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Zinc in PDB 2g9t: Crystal Structure of the Sars Coronavirus NSP10 at 2.1A

Protein crystallography data

The structure of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A, PDB code: 2g9t was solved by D.Su, Z.Lou, H.Yang, F.Sun, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group C 2 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 159.111, 321.829, 161.957, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A (pdb code 2g9t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 48 binding sites of Zinc where determined in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A, PDB code: 2g9t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 48 in 2g9t

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Zinc binding site 1 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


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 Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn998

b:27.1
occ:1.00
 NE2 A:HIS83 2.0 34.0 1.0
SG A:CYS74 2.2 24.1 1.0
SG A:CYS77 2.3 29.1 1.0
SG A:CYS90 2.4 35.2 1.0
CD2 A:HIS83 3.0 32.8 1.0
CB A:CYS74 3.0 23.5 1.0
CE1 A:HIS83 3.1 33.2 1.0
CB A:CYS90 3.3 39.2 1.0
CB A:CYS77 3.5 28.2 1.0
N A:CYS77 3.6 24.9 1.0
CA A:CYS77 4.0 26.0 1.0
CG A:HIS83 4.1 34.6 1.0
ND1 A:HIS83 4.2 32.8 1.0
O A:HOH1040 4.2 44.6 1.0
CA A:CYS90 4.4 41.5 1.0
CB A:TYR76 4.5 23.3 1.0
CA A:CYS74 4.5 22.4 1.0
C A:TYR76 4.5 23.0 1.0
CB A:LYS93 4.8 33.6 1.0
N A:LYS93 4.8 32.5 1.0
CA A:TYR76 4.8 23.8 1.0
C A:CYS74 4.9 20.4 1.0
N A:TYR76 4.9 21.9 1.0
O A:CYS74 5.0 20.0 1.0

Zinc binding site 2 out of 48 in 2g9t

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Zinc binding site 2 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


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 Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn999

b:36.6
occ:1.00
 SG A:CYS120 2.3 28.5 1.0
SG A:CYS128 2.3 34.7 1.0
SG A:CYS117 2.4 33.9 1.0
O A:HOH1068 2.5 24.5 1.0
CB A:CYS117 3.1 30.5 1.0
CB A:CYS128 3.3 37.6 1.0
CB A:CYS120 3.4 31.9 1.0
N A:CYS120 3.7 32.4 1.0
N A:SER129 3.8 45.6 1.0
CA A:CYS128 3.9 39.9 1.0
OG A:SER129 3.9 50.5 1.0
C A:CYS128 4.1 42.3 1.0
CA A:CYS120 4.2 31.7 1.0
CB A:VAL119 4.4 32.6 1.0
NZ A:LYS124 4.6 43.7 1.0
CA A:CYS117 4.6 31.4 1.0
CA A:SER129 4.6 47.9 1.0
CB A:SER129 4.6 48.5 1.0
C A:VAL119 4.8 33.6 1.0
C A:CYS120 5.0 30.4 1.0

Zinc binding site 3 out of 48 in 2g9t

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Zinc binding site 3 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


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 Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn998

b:27.3
occ:1.00
 NE2 B:HIS83 2.1 30.3 1.0
SG B:CYS74 2.2 24.5 1.0
SG B:CYS77 2.3 24.7 1.0
SG B:CYS90 2.4 30.8 1.0
CD2 B:HIS83 2.8 32.5 1.0
CB B:CYS74 3.1 22.3 1.0
CB B:CYS90 3.2 39.7 1.0
CE1 B:HIS83 3.2 32.6 1.0
CB B:CYS77 3.5 24.5 1.0
N B:CYS77 3.6 24.0 1.0
CA B:CYS77 4.0 23.2 1.0
O B:HOH1024 4.0 39.5 1.0
CG B:HIS83 4.1 33.4 1.0
ND1 B:HIS83 4.2 31.3 1.0
CA B:CYS90 4.5 42.5 1.0
C B:TYR76 4.5 23.6 1.0
CB B:TYR76 4.5 25.3 1.0
CA B:CYS74 4.6 22.6 1.0
CB B:LYS93 4.8 32.3 1.0
CA B:TYR76 4.9 23.2 1.0
N B:LYS93 4.9 31.7 1.0
N B:TYR76 5.0 21.6 1.0
C B:CYS74 5.0 22.1 1.0

Zinc binding site 4 out of 48 in 2g9t

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Zinc binding site 4 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


