Magnesium in PDB 7n0d: Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex

Other elements in 7n0d:

The structure of Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex also contains other interesting chemical elements:

Zinc (Zn) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex (pdb code 7n0d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex, PDB code: 7n0d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7n0d

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:95.0
occ:1.00
OP1 K:C71 2.2 88.6 1.0
OD2 B:ASP90 2.3 81.7 1.0
OD1 B:ASP273 2.3 87.5 1.0
OE2 B:GLU92 2.3 84.8 1.0
OD1 B:ASP90 3.0 81.7 1.0
CG B:ASP90 3.0 81.7 1.0
MG B:MG602 3.0 102.0 1.0
CG B:ASP273 3.4 87.5 1.0
P K:C71 3.5 88.6 1.0
CD B:GLU92 3.5 84.8 1.0
CB B:ASP273 3.8 87.5 1.0
OP2 K:C71 4.0 88.6 1.0
OE1 B:GLU92 4.1 84.8 1.0
O5' K:C71 4.4 88.6 1.0
CB B:ASP90 4.4 81.7 1.0
OD2 B:ASP273 4.5 87.5 1.0
ND1 B:HIS268 4.5 97.7 1.0
CA B:HIS268 4.5 97.7 1.0
O3' K:C70 4.6 91.2 1.0
CG B:GLU92 4.7 84.8 1.0
O B:VAL91 4.7 80.5 1.0
C5' K:C71 4.8 88.6 1.0
N B:HIS268 5.0 97.7 1.0

Magnesium binding site 2 out of 6 in 7n0d

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:102.0
occ:1.00
OD1 B:ASP90 2.4 81.7 1.0
MG B:MG601 3.0 95.0 1.0
OP1 K:C71 3.0 88.6 1.0
CG B:ASP90 3.3 81.7 1.0
OD2 B:ASP90 3.8 81.7 1.0
P K:C71 3.9 88.6 1.0
O3' K:C70 4.0 91.2 1.0
CD1 B:TRP186 4.0 80.7 1.0
OD1 B:ASP273 4.1 87.5 1.0
O B:HOH801 4.1 84.4 1.0
CB B:TRP186 4.3 80.7 1.0
CD2 B:LEU253 4.3 85.3 1.0
CB B:ASP273 4.3 87.5 1.0
OP2 K:C71 4.3 88.6 1.0
CG B:ASP273 4.4 87.5 1.0
CB B:ASP90 4.5 81.7 1.0
CG B:TRP186 4.5 80.7 1.0

Magnesium binding site 3 out of 6 in 7n0d

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:90.4
occ:1.00
OP1 P:C71 2.2 93.8 1.0
OD2 D:ASP90 2.3 81.4 1.0
OD1 D:ASP273 2.4 84.6 1.0
OD1 D:ASP90 2.4 81.4 1.0
OE2 D:GLU92 2.4 88.8 1.0
CG D:ASP90 2.6 81.4 1.0
CG D:ASP273 3.4 84.6 1.0
P P:C71 3.5 93.8 1.0
CD D:GLU92 3.6 88.8 1.0
CB D:ASP273 3.7 84.6 1.0
OP2 P:C71 4.1 93.8 1.0
CB D:ASP90 4.1 81.4 1.0
OE1 D:GLU92 4.2 88.8 1.0
O D:VAL91 4.3 83.1 1.0
O5' P:C71 4.5 93.8 1.0
OD2 D:ASP273 4.5 84.6 1.0
O3' P:C70 4.5 93.1 1.0
CA D:HIS268 4.6 96.9 1.0
CG D:GLU92 4.7 88.8 1.0
ND1 D:HIS268 4.7 96.9 1.0
C5' P:C71 4.9 93.8 1.0
C D:VAL91 4.9 83.1 1.0
O D:HOH801 4.9 86.0 1.0
N D:VAL91 5.0 83.1 1.0

