Magnesium in PDB 8qrn: Mt-Ssu in GTPBP8 Knock-Out Cells, State 4

The structure of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 also contains other interesting chemical elements:

Potassium	(K)	18 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 - 58;

Binding sites:

The binding sites of Magnesium atom in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 (pdb code 8qrn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 58 binding sites of Magnesium where determined in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4, PDB code: 8qrn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1704 b:71.9 occ:1.00 OP2 A:G791 1.7 78.2 1.0 OP2 A:G719 2.1 78.9 1.0 OP2 A:A718 2.1 83.2 1.0 P A:G791 3.1 78.5 1.0 P A:A718 3.2 88.0 1.0 O5' A:A718 3.3 78.3 1.0 P A:G719 3.5 82.4 1.0 O5' A:G791 3.7 76.6 1.0 OP1 A:G791 4.0 76.4 1.0 OP1 A:A718 4.0 76.4 1.0 O3' A:A790 4.2 83.2 1.0 C3' A:A790 4.2 78.7 1.0 O5' A:A790 4.2 82.5 1.0 O3' A:A718 4.3 81.0 1.0 OP1 A:G719 4.4 75.1 1.0 O5' A:G719 4.4 78.2 1.0 N7 A:G719 4.4 75.7 1.0 K A:K1759 4.4 89.1 1.0 O3' A:G717 4.4 71.3 1.0 C3' A:A718 4.5 76.4 1.0 O4 A:U720 4.6 87.9 1.0 C5' A:A718 4.7 74.3 1.0 OP2 A:A790 4.7 82.9 1.0 C8 A:G719 4.7 77.5 1.0 P A:A790 4.9 86.2 1.0 C5' A:G791 5.0 76.7 1.0

Magnesium binding site 2 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1705 b:39.0 occ:1.00 OP2 A:A940 2.2 34.9 1.0 OP2 A:A939 2.2 46.5 1.0 OP2 A:A938 2.5 55.0 1.0 P A:A939 3.4 54.2 1.0 P A:A940 3.7 54.2 1.0 OP1 A:A939 3.8 48.6 1.0 P A:A938 3.8 48.6 1.0 OP1 A:A938 4.3 40.0 1.0 OP1 A:U937 4.3 39.6 1.0 C5' A:A940 4.4 43.8 1.0 C3' A:A939 4.4 41.4 1.0 C5' A:A938 4.4 40.0 1.0 OP1 A:A940 4.4 52.1 1.0 O5' A:A938 4.5 39.6 1.0 O5' A:A939 4.5 34.1 1.0 O5' A:A940 4.5 38.6 1.0 O3' A:A938 4.5 42.3 1.0 O3' A:A939 4.6 44.5 1.0 O5' A:U937 4.6 35.1 1.0 C3' A:A938 4.7 30.3 1.0 C5' A:A939 4.8 39.9 1.0 C8 A:A940 4.8 31.8 1.0 N7 A:A940 4.9 38.1 1.0 P A:U937 4.9 44.3 1.0

Magnesium binding site 3 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1706 b:43.2 occ:1.00 OP2 A:G1028 3.3 40.7 1.0 OP2 A:A1104 4.2 28.4 1.0 N1 A:A1102 4.3 26.0 1.0 P A:G1028 4.4 39.3 1.0 O2' A:A1104 4.4 34.0 1.0 C4' A:A1104 4.5 25.8 1.0 C5' A:A1027 4.6 15.5 1.0 OP1 A:C1106 4.6 51.6 1.0 O3' A:C1591 4.6 31.2 1.0 OP1 A:G1028 4.6 35.4 1.0 OP2 A:C1106 4.6 55.4 1.0 C2 A:A1102 4.6 27.9 1.0 O2' A:C1591 4.6 37.7 1.0 OP1 A:A1027 4.7 29.7 1.0 O3' A:A1027 4.8 35.8 1.0

Magnesium binding site 4 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1707 b:43.7 occ:1.00 OP2 A:A1054 2.3 42.0 1.0 O2 A:C1100 3.6 42.1 1.0 N4 A:C1099 3.7 44.3 1.0 P A:A1054 3.7 37.3 1.0 N3 A:C1099 3.9 31.6 1.0 O4 A:U1101 4.1 39.3 1.0 C4 A:C1099 4.2 35.8 1.0 C2 A:C1100 4.2 37.1 1.0 N3 A:C1100 4.3 36.1 1.0 OP1 A:A1054 4.3 37.9 1.0 C3' A:A1053 4.6 28.9 1.0 C4 A:U1101 4.6 32.3 1.0 O5' A:A1054 4.6 32.8 1.0 O3' A:A1053 4.6 24.8 1.0 O4 A:U1055 4.7 45.6 1.0 N6 A:A1056 4.8 44.0 1.0 C2' A:A1053 4.9 31.8 1.0 C2 A:C1099 5.0 39.3 1.0

Magnesium binding site 5 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1708 b:58.6 occ:1.00 OP2 A:A1067 2.4 63.8 1.0 N7 A:A1067 3.8 58.1 1.0 OP2 A:C1088 3.8 68.3 1.0 P A:A1067 3.9 64.1 1.0 N6 A:A1068 4.1 56.2 1.0 C8 A:A1067 4.2 60.7 1.0 N7 A:A1068 4.2 56.1 1.0 O5' A:A1067 4.3 55.2 1.0 OP1 A:A1067 4.8 62.5 1.0 O5' A:C1066 4.8 70.4 1.0 C3' A:C1066 4.8 66.8 1.0 C5 A:A1068 4.8 50.9 1.0 O3' A:C1066 4.9 66.1 1.0 P A:C1088 4.9 70.5 1.0 C6 A:A1068 4.9 52.9 1.0 O5' A:C1088 5.0 69.6 1.0