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 Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn999

b:41.2
occ:1.00
 SG B:CYS117 2.4 32.5 1.0
SG B:CYS128 2.5 40.9 1.0
SG B:CYS120 2.5 38.4 1.0
O B:HOH1058 2.5 22.4 1.0
CB B:CYS117 3.1 30.4 1.0
CB B:CYS120 3.4 35.6 1.0
CB B:CYS128 3.4 43.5 1.0
N B:CYS120 3.7 34.2 1.0
OG B:SER129 3.8 53.5 1.0
N B:SER129 3.8 49.8 1.0
CA B:CYS128 3.9 44.6 1.0
CA B:CYS120 4.1 34.2 1.0
C B:CYS128 4.3 47.2 1.0
CB B:VAL119 4.5 36.5 1.0
CA B:CYS117 4.5 31.9 1.0
CB B:SER129 4.6 52.4 1.0
CA B:SER129 4.7 51.6 1.0
C B:VAL119 4.8 35.8 1.0
CG1 B:VAL119 4.9 36.1 1.0
C B:CYS120 5.0 32.5 1.0
NZ B:LYS124 5.0 36.6 1.0

Zinc binding site 5 out of 48 in 2g9t

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Zinc binding site 5 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn998

b:27.4
occ:1.00
 SG C:CYS77 2.2 27.0 1.0
NE2 C:HIS83 2.2 33.6 1.0
SG C:CYS74 2.3 26.1 1.0
SG C:CYS90 2.3 32.0 1.0
CD2 C:HIS83 2.9 33.7 1.0
CB C:CYS74 3.2 27.0 1.0
CB C:CYS90 3.3 38.8 1.0
CB C:CYS77 3.3 25.0 1.0
CE1 C:HIS83 3.3 32.4 1.0
N C:CYS77 3.6 25.5 1.0
CA C:CYS77 3.9 26.0 1.0
CG C:HIS83 4.2 35.6 1.0
ND1 C:HIS83 4.3 33.3 1.0
O C:HOH1054 4.5 46.5 1.0
C C:TYR76 4.5 25.5 1.0
CA C:CYS90 4.5 41.1 1.0
CB C:TYR76 4.6 26.3 1.0
CA C:CYS74 4.6 25.4 1.0
CB C:LYS93 4.8 30.9 1.0
N C:LYS93 4.9 29.3 1.0
CA C:TYR76 4.9 25.3 1.0
C C:CYS74 4.9 25.2 1.0
N C:TYR76 5.0 23.0 1.0
O C:CYS74 5.0 24.0 1.0

Zinc binding site 6 out of 48 in 2g9t

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Zinc binding site 6 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn999

b:36.0
occ:1.00
 SG C:CYS120 2.4 28.1 1.0
O C:HOH1065 2.4 19.6 1.0
SG C:CYS128 2.4 36.0 1.0
SG C:CYS117 2.4 31.9 1.0
CB C:CYS117 3.1 30.8 1.0
CB C:CYS120 3.3 30.8 1.0
CB C:CYS128 3.6 37.0 1.0
N C:CYS120 3.7 33.7 1.0
N C:SER129 3.8 45.1 1.0
O C:HOH1060 3.8 59.8 1.0
OG C:SER129 4.0 46.4 1.0
CA C:CYS128 4.0 39.5 1.0
CA C:CYS120 4.1 31.4 1.0
C C:CYS128 4.3 42.0 1.0
NZ C:LYS124 4.5 43.6 1.0
CA C:CYS117 4.6 32.4 1.0
CB C:VAL119 4.6 35.2 1.0
CA C:SER129 4.7 47.5 1.0
CB C:SER129 4.8 47.5 1.0
C C:VAL119 4.8 35.6 1.0
C C:CYS120 4.9 30.8 1.0

Zinc binding site 7 out of 48 in 2g9t

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Zinc binding site 7 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn998

b:27.5
occ:1.00
 NE2 D:HIS83 2.0 34.6 1.0
SG D:CYS77 2.3 26.7 1.0
SG D:CYS90 2.3 30.6 1.0
SG D:CYS74 2.4 25.6 1.0
CE1 D:HIS83 2.9 34.1 1.0
CD2 D:HIS83 3.0 33.0 1.0
CB D:CYS74 3.2 23.6 1.0
CB D:CYS90 3.3 39.1 1.0
CB D:CYS77 3.5 23.9 1.0
N D:CYS77 3.6 21.8 1.0
CA D:CYS77 4.0 22.9 1.0
ND1 D:HIS83 4.0 32.8 1.0
CG D:HIS83 4.1 35.3 1.0
CB D:TYR76 4.4 24.8 1.0
CA D:CYS90 4.5 39.8 1.0
C D:TYR76 4.5 22.2 1.0
CA D:CYS74 4.6 24.0 1.0
CA D:TYR76 4.9 23.0 1.0
CB D:LYS93 4.9 31.5 1.0

