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Zinc in PDB 5nfy: Sars-Cov NSP10/NSP14 Dynamic Complex

Protein crystallography data

The structure of Sars-Cov NSP10/NSP14 Dynamic Complex, PDB code: 5nfy was solved by F.Ferron, L.Gluais, C.Vonrhein, G.Bricogne, B.Canard, I.Imbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.40 / 3.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 185.881, 189.786, 196.245, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.5

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Sars-Cov NSP10/NSP14 Dynamic Complex (pdb code 5nfy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Sars-Cov NSP10/NSP14 Dynamic Complex, PDB code: 5nfy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in 5nfy

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Zinc binding site 1 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:0.4
occ:1.00
SG A:CYS210 0.8 67.0 1.0
ND1 A:HIS229 1.9 77.5 1.0
SG A:CYS207 1.9 73.3 1.0
SG A:CYS226 2.4 83.1 1.0
CB A:CYS210 2.6 82.9 1.0
CE1 A:HIS229 2.7 77.3 1.0
CB A:CYS207 2.9 83.0 1.0
CG A:HIS229 3.0 81.3 1.0
CB A:CYS226 3.2 58.6 1.0
CB A:HIS229 3.5 81.5 1.0
N A:CYS226 3.7 61.5 1.0
O A:CYS208 3.7 0.5 1.0
CA A:CYS210 3.7 76.5 1.0
N A:CYS210 3.8 80.1 1.0
NE2 A:HIS229 3.8 68.8 1.0
CD2 A:HIS229 4.0 75.7 1.0
CA A:CYS226 4.0 59.7 1.0
CA A:CYS207 4.3 61.7 1.0
N A:HIS229 4.5 85.2 1.0
C A:CYS207 4.5 61.6 1.0
C A:CYS210 4.6 75.9 1.0
CA A:HIS229 4.6 85.4 1.0
C A:ALA225 4.8 54.2 1.0
O A:CYS207 4.8 71.5 1.0
C A:CYS226 4.8 56.4 1.0
CA A:ALA225 4.9 58.9 1.0
C A:CYS208 4.9 85.9 1.0
N A:CYS208 5.0 71.3 1.0

Zinc binding site 2 out of 20 in 5nfy

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Zinc binding site 2 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:0.2
occ:1.00
ND1 A:HIS264 2.3 89.9 1.0
SG A:CYS279 2.4 80.4 1.0
NE2 A:HIS257 2.4 0.8 1.0
SG A:CYS261 2.5 0.1 1.0
CG A:HIS264 3.1 86.6 1.0
CB A:CYS279 3.2 79.9 1.0
CB A:HIS264 3.2 99.7 1.0
CE1 A:HIS257 3.2 0.8 1.0
CE1 A:HIS264 3.4 0.4 1.0
CB A:CYS261 3.4 0.2 1.0
CD2 A:HIS257 3.4 96.2 1.0
N A:HIS264 4.1 0.2 1.0
CD2 A:HIS264 4.3 90.9 1.0
CA A:HIS264 4.3 0.2 1.0
NE2 A:HIS264 4.4 0.8 1.0
ND1 A:HIS257 4.4 0.3 1.0
CG A:HIS257 4.5 0.1 1.0
CA A:CYS279 4.6 83.6 1.0
CA A:CYS261 4.9 0.9 1.0
N A:ASP415 4.9 0.6 1.0

Zinc binding site 3 out of 20 in 5nfy

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Zinc binding site 3 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:92.2
occ:1.00
SG A:CYS477 1.1 0.0 1.0
CB A:CYS477 2.5 0.5 1.0
SG A:CYS484 2.6 73.0 1.0
NE2 A:HIS487 2.6 0.5 1.0
CB A:CYS484 2.6 0.1 1.0
SG A:CYS452 2.6 86.5 1.0
CD2 A:HIS487 2.8 90.1 1.0
CE1 A:HIS487 3.6 0.8 1.0
CA A:CYS477 3.7 1.0 1.0
CG A:HIS487 3.8 86.2 1.0
N A:CYS477 3.9 94.3 1.0
OG1 A:THR475 3.9 0.8 1.0
CB A:CYS452 4.0 88.7 1.0
O A:CYS477 4.0 91.9 1.0
CA A:CYS484 4.1 93.9 1.0
ND1 A:HIS487 4.2 0.2 1.0
O A:ALA482 4.3 0.1 1.0
C A:CYS477 4.3 86.9 1.0
CG2 A:THR475 4.4 82.0 1.0
N A:CYS484 4.6 0.0 1.0
O A:CYS484 4.7 0.6 1.0
CB A:THR475 4.8 80.0 1.0
C A:CYS484 4.9 0.8 1.0
CB A:HIS487 4.9 0.3 1.0
CA A:CYS452 4.9 85.5 1.0

