Magnesium in PDB 7of0: Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).

Enzymatic activity of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).

All present enzymatic activity of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).:
3.1.1.29;

Other elements in 7of0:

The structure of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

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 - 60; Page 7, Binding sites: 61 - 61;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). (pdb code 7of0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 61 binding sites of Magnesium where determined in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1)., PDB code: 7of0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 61 in 7of0

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Magnesium binding site 1 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3301

b:71.2
occ:1.00
OP1 A:A2866 2.8 59.4 1.0
OP2 A:U2864 3.0 87.7 1.0
C2 A:U2863 3.6 72.0 1.0
C2' A:U2863 3.7 72.0 1.0
O2 A:U2863 3.8 72.0 1.0
N3 A:U2863 3.9 72.0 1.0
N1 A:U2863 4.0 72.0 1.0
OP2 A:C2867 4.1 56.4 1.0
P A:A2866 4.1 59.4 1.0
C3' A:U2863 4.3 72.0 1.0
P A:U2864 4.4 87.7 1.0
C1' A:U2863 4.4 72.0 1.0
C4 A:U2863 4.5 72.0 1.0
C6 A:U2863 4.5 72.0 1.0
OP2 A:A2866 4.6 59.4 1.0
O2' A:U2863 4.6 72.0 1.0
N6 A:A2869 4.6 58.0 1.0
C5' A:U2864 4.7 87.7 1.0
C5 A:U2863 4.7 72.0 1.0
O3' A:U2863 4.7 72.0 1.0
O3' A:C2865 4.9 81.6 1.0

Magnesium binding site 2 out of 61 in 7of0

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Magnesium binding site 2 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3302

b:56.0
occ:1.00
O4 A:U1758 2.0 62.3 1.0
OP2 A:A1757 2.1 58.7 1.0
C4 A:U1758 3.1 62.3 1.0
P A:A1757 3.5 58.7 1.0
O4 A:U1759 3.6 70.3 1.0
C5 A:U1758 3.8 62.3 1.0
O5' A:A1756 3.9 54.0 1.0
N1 A:A1740 4.0 52.1 1.0
N6 A:A1739 4.1 61.3 1.0
OP1 A:A1757 4.2 58.7 1.0
N3 A:U1758 4.3 62.3 1.0
O3' A:A1756 4.3 54.0 1.0
C3' A:A1756 4.3 54.0 1.0
C2 A:A1740 4.5 52.1 1.0
OP2 A:A1756 4.5 54.0 1.0
O5' A:A1757 4.5 58.7 1.0
P A:A1756 4.6 54.0 1.0
C4 A:U1759 4.6 70.3 1.0
OP1 A:A1756 4.7 54.0 1.0
C5' A:A1756 4.8 54.0 1.0

Magnesium binding site 3 out of 61 in 7of0

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Magnesium binding site 3 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3303

b:48.9
occ:1.00
OP1 A:C1725 1.9 51.6 1.0
OP2 A:C1726 2.0 51.7 1.0
N7 A:A1723 2.2 48.2 1.0
C8 A:A1723 3.1 48.2 1.0
P A:C1725 3.4 51.6 1.0
C5 A:A1723 3.4 48.2 1.0
P A:C1726 3.4 51.7 1.0
N6 A:A1723 3.7 48.2 1.0
C6 A:A1723 4.0 48.2 1.0
N7 A:A1722 4.0 48.2 1.0
OP2 A:C1725 4.1 51.6 1.0
OP2 A:A1723 4.1 48.2 1.0
OP2 A:A1722 4.1 48.2 1.0
OP1 A:C1726 4.2 51.7 1.0
O5' A:C1725 4.2 51.6 1.0
O3' A:C1725 4.2 51.6 1.0
C8 A:A1722 4.3 48.2 1.0
O3' A:A1724 4.3 50.2 1.0
N9 A:A1723 4.3 48.2 1.0
O5' A:C1726 4.4 51.7 1.0
C5' A:C1725 4.4 51.6 1.0
C4 A:A1723 4.5 48.2 1.0
C5 A:C1726 4.6 51.7 1.0
C3' A:C1725 4.7 51.6 1.0
C5 A:A1722 4.7 48.2 1.0
O5' A:A1722 4.9 48.2 1.0