Zinc binding site 8 out of 48 in 2g9t

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Zinc binding site 8 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn999

b:37.0
occ:1.00
 SG D:CYS128 1.8 61.4 1.0
SG D:CYS120 2.2 53.2 1.0
SG D:CYS117 2.2 33.3 1.0
O D:HOH1062 2.4 22.3 1.0
CB D:CYS120 2.8 43.7 1.0
CB D:CYS117 3.0 33.5 1.0
N D:CYS120 3.3 39.6 1.0
CB D:CYS128 3.6 56.1 1.0
CA D:CYS120 3.7 40.0 1.0
OG D:SER129 3.9 55.4 1.0
N D:SER129 4.1 57.7 1.0
O D:HOH1044 4.3 40.3 1.0
CB D:VAL119 4.4 36.9 1.0
CA D:CYS128 4.4 56.3 1.0
C D:CYS128 4.5 57.0 1.0
CA D:CYS117 4.5 33.1 1.0
C D:VAL119 4.5 38.8 1.0
NZ D:LYS124 4.5 46.1 1.0
CB D:SER129 4.6 57.4 1.0
CA D:SER129 4.7 58.3 1.0
C D:CYS120 4.7 38.1 1.0
CA D:VAL119 4.8 36.7 1.0
N D:GLY121 4.8 36.2 1.0
N D:VAL119 4.9 36.2 1.0
C D:CYS117 5.0 33.8 1.0

Zinc binding site 9 out of 48 in 2g9t

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Zinc binding site 9 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn998

b:27.6
occ:1.00
 NE2 E:HIS83 2.1 33.3 1.0
SG E:CYS77 2.2 26.3 1.0
SG E:CYS74 2.3 24.1 1.0
SG E:CYS90 2.3 32.9 1.0
CD2 E:HIS83 2.9 34.0 1.0
CE1 E:HIS83 3.2 35.9 1.0
CB E:CYS74 3.2 23.9 1.0
CB E:CYS90 3.2 39.0 1.0
CB E:CYS77 3.4 27.2 1.0
N E:CYS77 3.5 24.7 1.0
CA E:CYS77 3.9 24.7 1.0
O E:HOH1029 4.0 47.9 1.0
CG E:HIS83 4.1 35.7 1.0
ND1 E:HIS83 4.2 33.9 1.0
CB E:TYR76 4.3 24.8 1.0
CA E:CYS90 4.4 41.3 1.0
C E:TYR76 4.5 24.6 1.0
CA E:CYS74 4.6 22.5 1.0
CA E:TYR76 4.8 25.6 1.0
N E:LYS93 4.9 31.4 1.0
CB E:LYS93 4.9 33.7 1.0
N E:TYR76 4.9 25.2 1.0
C E:CYS74 5.0 22.1 1.0

Zinc binding site 10 out of 48 in 2g9t

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Zinc binding site 10 out of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn999

b:36.0
occ:1.00
 SG E:CYS120 2.3 32.3 1.0
SG E:CYS128 2.4 39.9 1.0
SG E:CYS117 2.4 34.5 1.0
O E:HOH1062 2.5 24.5 1.0
CB E:CYS117 3.0 33.2 1.0
CB E:CYS120 3.3 33.3 1.0
CB E:CYS128 3.4 41.6 1.0
N E:CYS120 3.8 33.0 1.0
CA E:CYS128 3.9 43.0 1.0
OG E:SER129 4.0 50.4 1.0
N E:SER129 4.1 47.0 1.0
CA E:CYS120 4.1 32.4 1.0
C E:CYS128 4.3 45.3 1.0
O E:HOH1037 4.4 68.1 1.0
NZ E:LYS124 4.5 47.7 1.0
CA E:CYS117 4.5 33.5 1.0
CB E:VAL119 4.7 36.6 1.0
CB E:SER129 4.8 49.3 1.0
C E:VAL119 4.9 35.4 1.0
C E:CYS120 4.9 32.0 1.0
CA E:SER129 5.0 49.7 1.0

Reference:

D.Su, Z.Lou, F.Sun, Y.Zhai, H.Yang, R.Zhang, A.Joachimiak, X.C.Zhang, M.Bartlam, Z.Rao. Dodecamer Structure of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein NSP10 J.Virol. V. 80 7902 2006.
ISSN: ISSN 0022-538X
PubMed: 16873247
DOI: 10.1128/JVI.00483-06
Page generated: Thu Oct 17 00:05:39 2024

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