Zinc binding site 4 out of 20 in 5nfy

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Zinc binding site 4 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:0.8
occ:1.00
O B:HOH707 2.1 0.5 1.0
ND1 B:HIS229 2.2 92.2 1.0
SG B:CYS210 2.5 0.8 1.0
SG B:CYS226 2.5 0.9 1.0
CE1 B:HIS229 3.1 0.8 1.0
CB B:CYS210 3.2 85.1 1.0
CG B:HIS229 3.2 0.9 1.0
SG B:CYS207 3.5 0.7 1.0
CB B:HIS229 3.6 0.3 1.0
O B:LEU209 3.9 0.5 1.0
CB B:CYS226 3.9 97.9 1.0
N B:HIS229 4.0 0.6 1.0
CB B:CYS207 4.1 84.7 1.0
O B:CYS208 4.1 0.2 1.0
NE2 B:HIS229 4.2 0.6 1.0
C B:LEU209 4.2 95.2 1.0
CD2 B:HIS229 4.3 0.3 1.0
N B:CYS226 4.3 0.9 1.0
CA B:CYS210 4.4 91.8 1.0
N B:CYS210 4.4 98.0 1.0
CA B:HIS229 4.4 0.7 1.0
CA B:CYS226 4.6 96.5 1.0
CB B:ASN228 4.7 98.2 1.0
CB B:LEU209 4.7 93.7 1.0
C B:ASN228 4.9 0.7 1.0
O B:CYS226 5.0 86.3 1.0

Zinc binding site 5 out of 20 in 5nfy

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Zinc binding site 5 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:0.2
occ:1.00
ND1 B:HIS264 2.2 74.0 1.0
NE2 B:HIS257 2.3 86.2 1.0
SG B:CYS279 2.3 63.9 1.0
SG B:CYS261 2.4 0.3 1.0
CG B:HIS264 2.8 83.6 1.0
CB B:HIS264 3.0 93.4 1.0
CE1 B:HIS257 3.1 88.8 1.0
CB B:CYS261 3.2 91.8 1.0
CE1 B:HIS264 3.3 82.2 1.0
CD2 B:HIS257 3.4 82.1 1.0
CB B:CYS279 3.6 87.3 1.0
CD2 B:HIS264 3.9 85.6 1.0
N B:HIS264 3.9 0.4 1.0
CA B:HIS264 4.1 0.2 1.0
NE2 B:HIS264 4.1 99.4 1.0
ND1 B:HIS257 4.2 85.7 1.0
CG B:HIS257 4.4 82.5 1.0
CA B:CYS261 4.6 88.3 1.0
O B:HIS264 4.8 99.5 1.0
O B:CYS414 4.9 0.5 1.0
C B:HIS264 4.9 99.8 1.0
C B:CYS261 5.0 87.3 1.0

Zinc binding site 6 out of 20 in 5nfy

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Zinc binding site 6 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:0.2
occ:1.00
SG B:CYS477 2.1 0.2 1.0
CB B:CYS477 2.2 0.3 1.0
SG B:CYS484 2.2 0.5 1.0
CB B:CYS484 2.5 0.3 1.0
SG B:CYS452 2.9 87.0 1.0
ND1 B:HIS487 2.9 0.9 1.0
CA B:CYS477 3.4 0.2 1.0
N B:CYS477 3.6 0.8 1.0
CG B:HIS487 3.7 95.5 1.0
CB B:HIS487 3.7 87.4 1.0
OG1 B:THR475 3.9 0.1 1.0
CE1 B:HIS487 3.9 0.4 1.0
CB B:CYS452 3.9 0.3 1.0
CA B:CYS484 4.0 0.7 1.0
O B:HOH717 4.0 0.7 1.0
CG2 B:THR475 4.1 86.4 1.0
C B:CYS477 4.3 0.4 1.0
O B:CYS477 4.6 0.3 1.0
CB B:THR475 4.6 84.8 1.0
N B:CYS484 4.7 0.7 1.0
C B:ARG476 4.7 85.4 1.0
CD2 B:HIS487 4.8 0.9 1.0
C B:CYS484 4.9 0.8 1.0
NE2 B:HIS487 4.9 98.9 1.0
CA B:CYS452 5.0 0.9 1.0

Zinc binding site 7 out of 20 in 5nfy

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Zinc binding site 7 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:0.8
occ:1.00
SG C:CYS210 1.3 71.0 1.0
ND1 C:HIS229 1.9 68.5 1.0
SG C:CYS207 2.1 60.3 1.0
CE1 C:HIS229 2.4 82.7 1.0
SG C:CYS226 2.5 68.5 1.0
CB C:CYS210 2.8 76.4 1.0
CG C:HIS229 3.2 79.2 1.0
CB C:CYS207 3.3 79.5 1.0
N C:CYS210 3.5 71.5 1.0
NE2 C:HIS229 3.6 64.6 1.0
CA C:CYS210 3.7 81.8 1.0
CB C:CYS226 3.7 61.8 1.0
O C:CYS208 3.9 92.7 1.0
CD2 C:HIS229 4.0 72.8 1.0
CB C:HIS229 4.0 74.1 1.0
N C:CYS226 4.3 60.1 1.0
C C:CYS210 4.4 73.7 1.0
CA C:CYS226 4.6 57.6 1.0
N C:HIS229 4.6 69.5 1.0
C C:LEU209 4.8 80.9 1.0
CA C:CYS207 4.8 67.0 1.0
O C:CYS210 4.8 65.8 1.0
CB C:LEU209 4.9 66.3 1.0
CA C:HIS229 5.0 77.2 1.0