Magnesium binding site 4 out of 61 in 7of0

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Magnesium binding site 4 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3304

b:50.1
occ:1.00
OP2 A:U1778 2.3 46.8 1.0
OP2 A:G1776 3.1 39.6 1.0
P A:U1778 3.8 46.8 1.0
O F:GLY148 4.0 44.3 1.0
OP2 A:A1777 4.2 52.9 1.0
P A:G1776 4.4 39.6 1.0
C5' A:U1778 4.5 46.8 1.0
OP1 A:U1778 4.5 46.8 1.0
C F:GLY148 4.5 44.3 1.0
O5' A:U1778 4.5 46.8 1.0
C5' A:A1777 4.6 52.9 1.0
CA F:GLY148 4.6 44.3 1.0
CG1 F:VAL120 4.7 45.3 1.0
O F:GLY149 4.7 43.1 1.0
O5' A:G1776 4.7 39.6 1.0
OP2 A:A1775 4.7 52.5 1.0
O3' A:A1777 4.8 52.9 1.0
N7 A:G1776 4.8 39.6 1.0
OP2 A:A1779 4.9 45.9 1.0
C8 A:G1776 4.9 39.6 1.0

Magnesium binding site 5 out of 61 in 7of0

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Magnesium binding site 5 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3305

b:52.1
occ:1.00
OP2 A:A1815 2.1 47.7 1.0
OP1 A:A1814 2.1 53.9 1.0
P A:A1815 3.5 47.7 1.0
P A:A1814 3.5 53.9 1.0
O6 A:G1816 3.6 46.2 1.0
N7 A:G1816 3.8 46.2 1.0
O5' A:A1814 4.2 53.9 1.0
OP1 A:A1815 4.2 47.7 1.0
O5' A:A1815 4.2 47.7 1.0
OP2 A:A1814 4.3 53.9 1.0
N4 A:C1817 4.3 47.8 1.0
C6 A:G1816 4.4 46.2 1.0
N7 A:A1815 4.4 47.7 1.0
C5 A:G1816 4.5 46.2 1.0
O3' A:A1814 4.5 53.9 1.0
O3' A:C1813 4.6 70.8 1.0
C3' A:A1814 4.6 53.9 1.0
C8 A:A1815 4.7 47.7 1.0
C5' A:A1814 4.7 53.9 1.0
OP2 A:C1813 4.9 70.8 1.0
C8 A:G1816 5.0 46.2 1.0

Magnesium binding site 6 out of 61 in 7of0

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Magnesium binding site 6 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3306

b:45.1
occ:1.00
OP1 A:A1779 2.0 45.9 1.0
O6 A:G1776 2.1 39.6 1.0
C6 A:G1776 3.2 39.6 1.0
P A:A1779 3.4 45.9 1.0
C5 A:G1776 3.9 39.6 1.0
N7 A:G1776 4.0 39.6 1.0
O5' A:A1779 4.0 45.9 1.0
OP2 A:A1779 4.2 45.9 1.0
N7 A:A1775 4.2 52.5 1.0
C5' A:A1779 4.3 45.9 1.0
N1 A:G1776 4.3 39.6 1.0
O3' A:U1778 4.4 46.8 1.0
OP2 A:A1775 4.4 52.5 1.0
N6 A:A1775 4.7 52.5 1.0
OP1 A:A1795 4.9 50.1 1.0
C5' A:U1774 5.0 48.4 1.0
C5 A:A1775 5.0 52.5 1.0

Magnesium binding site 7 out of 61 in 7of0

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Magnesium binding site 7 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3307

b:45.3
occ:1.00
OP2 A:G1918 2.0 46.8 1.0
P A:G1918 3.3 46.8 1.0
O3' A:A1917 3.7 46.4 1.0
OP2 A:C1919 3.8 48.4 1.0
O5' A:G1918 4.1 46.8 1.0
O6 A:G1981 4.2 50.8 1.0
O4 A:U1920 4.2 48.7 1.0
O6 A:G1982 4.3 49.6 1.0
OP1 A:G1918 4.5 46.8 1.0
N4 A:C1922 4.8 51.3 1.0

