Magnesium in PDB 8qu5: Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2

All present enzymatic activity of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2:
3.1.1.29;

The structure of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

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 - 48;

Binding sites:

The binding sites of Magnesium atom in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 (pdb code 8qu5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 48 binding sites of Magnesium where determined in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2, PDB code: 8qu5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ g:Mg201 b:43.0 occ:1.00 OD1 g:ASP99 2.1 37.9 1.0 CG g:ASP99 3.3 31.7 1.0 O2' A:A1893 3.6 17.8 1.0 N7 A:G1894 3.7 12.9 1.0 OP2 A:G1894 4.0 18.8 1.0 OD2 g:ASP99 4.0 34.4 1.0 O g:ILE100 4.1 27.9 1.0 CA g:ASP99 4.3 25.5 1.0 C8 A:G1894 4.3 13.0 1.0 CB g:ASP99 4.3 28.3 1.0 O3' A:A1893 4.4 18.4 1.0 N g:ILE100 4.4 25.6 1.0 C g:ASP99 4.8 25.1 1.0 P A:G1894 4.8 18.2 1.0 C2' A:A1893 4.9 17.8 1.0 C5 A:G1894 4.9 12.8 1.0

Magnesium binding site 2 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3301 b:47.8 occ:1.00 O W:GLY44 3.7 42.9 1.0 N4 A:C2829 3.8 36.5 1.0 O W:SER46 4.1 35.2 1.0 O6 A:G2828 4.1 35.7 1.0 N6 A:A2827 4.3 33.4 1.0 N7 A:A2827 4.3 35.4 1.0 N7 A:G2828 4.5 33.9 1.0 C W:GLY44 4.6 41.9 1.0 C4 A:C2829 4.9 36.5 1.0 C5 A:A2827 4.9 34.5 1.0 C6 A:A2827 4.9 33.4 1.0 C6 A:G2828 5.0 35.0 1.0

Magnesium binding site 3 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3302 b:34.7 occ:1.00 OP2 A:U2864 2.0 34.4 1.0 OP1 A:A2866 2.1 29.3 1.0 OP1 A:U2864 2.1 33.7 1.0 P A:U2864 2.5 31.2 1.0 O5' A:U2864 3.3 30.4 1.0 P A:A2866 3.4 25.3 1.0 O3' A:C2865 3.4 29.0 1.0 C5' A:U2864 3.9 30.4 1.0 O3' A:U2863 3.9 29.0 1.0 C5' A:A2866 4.3 20.9 1.0 C3' A:U2863 4.3 27.1 1.0 O5' A:A2866 4.4 22.8 1.0 OP2 A:A2866 4.4 27.4 1.0 C3' A:C2865 4.8 32.4 1.0 O2' A:C2865 4.9 36.7 1.0 C2' A:U2863 4.9 26.7 1.0

Magnesium binding site 4 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3303 b:29.6 occ:1.00 OP2 A:C1726 2.0 28.8 1.0 OP1 A:C1725 2.0 28.5 1.0 N7 A:A1723 2.7 22.6 1.0 C8 A:A1723 3.4 22.3 1.0 P A:C1726 3.4 27.5 1.0 P A:C1725 3.5 27.6 1.0 C5 A:A1723 3.8 22.1 1.0 OP2 A:A1723 4.0 26.6 1.0 OP2 A:A1722 4.0 32.5 1.0 N7 A:A1722 4.1 28.3 1.0 OP1 A:C1726 4.1 31.5 1.0 N6 A:A1723 4.2 21.9 1.0 O5' A:C1725 4.3 27.9 1.0 O3' A:C1725 4.3 28.6 1.0 C8 A:A1722 4.3 28.1 1.0 OP2 A:C1725 4.3 29.7 1.0 C5' A:C1725 4.4 28.5 1.0 O5' A:C1726 4.4 28.7 1.0 O3' A:A1724 4.5 28.4 1.0 C6 A:A1723 4.5 21.9 1.0 C5 A:C1726 4.7 25.6 1.0 N9 A:A1723 4.7 22.6 1.0 C3' A:C1725 4.7 29.2 1.0 O5' A:A1722 4.8 29.2 1.0 C5 A:A1722 4.8 27.5 1.0 C4 A:A1723 4.9 22.2 1.0

Magnesium binding site 5 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3304 b:24.5 occ:1.00 MG A:MG3306 1.8 23.8 1.0 OP2 A:G1776 2.0 21.0 1.0 OP1 A:G1776 2.2 19.3 1.0 P A:G1776 2.7 15.3 1.0 O F:GLY149 3.0 13.3 1.0 OP1 A:A1775 3.5 14.0 1.0 O3' A:A1775 3.7 14.0 1.0 O5' A:G1776 4.1 15.1 1.0 P A:A1775 4.1 13.4 1.0 OP2 A:A1775 4.2 14.1 1.0 C3' A:A1775 4.2 12.9 1.0 C F:GLY149 4.2 12.7 1.0 C F:GLY148 4.3 13.1 1.0 C5' A:A1775 4.3 12.2 1.0 O F:GLY148 4.4 13.5 1.0 O5' A:A1775 4.5 12.8 1.0 CA F:GLY148 4.6 13.2 1.0 N F:GLY149 4.6 12.8 1.0 CG2 F:VAL151 4.8 13.5 1.0 C4' A:A1775 4.9 12.3 1.0

