.0 1.0 O4 A:U1055 4.7 67.0 1.0 C4 A:U1101 4.7 57.2 1.0 C2' A:A1053 4.8 57.3 1.0 N6 A:A1056 4.9 68.0 1.0

Magnesium binding site 5 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1708 b:71.1 occ:1.00 OP2 A:A1067 2.0 102.3 1.0 P A:A1067 3.5 104.2 1.0 N7 A:A1067 4.0 95.9 1.0 OP2 A:C1088 4.0 117.5 1.0 O5' A:A1067 4.1 98.8 1.0 C8 A:A1067 4.1 96.0 1.0 O5' A:C1066 4.3 104.8 1.0 C3' A:C1066 4.4 103.0 1.0 OP1 A:A1067 4.4 100.0 1.0 O3' A:C1066 4.4 105.7 1.0 N7 A:A1068 4.6 92.1 1.0 N6 A:A1068 4.6 92.2 1.0 OP2 A:C1066 4.9 106.6 1.0

Magnesium binding site 6 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1709 b:83.5 occ:1.00 OP1 A:C1070 1.9 92.3 1.0 OP1 A:A1082 1.9 106.5 1.0 P A:A1082 3.2 116.0 1.0 P A:C1070 3.2 103.2 1.0 OP2 A:A1082 3.7 111.0 1.0 O5' A:C1070 3.7 90.8 1.0 OP2 A:U1071 3.8 115.5 1.0 OP2 A:C1070 3.9 95.4 1.0 O5' A:A1082 4.0 107.9 1.0 C5' A:C1070 4.2 84.9 1.0 O3' A:A1069 4.4 90.5 1.0 O3' A:U1081 4.4 110.0 1.0 C5' A:A1082 4.5 102.8 1.0 N2 A:G1586 4.7 79.1 1.0 O2' A:G1586 5.0 81.1 1.0 N3 A:G1586 5.0 80.8 1.0

Magnesium binding site 7 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1710 b:89.6 occ:1.00 OP2 A:A1090 2.3 91.1 1.0 O4 A:U1091 2.3 90.9 1.0 C4 A:U1091 3.3 89.5 1.0 P A:A1090 3.6 100.9 1.0 N6 A:A1067 3.8 97.9 1.0 C5 A:U1091 3.8 85.9 1.0 N3 A:C1064 3.8 119.5 1.0 OP1 A:A1090 4.2 93.8 1.0 O2 A:C1064 4.3 119.3 1.0 O6 A:G1092 4.3 83.7 1.0 N1 A:A1068 4.4 86.6 1.0 C2 A:C1064 4.5 119.8 1.0 N3 A:U1091 4.5 91.5 1.0 O5' A:A1090 4.6 93.9 1.0 O5' A:U1089 4.6 107.3 1.0 O3' A:U1089 4.6 99.5 1.0 N4 A:C1064 4.7 119.4 1.0 C4 A:C1064 4.7 117.5 1.0 C3' A:U1089 4.8 98.3 1.0 C2 A:A1068 4.8 92.4 1.0 C6 A:A1067 5.0 97.0 1.0

Magnesium binding site 8 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1711 b:220.8 occ:1.00 OP1 A:U1259 2.7 288.1 1.0 OP2 A:G1328 2.9 263.5 1.0 OP1 A:G1328 3.2 262.9 1.0 P A:G1328 3.5 262.8 1.0 OP1 A:G1327 3.6 245.8 1.0 P A:U1259 4.1 291.4 1.0 O3' A:G1327 4.3 244.9 1.0 OP2 A:U1259 4.8 290.7 1.0 O5' A:U1259 4.9 289.2 1.0 P A:G1327 4.9 249.2 1.0 O5' A:G1328 4.9 264.8 1.0

Magnesium binding site 9 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1712 b:174.8 occ:1.00 OP1 A:A1266 2.3 224.8 1.0 CD2 H:HIS130 2.8 144.1 1.0 O5' A:A1266 2.9 227.2 1.0 P A:A1266 3.2 229.0 1.0 C5' A:A1266 3.4 224.0 1.0 CG H:HIS130 3.5 144.6 1.0 OP2 A:U1267 3.6 211.4 1.0 NE2 H:HIS130 3.7 144.2 1.0 OE1 H:GLN122 3.7 164.7 1.0 CB H:HIS130 3.9 146.2 1.0 O3' A:C1265 3.9 232.0 1.0 OP1 A:U1267 4.2 204.8 1.0 P A:U1267 4.2 207.9 1.0 OP2 A:A1266 4.4 226.5 1.0 O3' A:A1266 4.5 223.2 1.0 ND1 H:HIS130 4.5 145.0 1.0 C4' A:A1266 4.5 223.7 1.0 CE1 H:HIS130 4.6 144.7 1.0 CD H:GLN122 4.6 165.2 1.0 C3' A:A1266 4.7 224.6 1.0 NE2 H:GLN122 4.8 165.3 1.0

Magnesium binding site 10 out of 59 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1713 b:262.6 occ:1.00 OP2 A:A1434 2.6 235.1 1.0 P A:A1434 3.5 238.9 1.0 OP2 A:A1435 3.5 237.6 1.0 OE1 G:GLU385 3.6 106.5 1.0 O5' A:A1434 3.8 236.4 1.0 OP1 A:A1434 3.9 234.4 1.0 CD G:GLU385 4.7 105.9 1.0 N7 A:A1435 4.7 237.3 1.0 CG G:GLU385 4.9 104.6 1.0 O3' A:A1433 4.9 228.7 1.0 P A:A1435 5.0 238.6 1.0

M.Cipullo, G.Valentin Gese, S.Gopalakrishna, A.Krueger, V.Lobo, M.A.Pirozhkova, J.Marks, P.Palenkova, D.Shiriaev, Y.Liu, J.Misic, Y.Cai, M.Nguyen, A.Abdelbagi, X.Li, M.Minczuk, M.Hafner, D.Benhalevy, A.A.Sarshad, I.Attanasov, B.M.Hallberg, J.Rorbach. GTPBP8 Plays A Role in Mitoribosome Formation in Human Mitochondria Nat Commun 2024.
ISSN: ESSN 2041-1723