Potassium 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:

Iron	(Fe)	4 atoms
Zinc	(Zn)	1 atom
Magnesium	(Mg)	58 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Potassium 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 Potassium atom.
In total 18 binding sites of Potassium where determined in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4, PDB code: 8qrn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1758 b:114.0 occ:1.00 O2' A:C842 2.8 75.2 1.0 O3' A:C842 3.1 76.9 1.0 N3 A:C707 3.2 95.7 1.0 O2 A:C702 3.2 76.5 1.0 C5' A:G843 3.3 75.7 1.0 N4 A:C707 3.6 91.6 1.0 C2' A:C842 3.8 70.3 1.0 C4 A:C707 3.8 94.1 1.0 C3' A:C842 3.9 73.8 1.0 O2 A:C708 4.0 87.1 1.0 P A:G843 4.1 86.1 1.0 O5' A:G843 4.1 78.8 1.0 OP1 A:G843 4.1 83.3 1.0 C2 A:C707 4.1 95.7 1.0 O2 A:C707 4.2 96.0 1.0 C2 A:C708 4.3 85.7 1.0 C4' A:C842 4.3 72.7 1.0 C4' A:G843 4.4 80.7 1.0 C2 A:C702 4.4 74.9 1.0 N3 A:C708 4.5 85.0 1.0 N4 A:C706 4.5 100.5 1.0 O4' A:G843 4.9 79.1 1.0 O4' A:A703 4.9 82.1 1.0 N1 A:C708 4.9 84.4 1.0 N3 A:C702 5.0 77.2 1.0 C1' A:C842 5.0 69.5 1.0 C1' A:A703 5.0 77.1 1.0

Potassium binding site 2 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1759 b:89.1 occ:1.00 O6 A:G719 2.5 82.8 1.0 O2' A:G717 2.7 68.6 1.0 O4' A:G791 2.7 75.7 1.0 N7 A:G719 3.0 75.7 1.0 C6 A:G719 3.2 77.5 1.0 OP2 A:A718 3.4 83.2 1.0 C5 A:G719 3.4 76.2 1.0 C1' A:G791 3.5 74.2 1.0 O5' A:G791 3.6 76.6 1.0 N7 A:A718 3.6 76.9 1.0 N3 A:G717 3.7 65.3 1.0 C2' A:G717 3.8 69.1 1.0 O3' A:G717 3.9 71.3 1.0 C4' A:G791 3.9 75.1 1.0 C8 A:G791 3.9 79.4 1.0 N9 A:G791 3.9 77.2 1.0 C1' A:G717 4.0 70.6 1.0 C5' A:G791 4.2 76.7 1.0 C8 A:G719 4.2 77.5 1.0 P A:A718 4.3 88.0 1.0 C8 A:A718 4.3 78.6 1.0 O4 A:U720 4.3 87.9 1.0 C5 A:A718 4.4 76.0 1.0 N6 A:A718 4.4 79.3 1.0 MG A:MG1704 4.4 71.9 1.0 C3' A:G717 4.5 69.4 1.0 N2 A:G717 4.5 66.3 1.0 C2 A:G717 4.5 65.9 1.0 C4 A:G717 4.5 68.2 1.0 N1 A:G719 4.6 72.6 1.0 N9 A:G717 4.6 72.0 1.0 C4 A:U720 4.7 82.4 1.0 OP2 A:G791 4.7 78.2 1.0 C6 A:A718 4.7 76.7 1.0 P A:G791 4.8 78.5 1.0 C4 A:G719 4.8 71.8 1.0 C2' A:G791 4.9 76.7 1.0 N7 A:G791 4.9 78.5 1.0

Potassium binding site 3 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1760 b:97.7 occ:1.00 OD1 J:ASN74 2.5 69.1 1.0 O6 A:G901 2.8 54.6 1.0 N7 A:G901 3.0 56.3 1.0 C6 A:G901 3.5 49.8 1.0 C5 A:G901 3.6 55.2 1.0 C5 A:C900 3.6 43.3 1.0 CG J:ASN74 3.6 65.5 1.0 N3 A:C890 3.7 71.7 1.0 O J:PRO73 3.8 69.1 1.0 N4 A:C900 3.9 49.5 1.0 C4 A:C900 4.1 45.8 1.0 CA J:ASN74 4.1 62.4 1.0 O2 A:C890 4.1 68.1 1.0 C2 A:C890 4.2 70.8 1.0 C8 A:G901 4.2 52.0 1.0 C J:PRO73 4.3 68.2 1.0 C4 A:C890 4.4 73.0 1.0 CB J:ASN74 4.4 60.1 1.0 N J:ASN74 4.4 69.0 1.0 C6 A:C900 4.5 38.7 1.0 ND2 J:ASN74 4.6 64.5 1.0 N4 A:C890 4.6 68.2 1.0 N1 A:G901 4.8 41.4 1.0 C4 A:G901 4.9 55.3 1.0

