Magnesium in PDB 8qrk: Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1

The structure of Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1 also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Potassium	(K)	17 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 - 49;

Binding sites:

The binding sites of Magnesium atom in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1 (pdb code 8qrk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 49 binding sites of Magnesium where determined in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1, PDB code: 8qrk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg201 b:232.9 occ:1.00 OD1 3:ASN139 2.1 296.2 1.0 CG 3:ASN139 3.1 299.0 1.0 ND2 3:ASN139 3.5 299.9 1.0 O 3:ARG135 4.1 294.4 1.0 OP1 A:G1554 4.3 405.9 1.0 CB 3:ASN139 4.4 299.3 1.0 OP1 A:C1141 4.5 375.3 1.0 CA 3:ASN139 4.6 295.8 1.0 N 3:ASN139 4.6 295.8 1.0 CG 3:ARG135 4.7 281.8 1.0

Magnesium binding site 2 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1704 b:383.4 occ:1.00 OP2 A:A940 1.8 366.9 1.0 OP2 A:A939 2.2 404.8 1.0 OP2 A:A938 2.9 391.2 1.0 P A:A940 3.2 367.7 1.0 P A:A939 3.3 397.2 1.0 OP1 A:A939 3.6 395.7 1.0 OP1 A:A940 3.9 364.9 1.0 C3' A:A939 4.0 402.8 1.0 O3' A:A939 4.1 402.8 1.0 P A:A938 4.1 388.9 1.0 C5' A:A940 4.1 365.5 1.0 O5' A:A940 4.1 366.5 1.0 O5' A:A939 4.2 400.9 1.0 C5' A:A939 4.4 401.5 1.0 OP1 A:A938 4.4 387.3 1.0 O3' A:A938 4.5 388.1 1.0 OP1 A:U937 4.7 367.0 1.0 C5' A:A938 4.7 390.8 1.0 O5' A:A938 4.7 388.5 1.0 C4' A:A939 4.8 403.5 1.0 C3' A:A938 4.8 391.4 1.0 C8 A:A940 4.8 364.3 1.0 N7 A:A940 5.0 365.5 1.0

Magnesium binding site 3 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1705 b:381.8 occ:1.00 OP2 A:G1028 3.4 402.4 1.0 N1 A:A1102 4.0 429.3 1.0 OP2 A:A1104 4.1 396.3 1.0 C4' A:A1104 4.2 397.8 1.0 C2 A:A1102 4.3 430.2 1.0 O2' A:A1104 4.3 399.7 1.0 P A:G1028 4.3 405.9 1.0 O2' A:C1591 4.4 403.8 1.0 OP1 A:G1028 4.5 400.4 1.0 C5' A:A1027 4.6 395.5 1.0 O3' A:C1591 4.6 402.7 1.0 O3' A:A1027 4.7 395.6 1.0 O4' A:A1104 4.7 399.6 1.0 OP1 A:C1106 4.8 453.2 1.0 O5' A:A1104 4.9 399.6 1.0 OP2 A:C1106 4.9 455.4 1.0 C6 A:A1102 4.9 428.7 1.0 OP1 A:A1027 5.0 391.1 1.0 C5' A:A1104 5.0 397.1 1.0 P A:A1104 5.0 398.9 1.0

Magnesium binding site 4 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1706 b:372.7 occ:1.00 OP2 A:A1054 2.7 403.7 1.0 N4 A:C1099 3.4 388.6 1.0 N3 A:C1099 3.5 385.9 1.0 O2 A:C1100 3.6 422.4 1.0 C4 A:C1099 3.9 386.8 1.0 P A:A1054 4.1 408.7 1.0 C2 A:C1100 4.2 425.7 1.0 N3 A:C1100 4.2 424.9 1.0 O4 A:U1101 4.3 410.6 1.0 N6 A:A1056 4.4 347.2 1.0 O4 A:U1055 4.5 386.6 1.0 C2 A:C1099 4.6 387.6 1.0 OP1 A:A1054 4.6 406.0 1.0 C4 A:U1101 4.7 409.5 1.0 O2 A:C1099 4.8 387.1 1.0 O5' A:A1054 4.9 405.8 1.0 C3' A:A1053 5.0 361.8 1.0

Magnesium binding site 5 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1707 b:372.1 occ:1.00 OP2 A:A1067 2.5 383.3 1.0 OP2 A:C1088 3.6 457.6 1.0 P A:A1067 3.9 380.6 1.0 N7 A:A1067 4.0 385.9 1.0 N6 A:A1068 4.1 408.5 1.0 N7 A:A1068 4.2 402.7 1.0 C8 A:A1067 4.3 387.8 1.0 O5' A:A1067 4.4 383.9 1.0 P A:C1088 4.7 456.3 1.0 OP1 A:A1067 4.7 384.2 1.0 O5' A:C1088 4.8 456.0 1.0 C5 A:A1068 4.8 403.5 1.0 C6 A:A1068 4.9 406.1 1.0 C5 A:C1088 4.9 459.9 1.0 C3' A:C1066 5.0 395.6 1.0 O3' A:C1066 5.0 394.8 1.0 O5' A:C1066 5.0 395.7 1.0

