Zinc in PDB 7mc5: Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex, PDB code: 7mc5 was solved by N.M.Moeller, K.Shi, S.Banerjee, L.Yin, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.70 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.735, 67.48, 111.249, 90, 90, 90
R / Rfree (%) 16.6 / 19.7

Other elements in 7mc5:

The structure of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex (pdb code 7mc5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex, PDB code: 7mc5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7mc5

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Zinc binding site 1 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:26.3
occ:1.00
 ND1 A:HIS229 2.0 28.8 1.0
SG A:CYS207 2.3 26.3 1.0
SG A:CYS210 2.3 30.0 1.0
SG A:CYS226 2.4 25.0 1.0
CE1 A:HIS229 2.9 32.0 1.0
CB A:CYS207 3.0 20.3 1.0
CG A:HIS229 3.1 25.9 1.0
CB A:CYS210 3.5 33.6 1.0
CB A:CYS226 3.5 22.7 1.0
CB A:HIS229 3.5 24.0 1.0
N A:CYS210 3.8 29.0 1.0
N A:CYS226 4.0 20.4 1.0
NE2 A:HIS229 4.0 28.4 1.0
CD2 A:HIS229 4.2 30.1 1.0
CA A:CYS210 4.2 27.7 1.0
CA A:CYS226 4.3 19.6 1.0
C A:LEU209 4.4 32.4 1.0
N A:HIS229 4.5 22.9 1.0
CB A:LEU209 4.5 26.3 1.0
CA A:CYS207 4.5 24.7 1.0
NH1 A:ARG212 4.6 30.8 1.0
CD A:ARG212 4.7 27.3 1.0
CA A:HIS229 4.7 25.2 1.0
C A:CYS210 4.7 30.1 1.0
N A:LEU209 4.7 29.0 1.0
CB A:ARG212 4.8 28.3 1.0
CA A:LEU209 4.8 28.6 1.0
CB A:HIS228 4.9 24.5 1.0
O A:CYS210 4.9 31.4 1.0
C A:CYS226 4.9 19.3 1.0

Zinc binding site 2 out of 4 in 7mc5

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Zinc binding site 2 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:20.2
occ:1.00
 ND1 A:HIS264 2.1 19.6 1.0
NE2 A:HIS257 2.1 19.7 1.0
SG A:CYS279 2.2 20.6 1.0
SG A:CYS261 2.3 20.1 1.0
CE1 A:HIS257 3.0 19.4 1.0
CE1 A:HIS264 3.0 24.9 1.0
CD2 A:HIS257 3.1 18.6 1.0
CG A:HIS264 3.1 21.8 1.0
CB A:CYS261 3.1 23.4 1.0
CB A:CYS279 3.2 20.7 1.0
CB A:HIS264 3.5 23.7 1.0
ND1 A:HIS257 4.1 22.7 1.0
NE2 A:HIS264 4.1 23.4 1.0
O A:HOH637 4.1 26.6 1.0
CG A:HIS257 4.2 20.6 1.0
CD2 A:HIS264 4.2 19.9 1.0
O2 A:EDO308 4.3 30.6 1.0
O A:HOH626 4.4 20.7 1.0
N A:HIS264 4.5 21.8 1.0
CA A:CYS261 4.6 21.2 1.0
CA A:HIS264 4.6 25.3 1.0
CA A:CYS279 4.7 16.6 1.0
CG2 A:VAL263 4.8 23.0 1.0
C A:CYS261 4.9 21.3 1.0

Zinc binding site 3 out of 4 in 7mc5

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Zinc binding site 3 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:20.6
occ:1.00
 NE2 M:HIS83 2.1 20.7 1.0
SG M:CYS74 2.3 18.0 1.0
SG M:CYS77 2.3 20.5 1.0
SG M:CYS90 2.3 20.5 1.0
CD2 M:HIS83 3.0 20.4 1.0
CE1 M:HIS83 3.1 21.1 1.0
CB M:CYS74 3.1 17.9 1.0
CB M:CYS90 3.3 23.6 1.0
CB M:CYS77 3.4 15.4 1.0
N M:CYS77 3.6 18.4 1.0
CA M:CYS77 4.0 18.3 1.0
ND1 M:HIS83 4.2 23.0 1.0
CG M:HIS83 4.2 21.3 1.0
O M:HOH313 4.4 31.1 1.0
CA M:CYS90 4.4 24.3 1.0
CB M:TYR76 4.4 19.1 1.0
C M:TYR76 4.5 20.5 1.0
CA M:CYS74 4.5 18.0 1.0
CB M:LYS93 4.7 20.4 1.0
O1 M:EDO206 4.8 29.6 1.0
O M:CYS74 4.8 17.4 1.0
O M:HOH422 4.8 35.9 1.0
CA M:TYR76 4.8 20.5 1.0
C M:CYS74 4.9 20.4 1.0
N M:TYR76 4.9 19.2 1.0
N M:LYS93 5.0 18.9 1.0

Zinc binding site 4 out of 4 in 7mc5

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Zinc binding site 4 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn203

b:27.0
occ:1.00
 SG M:CYS120 2.3 28.0 1.0
SG M:CYS117 2.4 24.8 1.0
SG M:CYS128 2.4 27.6 1.0
SG M:CYS130 2.4 32.1 1.0
CB M:CYS117 3.1 20.5 1.0
CB M:CYS120 3.2 29.3 1.0
CB M:CYS130 3.4 36.4 1.0
CB M:CYS128 3.4 28.5 1.0
N M:CYS120 3.7 24.3 1.0
N M:CYS130 4.0 42.1 1.0
CA M:CYS128 4.0 29.3 1.0
CA M:CYS120 4.1 23.8 1.0
O M:HOH451 4.2 47.4 1.0
CA M:CYS130 4.3 41.9 1.0
O M:HOH302 4.3 44.2 1.0
N M:SER129 4.4 41.8 1.0
C M:CYS128 4.5 33.9 1.0
CA M:CYS117 4.5 22.3 1.0
CB M:VAL119 4.7 22.5 1.0
O M:HOH445 4.7 46.2 1.0
C M:VAL119 4.9 28.6 1.0
C M:CYS120 4.9 26.2 1.0
N M:GLY121 5.0 22.1 1.0

Reference:

N.H.Moeller, K.Shi, O.Demir, S.Banerjee, L.Yin, C.Belica, C.Durfee, R.E.Amaro, H.Aihara. Structure and Dynamics of Sars-Cov-2 Proofreading Exoribonuclease Exon. Biorxiv 2021.
PubMed: 33821277
DOI: 10.1101/2021.04.02.438274
Page generated: Tue Oct 29 23:12:16 2024

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