Potassium binding site 4 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1761 b:61.9 occ:1.00 O2 A:C1105 2.6 40.9 1.0 O2' A:C1105 2.7 47.4 1.0 C1' A:C1105 3.1 40.4 1.0 OP2 A:U1107 3.2 43.5 1.0 O3' A:C1105 3.3 37.1 1.0 O3' A:U1592 3.3 32.6 1.0 C2' A:C1105 3.3 39.2 1.0 C5' A:U1593 3.6 39.2 1.0 C2 A:C1105 3.6 38.6 1.0 O2' A:U1592 3.7 37.0 1.0 N1 A:C1105 3.9 38.7 1.0 C3' A:C1105 3.9 33.1 1.0 N2 A:G1594 4.0 39.9 1.0 C5' A:C1106 4.1 50.2 1.0 OP1 A:U1593 4.1 44.0 1.0 C5' A:U1107 4.2 45.1 1.0 O4' A:C1105 4.2 36.5 1.0 P A:U1593 4.3 42.1 1.0 C3' A:U1592 4.3 31.7 1.0 O5' A:U1593 4.4 38.3 1.0 P A:U1107 4.4 57.2 1.0 C4' A:U1592 4.5 27.3 1.0 P A:C1106 4.5 60.3 1.0 C4' A:C1105 4.5 32.5 1.0 C3' A:C1106 4.5 39.1 1.0 OP2 A:C1106 4.6 55.4 1.0 C2' A:U1592 4.6 29.2 1.0 O5' A:U1107 4.7 50.3 1.0 C4' A:U1107 4.7 43.2 1.0 O4' A:U1107 4.7 42.4 1.0 O5' A:C1106 4.8 53.3 1.0 C4' A:C1106 4.8 42.8 1.0 C4' A:U1593 4.8 42.7 1.0 N3 A:C1105 4.9 36.7 1.0

Potassium binding site 5 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1762 b:141.8 occ:1.00 OP2 A:A1198 1.9 91.3 1.0 P A:A1198 3.0 84.8 1.0 O6 A:G1200 3.0 110.3 1.0 N7 A:G1421 3.4 115.1 1.0 OP1 A:A1198 3.4 81.8 1.0 O5' A:A1198 3.4 83.4 1.0 OP2 A:G1199 3.5 103.0 1.0 N7 A:G1200 3.6 110.7 1.0 C6 A:G1200 3.9 111.2 1.0 C5 A:G1421 4.0 116.6 1.0 O6 A:G1421 4.0 118.2 1.0 N7 A:G1199 4.0 102.6 1.0 C5 A:G1200 4.1 112.2 1.0 C8 A:G1421 4.2 116.9 1.0 C6 A:G1421 4.2 116.8 1.0 O3' A:G1197 4.4 73.1 1.0 N6 A:A1365 4.4 108.4 1.0 C3' A:A1198 4.7 86.2 1.0 C8 A:G1199 4.7 102.3 1.0 C8 A:A1198 4.7 87.2 1.0 C5' A:A1198 4.7 84.8 1.0 C8 A:G1200 4.8 111.3 1.0 P A:G1199 4.8 105.7 1.0 C4 A:G1421 4.9 116.2 1.0

Potassium binding site 6 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1763 b:124.5 occ:1.00 N7 A:G1362 2.2 82.5 1.0 OP1 A:G1199 3.0 102.2 1.0 C5 A:G1362 3.1 77.4 1.0 C8 A:G1362 3.2 79.5 1.0 O6 A:G1362 3.3 78.2 1.0 O3' A:A1198 3.4 89.3 1.0 C6 A:G1362 3.5 76.2 1.0 P A:G1199 3.8 105.7 1.0 C4 A:G1362 4.3 74.6 1.0 N7 A:G1361 4.3 77.8 1.0 N9 A:G1362 4.3 75.8 1.0 N4 A:C1363 4.5 84.0 1.0 OP2 A:G1362 4.6 78.8 1.0 C5 A:G1361 4.6 73.8 1.0 C3' A:A1198 4.7 86.2 1.0 C8 A:G1361 4.8 78.7 1.0 K A:K1764 4.8 103.1 1.0 C4' A:A1198 4.8 86.6 1.0 OP2 A:G1199 4.8 103.0 1.0 N1 A:G1362 4.8 74.2 1.0 C5' A:G1199 4.9 104.5 1.0 O5' A:G1199 4.9 107.3 1.0 C6 A:G1361 4.9 75.1 1.0 O6 A:G1361 4.9 75.9 1.0

