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Magnesium in PDB 3j7y: Structure of the Large Ribosomal Subunit From Human Mitochondria

Other elements in 3j7y:

The structure of Structure of the Large Ribosomal Subunit From Human Mitochondria 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 - 66;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Large Ribosomal Subunit From Human Mitochondria (pdb code 3j7y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 66 binding sites of Magnesium where determined in the Structure of the Large Ribosomal Subunit From Human Mitochondria, PDB code: 3j7y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 66 in 3j7y

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Magnesium binding site 1 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3302

b:16.0
occ:1.00
OP1 A:A2866 2.2 14.3 1.0
OP2 A:U2864 2.3 17.0 1.0
P A:A2866 3.5 14.3 1.0
P A:U2864 3.7 17.0 1.0
O3' A:C2865 3.8 15.4 1.0
OP2 A:C2867 4.0 11.5 1.0
C5' A:A2866 4.3 12.6 1.0
O5' A:A2866 4.3 13.4 1.0
OP1 A:U2864 4.4 17.2 1.0
C2' A:U2863 4.5 16.8 1.0
C3' A:U2863 4.6 16.8 1.0
O5' A:U2864 4.6 17.2 1.0
O3' A:U2863 4.6 16.9 1.0
OP2 A:A2866 4.7 14.3 1.0
C5' A:U2864 4.8 17.6 1.0

Magnesium binding site 2 out of 66 in 3j7y

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Magnesium binding site 2 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3303

b:2.0
occ:1.00
OP1 A:U1848 2.4 8.2 1.0
O4 A:U2020 3.4 8.3 1.0
NE2 M:GLN58 3.6 11.3 1.0
P A:U1848 3.7 8.2 1.0
OE1 M:GLN58 3.8 11.2 1.0
CE M:LYS48 3.9 13.6 1.0
NZ M:LYS48 4.1 13.6 1.0
O3' A:U1847 4.1 8.2 1.0
CD M:GLN58 4.1 11.3 1.0
CD M:LYS48 4.2 13.5 1.0
ND1 M:HIS53 4.3 11.9 1.0
N7 A:G2019 4.3 7.1 1.0
C4 A:U2020 4.4 8.3 1.0
CE1 M:HIS53 4.6 11.9 1.0
OP2 A:U1848 4.6 8.2 1.0
O5' A:U1848 4.8 8.4 1.0
C5' A:U1848 4.9 8.6 1.0
C5 A:U2020 4.9 8.3 1.0
C8 A:G2019 5.0 7.1 1.0

Magnesium binding site 3 out of 66 in 3j7y

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Magnesium binding site 3 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3304

b:14.0
occ:1.00
OP2 A:A1757 2.2 25.6 1.0
O4 A:U1758 2.4 35.2 1.0
C4 A:U1758 3.3 34.7 1.0
P A:A1757 3.5 25.6 1.0
C5 A:U1758 3.6 34.4 1.0
OP1 A:A1757 4.0 25.8 1.0
O4 A:U1759 4.2 44.4 1.0
N6 A:A1739 4.4 34.2 1.0
O3' A:A1756 4.4 25.3 1.0
O5' A:A1757 4.6 26.3 1.0
N1 A:A1740 4.6 24.1 1.0
N3 A:U1758 4.6 34.7 1.0
O5' A:A1756 4.7 23.5 1.0
C3' A:A1756 4.8 25.0 1.0
C4 A:U1759 4.8 44.2 1.0
OP1 A:A1756 5.0 22.7 1.0
C6 A:U1758 5.0 34.5 1.0