Magnesium binding site 4 out of 6 in 7n0d

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:94.7
occ:1.00
OP1 L:C71 2.0 87.8 1.0
OD2 F:ASP90 2.3 81.4 1.0
OD1 F:ASP273 2.3 87.5 1.0
OE2 F:GLU92 2.3 84.8 1.0
OD1 F:ASP90 3.0 81.4 1.0
CG F:ASP90 3.0 81.4 1.0
MG F:MG602 3.0 101.5 1.0
P L:C71 3.3 87.8 1.0
CG F:ASP273 3.4 87.5 1.0
CD F:GLU92 3.5 84.8 1.0
CB F:ASP273 3.8 87.5 1.0
OP2 L:C71 3.8 87.8 1.0
OE1 F:GLU92 4.1 84.8 1.0
O5' L:C71 4.2 87.8 1.0
CB F:ASP90 4.4 81.4 1.0
O3' L:C70 4.4 90.7 1.0
OD2 F:ASP273 4.5 87.5 1.0
ND1 F:HIS268 4.5 97.5 1.0
CA F:HIS268 4.5 97.5 1.0
C5' L:C71 4.7 87.8 1.0
CG F:GLU92 4.7 84.8 1.0
O F:VAL91 4.7 80.5 1.0
N F:HIS268 5.0 97.5 1.0

Magnesium binding site 5 out of 6 in 7n0d

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:101.5
occ:1.00
OD1 F:ASP90 2.4 81.4 1.0
OP1 L:C71 3.0 87.8 1.0
MG F:MG601 3.0 94.7 1.0
CG F:ASP90 3.3 81.4 1.0
P L:C71 3.8 87.8 1.0
OD2 F:ASP90 3.8 81.4 1.0
O3' L:C70 3.9 90.7 1.0
CD1 F:TRP186 4.0 80.5 1.0
OD1 F:ASP273 4.1 87.5 1.0
O F:HOH801 4.1 84.5 1.0
OP2 L:C71 4.3 87.8 1.0
CB F:TRP186 4.3 80.5 1.0
CD2 F:LEU253 4.3 85.4 1.0
CB F:ASP273 4.3 87.5 1.0
CG F:ASP273 4.4 87.5 1.0
CB F:ASP90 4.5 81.4 1.0
CG F:TRP186 4.5 80.5 1.0
C5' L:C70 4.9 90.7 1.0

Magnesium binding site 6 out of 6 in 7n0d

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg702

b:90.3
occ:1.00
OP1 J:C71 2.2 93.1 1.0
OD2 H:ASP90 2.3 81.5 1.0
OD1 H:ASP273 2.4 84.8 1.0
OD1 H:ASP90 2.4 81.5 1.0
OE2 H:GLU92 2.4 88.8 1.0
CG H:ASP90 2.6 81.5 1.0
CG H:ASP273 3.4 84.8 1.0
P J:C71 3.6 93.1 1.0
CD H:GLU92 3.6 88.8 1.0
CB H:ASP273 3.7 84.8 1.0
OP2 J:C71 4.0 93.1 1.0
CB H:ASP90 4.1 81.5 1.0
OE1 H:GLU92 4.2 88.8 1.0
O H:VAL91 4.3 83.0 1.0
O5' J:C71 4.5 93.1 1.0
OD2 H:ASP273 4.5 84.8 1.0
O3' J:C70 4.6 92.5 1.0
CA H:HIS268 4.6 97.2 1.0
CG H:GLU92 4.7 88.8 1.0
ND1 H:HIS268 4.7 97.2 1.0
C H:VAL91 4.9 83.0 1.0
C5' J:C71 4.9 93.1 1.0
O H:HOH801 4.9 86.4 1.0
N H:VAL91 5.0 83.0 1.0

Reference:

C.Liu, W.Shi, S.T.Becker, D.G.Schatz, B.Liu, Y.Yang. Structural Basis of Mismatch Recognition By A Sars-Cov-2 Proofreading Enzyme Science 2021.
ISSN: ESSN 1095-9203
Page generated: Sat Aug 21 16:46:36 2021

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