Magnesium binding site 6 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1709 b:72.1 occ:1.00 OP1 A:A1082 1.8 61.3 1.0 OP1 A:C1070 2.1 51.2 1.0 P A:A1082 3.1 76.9 1.0 P A:C1070 3.4 62.9 1.0 OP2 A:U1071 3.6 68.3 1.0 OP2 A:A1082 3.7 67.4 1.0 O5' A:C1070 3.8 57.9 1.0 O5' A:A1082 4.1 55.0 1.0 C5' A:C1070 4.1 49.9 1.0 O3' A:U1081 4.2 75.0 1.0 OP2 A:C1070 4.3 64.5 1.0 N2 A:G1586 4.4 47.0 1.0 O3' A:A1069 4.5 48.7 1.0 C5' A:A1082 4.7 54.8 1.0 O2' A:U1580 4.7 58.8 1.0 N3 A:G1586 4.8 34.5 1.0 P A:U1071 4.9 70.9 1.0

Magnesium binding site 7 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1710 b:65.1 occ:1.00 OP2 A:A1090 1.8 60.5 1.0 O4 A:U1091 2.3 56.8 1.0 P A:A1090 3.2 70.0 1.0 C4 A:U1091 3.2 56.2 1.0 C5 A:U1091 3.5 55.4 1.0 OP1 A:A1090 3.8 62.7 1.0 N3 A:C1064 4.1 75.2 1.0 O5' A:A1090 4.1 57.4 1.0 N6 A:A1067 4.1 60.6 1.0 O3' A:U1089 4.2 55.8 1.0 C3' A:U1089 4.4 55.5 1.0 N3 A:U1091 4.5 60.0 1.0 N1 A:A1068 4.5 53.0 1.0 O5' A:U1089 4.6 64.2 1.0 N4 A:C1064 4.6 77.2 1.0 O6 A:G1092 4.7 57.2 1.0 O2 A:C1064 4.7 81.9 1.0 C2 A:A1068 4.8 53.3 1.0 C6 A:U1091 4.9 55.9 1.0 C4 A:C1064 4.9 75.7 1.0 C2 A:C1064 4.9 79.7 1.0

Magnesium binding site 8 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1711 b:27.0 occ:1.00 OP1 A:A1266 2.7 45.0 1.0 CD2 H:HIS130 4.0 54.0 1.0 P A:A1266 4.0 57.6 1.0 OE1 H:GLN122 4.1 78.0 1.0 O5' A:A1266 4.2 45.5 1.0 OP2 A:U1267 4.4 61.1 1.0 O6 A:G1320 4.5 57.0 1.0 NE2 H:GLN122 4.6 73.8 1.0 CD H:GLN122 4.8 71.9 1.0 CG H:HIS130 4.8 51.6 1.0 O3' A:C1265 4.9 37.5 1.0 NE2 H:HIS130 4.9 59.3 1.0 C5' A:A1266 4.9 43.3 1.0 OD1 C:ASN37 4.9 74.5 1.0

Magnesium binding site 9 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1712 b:63.3 occ:1.00 OP2 A:A1434 2.4 56.8 1.0 P A:A1434 3.8 62.0 1.0 N7 A:A1434 3.9 53.7 1.0 O5' A:A1434 4.0 48.3 1.0 N7 A:A1435 4.1 55.5 1.0 C8 A:A1434 4.2 52.8 1.0 O5' A:A1433 4.4 53.0 1.0 OP2 A:A1435 4.5 55.2 1.0 OP2 A:A1433 4.5 57.5 1.0 OP1 A:A1434 4.7 57.8 1.0 P A:A1433 4.8 53.2 1.0 O3' A:A1433 4.9 44.8 1.0 OP1 A:A1433 4.9 55.3 1.0 C5 A:A1434 4.9 42.2 1.0 C8 A:A1435 4.9 50.8 1.0 N6 A:A1435 5.0 54.8 1.0 C3' A:A1433 5.0 49.5 1.0

Magnesium binding site 10 out of 58 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mt-Ssu in GTPBP8 Knock-Out Cells, State 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1713 b:41.1 occ:1.00 OP2 A:A1564 2.0 42.9 1.0 OP2 A:A1565 2.2 53.0 1.0 OP2 A:G1570 2.5 43.3 1.0 O3' A:U1563 2.8 52.5 1.0 P A:A1564 2.9 59.7 1.0 O5' A:A1564 3.5 54.1 1.0 P A:A1565 3.7 50.6 1.0 P A:G1570 3.9 40.3 1.0 O2' A:U1563 3.9 50.8 1.0 C3' A:U1563 4.1 51.7 1.0 N7 A:A1565 4.1 47.8 1.0 O2' A:G1569 4.1 38.9 1.0 OP1 A:A1564 4.2 62.7 1.0 C3' A:A1564 4.3 44.1 1.0 C8 A:A1565 4.4 50.8 1.0 O3' A:G1569 4.4 48.6 1.0 O3' A:A1564 4.4 57.5 1.0 O5' A:A1565 4.5 32.2 1.0 C5' A:A1564 4.5 46.0 1.0 OP1 A:G1570 4.6 53.6 1.0 OP1 A:A1565 4.6 51.4 1.0 C2' A:U1563 4.6 52.4 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