Magnesium binding site 4 out of 66 in 3j7y

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Magnesium binding site 4 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3305

b:5.3
occ:1.00
OP2 A:C1726 1.9 11.0 1.0
OP1 A:C1725 2.2 10.2 1.0
N7 A:A1723 2.5 9.5 1.0
P A:C1726 3.3 11.1 1.0
C8 A:A1723 3.4 9.5 1.0
C5 A:A1723 3.6 9.5 1.0
P A:C1725 3.7 10.2 1.0
N6 A:A1723 3.8 9.5 1.0
N7 A:A1722 3.9 10.7 1.0
OP1 A:C1726 4.0 11.1 1.0
O3' A:C1725 4.0 11.1 1.0
C6 A:A1723 4.1 9.5 1.0
C8 A:A1722 4.3 10.7 1.0
OP2 A:A1722 4.3 11.3 1.0
O5' A:C1726 4.3 11.2 1.0
OP2 A:C1725 4.5 10.2 1.0
O3' A:A1724 4.5 10.1 1.0
O5' A:C1725 4.5 10.4 1.0
C5' A:C1725 4.6 10.6 1.0
OP2 A:A1723 4.6 10.1 1.0
C3' A:C1725 4.6 10.9 1.0
N9 A:A1723 4.6 9.5 1.0
C5 A:A1722 4.7 10.8 1.0
C4 A:A1723 4.7 9.5 1.0
C5 A:C1726 4.9 11.3 1.0
O5' A:A1722 5.0 11.0 1.0

Magnesium binding site 5 out of 66 in 3j7y

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Magnesium binding site 5 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3306

b:2.0
occ:1.00
OP2 A:G1776 2.6 11.0 1.0
OP2 A:U1778 3.4 12.6 1.0
CA F:GLY148 4.0 13.7 1.0
P A:G1776 4.1 11.0 1.0
O F:GLY148 4.1 13.5 1.0
C F:GLY148 4.1 13.6 1.0
OP2 A:A1775 4.2 12.1 1.0
O F:GLY149 4.3 13.4 1.0
OP1 A:A1775 4.4 12.1 1.0
OP2 A:A1777 4.5 11.4 1.0
CG2 F:VAL120 4.6 17.8 1.0
O5' A:G1776 4.6 10.9 1.0
P A:A1775 4.8 12.1 1.0
N F:GLY149 4.8 13.5 1.0
P A:U1778 4.9 12.6 1.0
O3' A:A1775 5.0 11.0 1.0
C F:GLY149 5.0 13.4 1.0
OP1 A:G1776 5.0 11.0 1.0

Magnesium binding site 6 out of 66 in 3j7y

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Magnesium binding site 6 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3307

b:2.0
occ:1.00
OP2 A:A1815 2.2 22.3 1.0
OP1 A:A1814 2.9 41.2 1.0
O6 A:G1816 3.5 17.2 1.0
P A:A1815 3.7 22.1 1.0
P A:A1814 3.8 41.2 1.0
N7 A:G1816 3.9 16.8 1.0
O5' A:A1814 4.0 35.8 1.0
OP2 A:A1814 4.2 40.8 1.0
C6 A:G1816 4.3 16.9 1.0
O5' A:A1815 4.4 20.7 1.0
N4 A:C1817 4.4 17.6 1.0
C5 A:G1816 4.5 16.8 1.0
N7 A:A1815 4.5 18.2 1.0
OP1 A:A1815 4.6 22.2 1.0
O3' A:A1814 4.6 24.0 1.0
C8 A:A1815 4.6 18.2 1.0
C3' A:A1814 4.6 26.2 1.0

Magnesium binding site 7 out of 66 in 3j7y

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Magnesium binding site 7 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3308

b:9.2
occ:1.00
O6 A:G1776 2.6 10.3 1.0
OP1 A:A1779 2.6 14.0 1.0
C6 A:G1776 3.4 10.2 1.0
N7 A:A1775 3.7 10.7 1.0
N7 A:G1776 3.8 10.2 1.0
C5 A:G1776 3.9 10.1 1.0
P A:A1779 4.0 14.0 1.0
N6 A:A1775 4.3 10.8 1.0
OP2 A:A1775 4.4 12.1 1.0
OP2 A:A1779 4.5 14.0 1.0
C5' A:A1779 4.6 15.1 1.0
N1 A:G1776 4.6 10.1 1.0
C5 A:A1775 4.6 10.7 1.0
C8 A:A1775 4.6 10.7 1.0
O5' A:A1779 4.7 14.5 1.0
C5' A:U1774 4.7 13.5 1.0
C6 A:A1775 4.9 10.7 1.0

