Zinc 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:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc 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 Zinc atom.
In total 20 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in 7n0d

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Zinc binding site 1 out of 20 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn201

b:114.2
occ:1.00
NE2 A:HIS83 1.8 90.1 1.0
SG A:CYS74 2.0 86.3 1.0
SG A:CYS90 2.2 94.0 1.0
SG A:CYS77 2.2 87.7 1.0
CD2 A:HIS83 2.8 90.1 1.0
CE1 A:HIS83 2.9 90.1 1.0
CB A:CYS74 3.1 86.3 1.0
CB A:CYS90 3.1 94.0 1.0
CB A:CYS77 3.6 87.7 1.0
N A:CYS77 3.8 87.7 1.0
CG A:HIS83 4.0 90.1 1.0
ND1 A:HIS83 4.0 90.1 1.0
CA A:CYS90 4.1 94.0 1.0
CA A:CYS77 4.2 87.7 1.0
CA A:CYS74 4.5 86.3 1.0
CB A:TYR76 4.5 83.6 1.0
C A:TYR76 4.6 83.6 1.0
C A:CYS74 4.9 86.3 1.0
N A:TYR76 4.9 83.6 1.0
CA A:TYR76 4.9 83.6 1.0
CD2 A:TYR76 5.0 83.6 1.0

Zinc binding site 2 out of 20 in 7n0d

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Zinc binding site 2 out of 20 in the Cryo-Em Structure of the Tetrameric Form of Sars-Cov-2 NSP10-NSP14 (E191A)-Rna Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn202

b:154.4
occ:1.00
SG A:CYS130 2.1 140.8 1.0
SG A:CYS120 2.2 124.5 1.0
SG A:CYS117 2.2 121.5 1.0
SG A:CYS128 2.3 126.9 1.0
CB A:CYS130 3.1 140.8 1.0
CB A:CYS117 3.2 121.5 1.0
CB A:CYS120 3.5 124.5 1.0
CB A:CYS128 3.7 126.9 1.0
CG2 A:VAL119 4.0 124.2 1.0
N A:CYS120 4.2 124.5 1.0
N A:CYS130 4.2 140.8 1.0
CA A:CYS128 4.2 126.9 1.0
CA A:CYS130 4.3 140.8 1.0
CA A:CYS120 4.4 124.5 1.0
CA A:CYS117 4.6 121.5 1.0
C A:CYS128 4.6 126.9 1.0
N A:SER129 4.8 135.8 1.0
C A:CYS117 4.9 121.5 1.0
C A:CYS120 5.0 124.5 1.0

Zinc binding site 3 out of 20 in 7n0d

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Zinc binding site 3 out of 20 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 Zinc with other atoms in the Zn 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
B:Zn603

b:122.0
occ:1.00
ND1 B:HIS229 1.8 96.8 1.0
SG B:CYS226 2.2 92.4 1.0
SG B:CYS207 2.3 98.1 1.0
CE1 B:HIS229 2.8 96.8 1.0
CG B:HIS229 2.8 96.8 1.0
SG B:CYS210 2.9 103.7 1.0
CB B:CYS210 2.9 103.7 1.0
CB B:HIS229 3.4 96.8 1.0
CB B:CYS207 3.5 98.1 1.0
CB B:CYS226 3.7 92.4 1.0
NE2 B:HIS229 3.9 96.8 1.0
CD2 B:HIS229 3.9 96.8 1.0
O B:CYS208 4.0 101.2 1.0
N B:CYS226 4.1 92.4 1.0
NH1 B:ARG212 4.1 98.6 1.0
N B:HIS229 4.1 96.8 1.0
CA B:HIS229 4.4 96.8 1.0
CA B:CYS210 4.4 103.7 1.0
CA B:CYS226 4.4 92.4 1.0
CB B:HIS228 4.7 93.5 1.0
N B:CYS210 4.9 103.7 1.0
CA B:CYS207 4.9 98.1 1.0
C B:CYS226 5.0 92.4 1.0

Zinc binding site 4 out of 20 in 7n0d

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Zinc binding site 4 out of 20 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 Zinc with other atoms in the Zn 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
B:Zn604