Potassium binding site 7 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1764 b:103.1 occ:1.00 OP1 A:G1199 2.4 102.2 1.0 N7 A:A1201 3.2 107.7 1.0 OP2 A:G1200 3.3 109.2 1.0 P A:G1199 3.4 105.7 1.0 OP2 A:G1199 3.5 103.0 1.0 N6 A:A1201 3.8 106.2 1.0 O5' A:G1199 4.0 107.3 1.0 C5 A:A1201 4.0 107.2 1.0 C8 A:A1201 4.1 107.9 1.0 O6 A:G1202 4.2 99.1 1.0 C6 A:A1201 4.3 106.5 1.0 O6 A:G1362 4.4 78.2 1.0 OP2 A:A1201 4.6 109.9 1.0 C5' A:G1199 4.6 104.5 1.0 P A:G1200 4.7 108.7 1.0 N7 A:G1202 4.8 96.1 1.0 K A:K1763 4.8 124.5 1.0 O3' A:A1198 4.8 89.3 1.0 N4 A:C1363 4.9 84.0 1.0

Potassium binding site 8 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1765 b:108.7 occ:1.00 O2 A:C1330 2.5 71.2 1.0 O4 A:U1335 2.8 65.4 1.0 O4 A:U1257 2.9 74.2 1.0 N3 A:U1335 3.0 62.2 1.0 C4 A:U1335 3.1 65.2 1.0 C2 A:C1330 3.3 68.8 1.0 O6 A:G1336 3.6 75.1 1.0 N3 A:C1330 4.0 67.6 1.0 C2 A:U1335 4.0 58.2 1.0 N1 A:C1330 4.1 68.7 1.0 C4 A:U1257 4.1 72.9 1.0 C1' A:C1330 4.2 66.0 1.0 O2' A:C1330 4.2 66.5 1.0 N6 A:A1256 4.3 73.3 1.0 C5 A:U1335 4.3 61.0 1.0 N7 A:G1336 4.4 70.6 1.0 O2 A:U1335 4.5 62.6 1.0 C6 A:G1336 4.6 69.5 1.0 O4 A:U1337 4.6 80.6 1.0 N3 A:U1257 4.8 75.9 1.0 C2' A:C1330 4.8 66.8 1.0 C5 A:G1336 4.9 70.6 1.0 N1 A:U1335 5.0 59.3 1.0

Potassium binding site 9 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1766 b:75.4 occ:1.00 O6 A:G1328 2.2 63.2 1.0 O4 A:U1329 3.0 61.9 1.0 C6 A:G1328 3.3 58.1 1.0 N4 A:C1264 3.3 57.4 1.0 O6 A:G1263 3.3 61.7 1.0 OP2 A:C1262 4.0 54.3 1.0 C4 A:U1329 4.1 62.4 1.0 N1 A:G1328 4.2 54.2 1.0 C5 A:G1328 4.2 60.2 1.0 O6 A:G1327 4.3 65.1 1.0 N4 A:C1265 4.4 44.5 1.0 C6 A:G1263 4.4 57.3 1.0 N7 A:G1328 4.5 64.9 1.0 C4 A:C1264 4.6 49.6 1.0 N3 A:U1329 4.6 58.1 1.0 MG A:MG1746 4.8 49.9 1.0 N7 A:G1263 4.8 55.3 1.0

Potassium binding site 10 out of 18 in the Mt-Ssu in GTPBP8 Knock-Out Cells, State 4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1767 b:97.4 occ:1.00 N7 A:G1333 3.0 43.5 1.0 N7 A:G1334 3.1 51.8 1.0 O6 A:G1334 3.3 56.5 1.0 C5 A:G1333 3.6 43.2 1.0 O6 A:G1333 3.7 58.2 1.0 O4' A:C1330 3.8 67.5 1.0 C8 A:G1333 3.8 45.6 1.0 C5 A:G1334 3.9 51.2 1.0 C6 A:G1333 3.9 52.8 1.0 OP2 A:G1333 3.9 59.8 1.0 C6 A:G1334 3.9 53.7 1.0 C4' A:C1330 4.0 64.8 1.0 O3' A:C1330 4.0 70.8 1.0 C8 A:G1334 4.2 51.9 1.0 O4 A:U1335 4.2 65.4 1.0 C5' A:A1331 4.4 61.4 1.0 OP1 A:A1332 4.4 56.9 1.0 C1' A:C1330 4.5 66.0 1.0 C4 A:G1333 4.6 45.1 1.0 C3' A:C1330 4.6 66.7 1.0 N9 A:G1333 4.7 46.5 1.0 N6 A:A1258 4.8 62.8 1.0 C4 A:U1335 4.9 65.2 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