Magnesium binding site 8 out of 66 in 3j7y

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Magnesium binding site 8 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3309

b:2.0
occ:1.00
OP2 A:C1942 2.1 32.6 1.0
OP2 A:A1971 2.4 16.8 1.0
P A:C1942 3.4 32.7 1.0
P A:A1971 3.9 16.9 1.0
OP1 A:C1942 4.0 32.9 1.0
O5' A:C1942 4.1 32.5 1.0
N7 A:A1971 4.2 19.3 1.0
N7 A:A1943 4.3 30.8 1.0
N6 A:A1943 4.3 30.4 1.0
O5' A:A1971 4.5 17.5 1.0
OP2 A:G1970 4.5 15.9 1.0
O5' A:G1970 4.5 15.7 1.0
C8 A:A1971 4.6 19.2 1.0
O3' A:G1941 4.6 31.9 1.0
OP1 A:A1971 4.7 17.1 1.0
O3' A:G1970 4.8 16.5 1.0
P A:G1970 4.8 15.8 1.0
OP1 A:G1970 4.9 15.8 1.0
C5 A:C1942 4.9 33.1 1.0
C3' A:G1970 4.9 16.1 1.0
C3' A:G1941 5.0 31.3 1.0

Magnesium binding site 9 out of 66 in 3j7y

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Magnesium binding site 9 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3310

b:5.6
occ:1.00
OP2 A:G1918 1.9 8.6 1.0
P A:G1918 3.2 8.6 1.0
O3' A:A1917 3.6 8.6 1.0
OP1 A:G1918 3.9 8.6 1.0
OP2 A:C1919 4.1 8.3 1.0
O6 A:G1981 4.1 11.0 1.0
O6 A:G1982 4.4 9.7 1.0
O5' A:G1918 4.4 8.5 1.0
N4 A:C1922 4.7 9.6 1.0
O2' A:A1917 4.8 8.8 1.0
O4 A:U1920 4.9 7.8 1.0
C3' A:A1917 5.0 8.6 1.0
C6 A:G1981 5.0 11.0 1.0

Magnesium binding site 10 out of 66 in 3j7y

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Magnesium binding site 10 out of 66 in the Structure of the Large Ribosomal Subunit From Human Mitochondria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Large Ribosomal Subunit From Human Mitochondria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3311

b:2.0
occ:1.00
OP2 A:A2504 2.2 10.4 1.0
OP1 A:A2503 2.6 11.4 1.0
OP2 A:U1950 2.7 16.1 1.0
OP1 A:U1950 2.8 16.0 1.0
P A:U1950 3.2 16.1 1.0
OP2 A:A2503 3.4 11.4 1.0
P A:A2503 3.4 11.4 1.0
P A:A2504 3.7 10.3 1.0
O5' A:U1950 4.3 15.8 1.0
O5' A:A2504 4.4 10.1 1.0
O3' A:G1949 4.4 16.1 1.0
O5' A:A2503 4.4 11.2 1.0
OP1 A:A2504 4.5 10.3 1.0
O3' A:A2503 4.6 10.5 1.0
C3' A:G1949 4.6 16.2 1.0
O3' A:C2502 4.7 11.6 1.0
C3' A:A2503 4.8 10.8 1.0
C5' A:U1950 4.9 15.6 1.0

Reference:

A.Brown, A.Amunts, X.C.Bai, Y.Sugimoto, P.C.Edwards, G.Murshudov, S.H.Scheres, V.Ramakrishnan. Structure of the Large Ribosomal Subunit From Human Mitochondria. Science 2014.
ISSN: ESSN 1095-9203
PubMed: 25278503
DOI: 10.1126/SCIENCE.1258026
Page generated: Mon Dec 14 08:18:23 2020

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