Zinc in PDB 7mc6: Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion, PDB code: 7mc6 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) 42.96 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.67, 70.32, 108.54, 90, 90, 90
R / Rfree (%) 19.7 / 21.9

Other elements in 7mc6:

The structure of Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion (pdb code 7mc6). 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 Containing MG2+ Ion, PDB code: 7mc6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7mc6

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Zinc binding site 1 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion


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 Containing MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:48.0
occ:1.00
 ND1 A:HIS229 2.0 49.6 1.0
SG A:CYS210 2.3 52.8 1.0
SG A:CYS207 2.3 49.1 1.0
SG A:CYS226 2.3 50.0 1.0
CE1 A:HIS229 2.6 48.0 1.0
CB A:CYS207 3.1 50.3 1.0
CG A:HIS229 3.2 55.5 1.0
CB A:CYS210 3.6 51.6 1.0
CB A:CYS226 3.6 45.1 1.0
NE2 A:HIS229 3.8 53.0 1.0
CB A:HIS229 3.9 49.4 1.0
N A:CYS210 3.9 54.1 1.0
N A:CYS226 4.0 44.4 1.0
CD2 A:HIS229 4.1 55.6 1.0
CA A:CYS210 4.3 50.6 1.0
CA A:CYS226 4.4 36.3 1.0
NH1 A:ARG212 4.4 54.3 1.0
C A:LEU209 4.5 56.9 1.0
CB A:LEU209 4.5 54.2 1.0
N A:HIS229 4.5 46.8 1.0
CA A:CYS207 4.6 50.8 1.0
N A:LEU209 4.7 54.0 1.0
CA A:LEU209 4.8 53.5 1.0
C A:CYS210 4.8 54.9 1.0
CA A:HIS229 4.8 48.7 1.0
CB A:HIS228 4.9 41.9 1.0
CB A:ARG212 4.9 48.1 1.0
CD A:ARG212 4.9 50.1 1.0

Zinc binding site 2 out of 4 in 7mc6

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Zinc binding site 2 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion


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 Containing MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:35.0
occ:1.00
 NE2 A:HIS257 2.0 36.1 1.0
ND1 A:HIS264 2.0 32.8 1.0
SG A:CYS261 2.3 36.1 1.0
SG A:CYS279 2.3 34.2 1.0
CE1 A:HIS264 3.0 36.7 1.0
CE1 A:HIS257 3.0 38.1 1.0
CB A:CYS261 3.0 38.6 1.0
CD2 A:HIS257 3.0 34.9 1.0
CG A:HIS264 3.1 34.0 1.0
CB A:CYS279 3.2 34.1 1.0
CB A:HIS264 3.5 36.9 1.0
ND1 A:HIS257 4.1 36.9 1.0
NE2 A:HIS264 4.1 32.9 1.0
CG A:HIS257 4.1 39.8 1.0
CD2 A:HIS264 4.2 39.0 1.0
O A:HOH517 4.3 50.1 1.0
N A:HIS264 4.4 36.9 1.0
O A:HOH491 4.4 36.1 1.0
CA A:CYS261 4.5 37.3 1.0
O A:HOH508 4.6 55.0 1.0
CA A:HIS264 4.6 41.8 1.0
CA A:CYS279 4.7 36.8 1.0
CG2 A:VAL263 4.7 34.6 1.0
C A:CYS261 4.9 37.5 1.0

Zinc binding site 3 out of 4 in 7mc6

Go back to Zinc Binding Sites List in 7mc6
Zinc binding site 3 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion


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 Containing MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:36.0
occ:1.00
 NE2 M:HIS83 2.0 39.1 1.0
SG M:CYS74 2.3 35.5 1.0
SG M:CYS77 2.3 34.8 1.0
SG M:CYS90 2.3 37.0 1.0
CD2 M:HIS83 2.9 38.2 1.0
CB M:CYS74 3.1 35.0 1.0
CE1 M:HIS83 3.1 39.9 1.0
CB M:CYS90 3.3 42.2 1.0
CB M:CYS77 3.4 33.7 1.0
N M:CYS77 3.6 34.2 1.0
CA M:CYS77 4.0 35.6 1.0
CG M:HIS83 4.1 43.1 1.0
ND1 M:HIS83 4.2 41.7 1.0
C M:TYR76 4.5 34.6 1.0
CA M:CYS74 4.5 33.8 1.0
CA M:CYS90 4.5 55.1 1.0
CB M:TYR76 4.5 36.6 1.0
CB M:LYS93 4.7 38.6 1.0
C M:CYS74 4.9 32.6 1.0
CA M:TYR76 4.9 31.9 1.0
O M:CYS74 4.9 31.6 1.0
N M:LYS93 5.0 38.8 1.0
N M:TYR76 5.0 30.6 1.0

Zinc binding site 4 out of 4 in 7mc6

Go back to Zinc Binding Sites List in 7mc6
Zinc binding site 4 out of 4 in the Crystal Structure of the Sars-Cov-2 Exon-NSP10 Complex Containing MG2+ Ion


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 Containing MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:66.3
occ:1.00
 SG M:CYS117 2.3 58.0 1.0
SG M:CYS128 2.3 65.5 1.0
SG M:CYS120 2.3 59.3 1.0
SG M:CYS130 2.3 75.5 1.0
CB M:CYS117 3.1 53.4 1.0
CB M:CYS120 3.3 55.2 1.0
CB M:CYS130 3.4 79.1 1.0
CB M:CYS128 3.4 61.3 1.0
N M:CYS120 3.7 59.2 1.0
N M:CYS130 3.9 78.2 1.0
CA M:CYS128 4.0 65.0 1.0
N M:SER129 4.1 77.9 1.0
CA M:CYS120 4.1 55.5 1.0
CA M:CYS130 4.3 83.2 1.0
CB M:VAL119 4.5 63.7 1.0
C M:CYS128 4.5 73.0 1.0
CA M:CYS117 4.6 55.0 1.0
C M:VAL119 4.8 60.9 1.0
C M:SER129 4.9 81.5 1.0
C M:CYS120 4.9 54.0 1.0
N M:VAL119 5.0 62.5 1.0
CA M:VAL119 5.0 62.5 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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