Magnesium binding site 8 out of 61 in 7of0

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Magnesium binding site 8 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3308

b:57.7
occ:1.00
OP2 A:U1950 1.9 61.0 1.0
OP1 A:A2503 1.9 61.0 1.0
OP2 A:A2504 2.1 57.9 1.0
P A:U1950 3.1 61.0 1.0
P A:A2504 3.2 57.9 1.0
P A:A2503 3.4 61.0 1.0
OP1 A:A2504 3.5 57.9 1.0
OP1 A:U1950 3.6 61.0 1.0
O5' A:U1950 4.0 61.0 1.0
OP2 A:A2503 4.1 61.0 1.0
O3' A:A2503 4.2 61.0 1.0
O5' A:A2503 4.2 61.0 1.0
O3' A:C2502 4.3 64.0 1.0
O3' A:G1949 4.3 59.1 1.0
O5' A:A2504 4.4 57.9 1.0
C5' A:A2503 4.4 61.0 1.0
OP2 A:C1951 4.4 61.0 1.0
C3' A:A2503 4.5 61.0 1.0
C3' A:G1949 4.7 59.1 1.0
C5' A:U1950 4.7 61.0 1.0

Magnesium binding site 9 out of 61 in 7of0

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Magnesium binding site 9 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3309

b:48.4
occ:1.00
OP2 A:G2011 2.0 46.5 1.0
P A:G2011 3.3 46.5 1.0
O3' A:U2010 3.6 49.7 1.0
OP2 A:G2009 4.0 45.0 1.0
OP1 A:G2011 4.2 46.5 1.0
O F:GLY122 4.2 47.5 1.0
O F:ALA118 4.3 45.6 1.0
OP1 A:G2008 4.3 49.7 1.0
O5' A:G2011 4.4 46.5 1.0
O F:GLY123 4.4 48.8 1.0
NZ i:LYS112 4.5 46.2 1.0
C5' A:G2011 4.6 46.5 1.0
O2' A:U2010 4.6 49.7 1.0
C3' A:U2010 4.7 49.7 1.0
CA F:GLY124 4.8 50.1 1.0
C F:GLY123 4.9 48.8 1.0
CA F:ALA118 4.9 45.6 1.0
O F:ARG117 5.0 45.7 1.0

Magnesium binding site 10 out of 61 in 7of0

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Magnesium binding site 10 out of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3310

b:62.4
occ:1.00
OP1 A:A3076 2.0 67.8 1.0
OP2 A:A1993 2.2 57.1 1.0
OP2 A:A1994 2.3 65.0 1.0
P A:A1993 3.3 57.1 1.0
P A:A3076 3.4 67.8 1.0
O3' A:C1992 3.5 57.8 1.0
P A:A1994 3.7 65.0 1.0
O5' A:A1993 3.9 57.1 1.0
O3' A:G3075 4.1 66.0 1.0
O5' A:A3076 4.2 67.8 1.0
C5' A:A1993 4.4 57.1 1.0
OP2 A:A3076 4.4 67.8 1.0
OP1 A:A1994 4.4 65.0 1.0
C5' A:A3076 4.4 67.8 1.0
O3' A:A1993 4.5 57.1 1.0
OP1 A:A1993 4.6 57.1 1.0
O5' A:A1994 4.8 65.0 1.0
C3' A:A1993 4.8 57.1 1.0
C3' A:C1992 4.9 57.8 1.0
O2' A:C1992 4.9 57.8 1.0

Reference:

H.S.Hillen, E.Lavdovskaia, F.Nadler, E.Hanitsch, A.Linden, K.E.Bohnsack, H.Urlaub, R.Richter-Dennerlein. Structural Basis of Gtpase-Mediated Mitochondrial Ribosome Biogenesis and Recycling Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Mon Jul 12 14:52:56 2021

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