Magnesium binding site 6 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1708 b:389.4 occ:1.00 OP1 A:G1327 2.2 400.7 1.0 OP1 A:U1259 2.4 460.3 1.0 OP2 A:G1328 3.1 375.6 1.0 P A:U1259 3.4 465.4 1.0 O2' A:A1326 3.5 447.4 1.0 P A:G1327 3.6 408.4 1.0 OP2 A:U1259 3.8 461.4 1.0 O5' A:U1259 3.9 465.6 1.0 P A:G1328 4.0 370.8 1.0 C2' A:A1326 4.3 443.4 1.0 OP1 A:G1328 4.3 369.3 1.0 OP2 A:G1327 4.3 396.7 1.0 O3' A:A1326 4.4 446.2 1.0 C3' A:A1326 4.4 444.8 1.0 O3' A:G1327 4.4 389.0 1.0 C6 A:U1259 4.5 460.1 1.0 C5 A:U1259 4.6 457.4 1.0 C5' A:G1327 4.6 394.4 1.0 O5' A:G1327 4.6 397.2 1.0 O3' A:A1258 4.8 386.5 1.0

Magnesium binding site 7 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1709 b:386.6 occ:1.00 OP1 A:A1266 1.9 410.9 1.0 O5' A:A1266 3.0 411.9 1.0 P A:A1266 3.0 414.9 1.0 OP2 A:U1267 3.3 428.0 1.0 CD2 H:HIS130 3.8 300.2 1.0 C5' A:A1266 3.8 408.5 1.0 OP2 A:A1266 4.0 412.5 1.0 O3' A:C1265 4.1 356.2 1.0 P A:U1267 4.2 427.1 1.0 OE1 H:GLN122 4.3 300.2 1.0 OP1 A:U1267 4.4 423.2 1.0 NE2 H:HIS130 4.5 300.2 1.0 CG H:HIS130 4.6 300.5 1.0 O3' A:A1266 4.8 409.4 1.0 C3' A:A1266 4.9 410.6 1.0 C4' A:A1266 4.9 408.6 1.0 NE2 H:GLN122 4.9 299.3 1.0 CB H:HIS130 5.0 300.9 1.0 OD1 C:ASN37 5.0 342.5 1.0

Magnesium binding site 8 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1710 b:368.0 occ:1.00 OP2 A:A1434 1.8 327.8 1.0 P A:A1434 2.7 335.2 1.0 OP1 A:A1434 3.1 331.0 1.0 OE1 G:GLU385 3.3 552.9 1.0 O5' A:A1434 3.4 332.2 1.0 OP2 A:A1435 4.0 329.5 1.0 O3' A:A1433 4.1 359.1 1.0 CD G:GLU385 4.2 551.8 1.0 CD G:ARG389 4.3 540.5 1.0 CG G:GLU385 4.5 552.1 1.0 C5' A:A1434 4.7 333.4 1.0 C3' A:A1433 4.8 357.5 1.0 NE G:ARG389 4.8 538.5 1.0 O5' A:A1433 4.8 353.4 1.0 C8 A:A1434 5.0 324.4 1.0

Magnesium binding site 9 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1711 b:403.8 occ:1.00 OP2 A:A1564 2.3 460.5 1.0 OP2 A:A1565 2.3 460.4 1.0 OP2 A:G1570 2.8 408.6 1.0 O3' A:U1563 3.2 463.6 1.0 P A:A1564 3.3 465.8 1.0 O2' A:U1563 3.7 457.1 1.0 P A:A1565 3.8 471.2 1.0 N7 A:A1565 4.0 451.0 1.0 O5' A:A1564 4.1 460.3 1.0 C3' A:A1564 4.1 461.3 1.0 P A:G1570 4.1 417.3 1.0 C8 A:A1565 4.3 451.7 1.0 C3' A:U1563 4.3 462.1 1.0 O2' A:G1569 4.4 420.3 1.0 O3' A:A1564 4.5 464.2 1.0 C5' A:A1564 4.6 458.0 1.0 OP1 A:A1564 4.6 459.2 1.0 C2' A:U1563 4.6 459.5 1.0 O5' A:A1565 4.6 461.0 1.0 C8 A:A1564 4.6 458.8 1.0 O3' A:G1569 4.7 421.3 1.0 OP1 A:A1565 4.8 460.2 1.0 OP1 A:G1570 4.8 413.2 1.0 N7 A:A1564 4.8 457.4 1.0 C4' A:A1564 4.9 459.3 1.0

Magnesium binding site 10 out of 49 in the Mt-Ssu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1712 b:363.4 occ:1.00 OP1 A:G1045 2.5 354.6 1.0 OP1 A:A1046 3.5 370.7 1.0 P A:G1045 3.8 360.2 1.0 O5' A:G1045 4.0 356.8 1.0 C5' A:G1045 4.2 358.4 1.0 O2 A:C1133 4.2 356.4 1.0 N3 A:A1109 4.6 369.7 1.0 O3' A:U1044 4.6 381.4 1.0 P A:A1046 4.7 366.6 1.0 N2 A:G941 4.7 330.4 1.0 C9 A:SPM1702 4.7 413.1 1.0 C8 A:SPM1702 4.8 412.5 1.0 O2' A:A1109 4.9 378.2 1.0 C2 A:A1109 4.9 371.3 1.0 O4' A:A1110 4.9 371.9 1.0 OP2 A:G1045 4.9 360.0 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 Is Essential For Mitoribosome Formation in Human Mitochondria Nat Commun 2024.
ISSN: ESSN 2041-1723