b:102.3
occ:1.00
NE2 B:HIS257 2.0 91.0 1.0
ND1 B:HIS264 2.0 89.9 1.0
SG B:CYS261 2.2 95.0 1.0
SG B:CYS279 2.2 86.2 1.0
CE1 B:HIS264 2.3 89.9 1.0
CB B:CYS261 2.8 95.0 1.0
CE1 B:HIS257 2.9 91.0 1.0
CD2 B:HIS257 3.1 91.0 1.0
CB B:CYS279 3.3 86.2 1.0
CG B:HIS264 3.4 89.9 1.0
NE2 B:HIS264 3.6 89.9 1.0
ND1 B:HIS257 4.1 91.0 1.0
CD2 B:HIS264 4.1 89.9 1.0
CG B:HIS257 4.2 91.0 1.0
N B:ASP415 4.2 94.9 1.0
CB B:HIS264 4.2 89.9 1.0
CA B:CYS261 4.3 95.0 1.0
N B:HIS264 4.5 89.9 1.0
CA B:CYS414 4.7 93.7 1.0
CA B:CYS279 4.7 86.2 1.0
SG B:CYS414 4.8 93.7 1.0
C B:CYS261 4.9 95.0 1.0
O B:GLY413 4.9 88.5 1.0
C B:CYS414 5.0 93.7 1.0
CA B:ASP415 5.0 94.9 1.0

Zinc binding site 5 out of 20 in 7n0d

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Zinc binding site 5 out of 20 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 Zinc with other atoms in the Zn 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
B:Zn605

b:164.3
occ:1.00
ND1 B:HIS487 1.8 144.7 1.0
SG B:CYS477 2.0 150.5 1.0
SG B:CYS484 2.3 150.3 1.0
SG B:CYS452 2.5 155.5 1.0
CE1 B:HIS487 2.6 144.7 1.0
CG B:HIS487 3.0 144.7 1.0
CB B:CYS477 3.3 150.5 1.0
CB B:CYS452 3.5 155.5 1.0
CB B:CYS484 3.7 150.3 1.0
CB B:HIS487 3.7 144.7 1.0
NE2 B:HIS487 3.8 144.7 1.0
CD2 B:HIS487 4.0 144.7 1.0
CA B:CYS452 4.3 155.5 1.0
N B:HIS487 4.4 144.7 1.0
CA B:CYS477 4.5 150.5 1.0
N B:CYS477 4.6 150.5 1.0
N B:CYS484 4.7 150.3 1.0
CA B:HIS487 4.8 144.7 1.0
CA B:CYS484 4.8 150.3 1.0
OG1 B:THR475 4.9 146.8 1.0
ND1 B:HIS486 4.9 145.5 1.0
N B:GLU453 5.0 155.9 1.0

Zinc binding site 6 out of 20 in 7n0d

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Zinc binding site 6 out of 20 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 Zinc with other atoms in the Zn 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
C:Zn201

b:129.5
occ:1.00
NE2 C:HIS83 1.8 111.0 1.0
SG C:CYS77 2.0 108.3 1.0
SG C:CYS90 2.2 120.6 1.0
SG C:CYS74 2.3 113.2 1.0
CE1 C:HIS83 2.8 111.0 1.0
CD2 C:HIS83 2.9 111.0 1.0
CB C:CYS90 2.9 120.6 1.0
CB C:CYS74 3.2 113.2 1.0
CB C:CYS77 3.5 108.3 1.0
N C:CYS77 3.6 108.3 1.0
ND1 C:HIS83 3.9 111.0 1.0
CA C:CYS90 3.9 120.6 1.0
CG C:HIS83 4.0 111.0 1.0
CA C:CYS77 4.0 108.3 1.0
C C:TYR76 4.4 105.7 1.0
CB C:TYR76 4.5 105.7 1.0
CA C:CYS74 4.6 113.2 1.0
CB C:LYS93 4.8 122.4 1.0
O C:CYS74 4.8 113.2 1.0
CA C:TYR76 4.8 105.7 1.0
N C:CYS90 4.9 120.6 1.0
C C:CYS74 4.9 113.2 1.0
C C:CYS90 4.9 120.6 1.0
N C:TYR76 5.0 105.7 1.0

Zinc binding site 7 out of 20 in 7n0d

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Zinc binding site 7 out of 20 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 Zinc with other atoms in the Zn binding site number 7 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
C:Zn202

b:182.1
occ:1.00
SG C:CYS130 2.1 163.7 1.0
SG C:CYS120 2.1 157.4 1.0
SG C:CYS117 2.3 155.0 1.0
SG C:CYS128 2.4 155.2 1.0
CB C:CYS117 3.0 155.0 1.0
CB C:CYS120 3.2 157.4 1.0
CB C:CYS130 3.3 163.7 1.0
CB C:CYS128 4.1 155.2 1.0
N C:CYS120 4.1 157.4 1.0
CG2 C:VAL119 4.3 157.0 1.0
N C:CYS130 4.3 163.7 1.0
CA C:CYS120 4.3 157.4 1.0
CA C:CYS130 4.4 163.7 1.0
CA C:CYS117 4.5 155.0 1.0
CA C:CYS128 4.8 155.2 1.0
O C:CYS130 5.0 163.7 1.0
C C:CYS117 5.0 155.0 1.0