Magnesium binding site 6 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3305 b:28.3 occ:1.00 OP2 A:A1815 2.0 22.3 1.0 OP1 A:A1814 2.0 30.3 1.0 P A:A1814 3.5 29.7 1.0 P A:A1815 3.5 19.0 1.0 O6 A:G1816 3.9 14.1 1.0 O5' A:A1814 4.1 26.0 1.0 N7 A:G1816 4.1 13.4 1.0 OP2 A:A1814 4.1 30.8 1.0 N7 A:A1815 4.2 21.0 1.0 OP1 A:A1815 4.3 19.4 1.0 O3' A:A1814 4.4 19.8 1.0 O5' A:A1815 4.4 17.6 1.0 C3' A:A1814 4.4 20.6 1.0 C8 A:A1815 4.5 20.0 1.0 N4 A:C1817 4.6 16.9 1.0 O3' A:C1813 4.6 32.3 1.0 C5' A:A1814 4.6 23.6 1.0 C6 A:G1816 4.7 13.2 1.0 C5 A:G1816 4.8 13.3 1.0

Magnesium binding site 7 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3306 b:23.8 occ:1.00 MG A:MG3304 1.8 24.5 1.0 OP2 A:G1776 2.1 21.0 1.0 OP1 A:G1776 3.0 19.3 1.0 P A:G1776 3.3 15.3 1.0 OP2 A:U1778 3.4 24.0 1.0 O F:GLY149 3.9 13.3 1.0 O5' A:G1776 4.0 15.1 1.0 OP2 A:A1777 4.1 16.9 1.0 O F:GLY148 4.1 13.5 1.0 OP2 A:A1775 4.3 14.1 1.0 C F:GLY148 4.5 13.1 1.0 OP1 A:A1775 4.6 14.0 1.0 O3' A:A1775 4.6 14.0 1.0 CG2 F:VAL120 4.6 23.5 1.0 CA F:GLY148 4.7 13.2 1.0 P A:U1778 4.7 21.3 1.0 N7 A:G1776 4.8 13.3 1.0 OP1 A:U1778 4.8 26.3 1.0 P A:A1775 4.9 13.4 1.0 C8 A:G1776 4.9 13.3 1.0 C F:GLY149 4.9 12.7 1.0 C3' A:A1775 5.0 12.9 1.0 C5' A:A1777 5.0 17.9 1.0

Magnesium binding site 8 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3307 b:211.4 occ:1.00 OP1 A:G1918 2.0 202.1 1.0 P A:G1918 2.6 200.7 1.0 O3' A:A1917 2.8 177.8 1.0 OP2 A:G1918 3.1 201.5 1.0 C3' A:A1917 3.1 157.6 1.0 O2' A:A1917 3.2 164.3 1.0 NZ 2:LYS59 3.6 91.4 1.0 C2' A:A1917 3.7 161.7 1.0 CE 2:LYS63 4.0 61.8 1.0 O5' A:G1918 4.1 209.6 1.0 NZ 2:LYS63 4.3 63.5 1.0 OP1 A:A1917 4.3 60.6 1.0 C4' A:A1917 4.6 134.9 1.0 C5' A:G1918 4.8 217.2 1.0 C1' A:A1917 5.0 161.0 1.0 CE 2:LYS59 5.0 89.7 1.0

Magnesium binding site 9 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3308 b:19.2 occ:1.00 OP2 A:G2011 2.0 17.3 1.0 P A:G2011 3.3 15.2 1.0 O3' A:U2010 3.7 15.6 1.0 OP1 A:G2011 4.2 15.8 1.0 OP2 A:G2009 4.3 16.4 1.0 O F:ALA118 4.3 20.4 1.0 O F:GLY123 4.3 21.1 1.0 OP1 A:G2008 4.5 15.5 1.0 O5' A:G2011 4.5 15.5 1.0 O F:GLY122 4.5 20.2 1.0 C5' A:G2011 4.6 15.0 1.0 NZ i:LYS112 4.8 15.2 1.0 CA F:ALA118 4.8 18.6 1.0 CA F:GLY124 4.8 21.3 1.0 C3' A:U2010 4.9 16.0 1.0 O2' A:U2010 4.9 16.3 1.0 C F:GLY123 4.9 20.2 1.0 C F:ALA118 5.0 19.4 1.0

Magnesium binding site 10 out of 48 in the Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mt-Lsu Assembly Intermediate in GTPBP8 Knock-Out Cells, State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3309 b:45.4 occ:1.00 OP2 A:A2027 2.0 42.1 1.0 P A:A2027 3.4 37.1 1.0 OP1 A:A2027 4.0 38.1 1.0 OP2 A:C2263 4.0 38.1 1.0 OP1 A:C2263 4.2 38.4 1.0 O5' A:A2027 4.2 36.8 1.0 N6 A:A2142 4.3 33.2 1.0 N7 A:G2028 4.4 29.0 1.0 O6 A:G2028 4.4 27.4 1.0 O3' A:A2026 4.5 34.7 1.0 N7 A:A2027 4.5 31.2 1.0 C3' A:A2026 4.5 34.0 1.0 O5' A:A2026 4.6 32.9 1.0 C8 A:A2027 4.6 31.3 1.0 P A:C2263 4.6 36.2 1.0 C5 A:C2263 4.9 31.6 1.0 OP1 A:A2026 5.0 36.6 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