Zinc binding site 8 out of 20 in 5nfy

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Zinc binding site 8 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:0.5
occ:1.00
ND1 C:HIS264 2.2 91.8 1.0
NE2 C:HIS257 2.4 91.9 1.0
SG C:CYS279 2.4 70.9 1.0
SG C:CYS261 2.5 0.2 1.0
CG C:HIS264 3.0 89.1 1.0
CB C:CYS279 3.1 69.5 1.0
CB C:HIS264 3.1 95.3 1.0
CE1 C:HIS257 3.3 0.7 1.0
CD2 C:HIS257 3.3 77.3 1.0
CE1 C:HIS264 3.4 0.3 1.0
CB C:CYS261 3.6 0.1 1.0
N C:HIS264 4.1 0.3 1.0
CA C:HIS264 4.2 0.2 1.0
CD2 C:HIS264 4.2 94.1 1.0
NE2 C:HIS264 4.4 0.1 1.0
ND1 C:HIS257 4.4 96.9 1.0
CG C:HIS257 4.5 85.5 1.0
CA C:CYS279 4.6 66.1 1.0
O C:HIS264 4.8 0.5 1.0
O C:CYS414 4.8 0.5 1.0
C C:HIS264 5.0 0.8 1.0

Zinc binding site 9 out of 20 in 5nfy

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Zinc binding site 9 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn603

b:0.7
occ:1.00
SG C:CYS452 2.3 96.4 1.0
SG C:CYS484 2.3 0.5 1.0
OG1 C:THR475 2.8 0.8 1.0
ND1 C:HIS487 2.8 0.7 1.0
CB C:CYS484 3.2 92.4 1.0
CB C:CYS477 3.2 1.0 1.0
N C:CYS477 3.6 0.8 1.0
O C:CYS477 3.6 0.4 1.0
CE1 C:HIS487 3.7 0.8 1.0
CG C:HIS487 3.8 1.0 1.0
O C:HOH708 3.8 0.5 1.0
CA C:CYS477 3.8 0.2 1.0
CB C:THR475 4.0 0.6 1.0
CB C:HIS487 4.0 88.6 1.0
CB C:CYS452 4.0 0.7 1.0
CG2 C:THR475 4.0 0.1 1.0
C C:CYS477 4.1 0.1 1.0
SG C:CYS477 4.5 0.8 1.0
CA C:CYS484 4.5 0.4 1.0
O C:ALA482 4.6 0.6 1.0
C C:ARG476 4.7 0.2 1.0
N C:ARG476 4.7 0.3 1.0
NE2 C:HIS487 4.8 0.3 1.0
CD2 C:HIS487 4.9 0.8 1.0
C C:THR475 5.0 0.6 1.0

Zinc binding site 10 out of 20 in 5nfy

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Zinc binding site 10 out of 20 in the Sars-Cov NSP10/NSP14 Dynamic Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Sars-Cov NSP10/NSP14 Dynamic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:0.4
occ:1.00
SG D:CYS210 1.4 0.6 1.0
SG D:CYS207 2.2 0.1 1.0
ND1 D:HIS229 2.3 0.7 1.0
SG D:CYS226 2.6 0.7 1.0
CB D:CYS210 3.1 99.5 1.0
CG D:HIS229 3.2 0.7 1.0
CE1 D:HIS229 3.3 0.9 1.0
CB D:HIS229 3.4 0.3 1.0
O D:LEU209 3.6 0.5 1.0
CB D:CYS226 3.9 0.0 1.0
CB D:CYS207 4.0 0.4 1.0
O D:CYS208 4.0 0.5 1.0
C D:LEU209 4.1 0.3 1.0
N D:HIS229 4.1 0.1 1.0
N D:CYS226 4.2 0.6 1.0
CA D:CYS210 4.3 0.7 1.0
CD2 D:HIS229 4.3 0.5 1.0
NE2 D:HIS229 4.3 0.1 1.0
N D:CYS210 4.4 0.1 1.0
CA D:HIS229 4.4 0.1 1.0
CA D:CYS226 4.6 0.2 1.0
C D:CYS208 4.7 0.7 1.0
O D:HOH706 4.7 0.2 1.0
CB D:ASN228 5.0 0.8 1.0
O D:CYS226 5.0 0.9 1.0

Reference:

F.Ferron, L.Subissi, A.T.Silveira De Morais, N.T.T.Le, M.Sevajol, L.Gluais, E.Decroly, C.Vonrhein, G.Bricogne, B.Canard, I.Imbert. Structural and Molecular Basis of Mismatch Correction and Ribavirin Excision From Coronavirus Rna. Proc. Natl. Acad. Sci. V. 115 E162 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29279395
DOI: 10.1073/PNAS.1718806115
Page generated: Wed Dec 16 06:35:24 2020

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