Zinc binding site 8 out of 20 in 7n0d

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Zinc binding site 8 out of 20 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 Zinc with other atoms in the Zn binding site number 8 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:Zn602

b:121.4
occ:1.00
ND1 D:HIS229 1.8 98.8 1.0
SG D:CYS210 2.0 105.8 1.0
SG D:CYS207 2.2 100.5 1.0
SG D:CYS226 2.3 92.5 1.0
CE1 D:HIS229 2.8 98.8 1.0
CG D:HIS229 2.9 98.8 1.0
CB D:CYS210 3.4 105.8 1.0
CB D:CYS207 3.4 100.5 1.0
CB D:HIS229 3.5 98.8 1.0
CB D:CYS226 3.7 92.5 1.0
NE2 D:HIS229 3.9 98.8 1.0
CD2 D:HIS229 4.0 98.8 1.0
O D:CYS208 4.0 105.2 1.0
N D:CYS226 4.0 92.5 1.0
NH1 D:ARG212 4.0 99.7 1.0
N D:CYS210 4.1 105.8 1.0
N D:HIS229 4.2 98.8 1.0
CA D:CYS210 4.2 105.8 1.0
CA D:CYS226 4.4 92.5 1.0
C D:LEU209 4.5 106.7 1.0
CA D:HIS229 4.5 98.8 1.0
O D:LEU209 4.8 106.7 1.0
CA D:CYS207 4.8 100.5 1.0
C D:CYS210 4.8 105.8 1.0
CB D:HIS228 4.9 95.0 1.0
CB D:LEU209 4.9 106.7 1.0
C D:CYS226 5.0 92.5 1.0

Zinc binding site 9 out of 20 in 7n0d

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Zinc binding site 9 out of 20 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 Zinc with other atoms in the Zn binding site number 9 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:Zn603

b:101.1
occ:1.00
NE2 D:HIS257 2.0 86.5 1.0
ND1 D:HIS264 2.0 86.5 1.0
SG D:CYS261 2.2 91.6 1.0
SG D:CYS279 2.2 80.3 1.0
CE1 D:HIS264 2.7 86.5 1.0
CD2 D:HIS257 2.7 86.5 1.0
CB D:CYS261 2.8 91.6 1.0
CB D:CYS279 3.2 80.3 1.0
CE1 D:HIS257 3.2 86.5 1.0
CG D:HIS264 3.2 86.5 1.0
CB D:HIS264 3.8 86.5 1.0
NE2 D:HIS264 3.9 86.5 1.0
CG D:HIS257 4.0 86.5 1.0
ND1 D:HIS257 4.2 86.5 1.0
CD2 D:HIS264 4.2 86.5 1.0
CA D:CYS261 4.3 91.6 1.0
N D:ASP415 4.5 95.0 1.0
CA D:CYS279 4.6 80.3 1.0
N D:HIS264 4.6 86.5 1.0
SG D:CYS414 4.8 91.4 1.0
C D:CYS261 4.9 91.6 1.0
CA D:HIS264 4.9 86.5 1.0
CG2 D:VAL263 4.9 89.3 1.0
C D:CYS279 4.9 80.3 1.0

Zinc binding site 10 out of 20 in 7n0d

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Zinc binding site 10 out of 20 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 Zinc with other atoms in the Zn binding site number 10 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:Zn604

b:168.5
occ:1.00
ND1 D:HIS487 1.8 150.9 1.0
SG D:CYS477 2.1 155.1 1.0
SG D:CYS452 2.1 157.4 1.0
CE1 D:HIS487 2.4 150.9 1.0
CG D:HIS487 2.5 150.9 1.0
CB D:CYS452 2.8 157.4 1.0
SG D:CYS484 2.9 154.3 1.0
NE2 D:HIS487 3.2 150.9 1.0
CB D:CYS477 3.2 155.1 1.0
CD2 D:HIS487 3.3 150.9 1.0
CB D:HIS487 3.3 150.9 1.0
O D:SER450 4.1 155.0 1.0
CA D:CYS452 4.1 157.4 1.0
N D:CYS452 4.3 157.4 1.0
N D:HIS487 4.3 150.9 1.0
CB D:CYS484 4.3 154.3 1.0
CA D:HIS487 4.4 150.9 1.0
OG1 D:THR475 4.5 152.0 1.0
CA D:CYS477 4.5 155.1 1.0
CB D:THR475 4.5 152.0 1.0
N D:CYS477 4.5 155.1 1.0
C D:PRO451 4.7 156.2 1.0
ND1 D:HIS486 4.8 151.4 1.0
OG D:SER448 4.9 150.4 1.0
CG2 D:THR475 5.0 152.0 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: Sun Aug 22 09:48:45 2021

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