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Zinc in PDB 5c8t: Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam

Protein crystallography data

The structure of Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam, PDB code: 5c8t was solved by Y.Y.Ma, L.J.Wu, R.G.Zhang, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.54 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 188.797, 196.840, 180.100, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 26.5

Other elements in 5c8t:

The structure of Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam (pdb code 5c8t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam, PDB code: 5c8t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5c8t

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Zinc binding site 1 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:0.4
occ:1.00
 NE2 A:HIS83 2.1 0.5 1.0
SG A:CYS90 2.3 0.3 1.0
SG A:CYS77 2.3 0.9 1.0
SG A:CYS74 2.4 91.9 1.0
CB A:CYS90 2.8 0.9 1.0
CD2 A:HIS83 3.0 0.2 1.0
CB A:CYS77 3.2 70.8 1.0
CE1 A:HIS83 3.2 0.9 1.0
N A:CYS77 3.4 0.8 1.0
CB A:CYS74 3.5 93.1 1.0
CA A:CYS77 3.7 0.5 1.0
CG A:HIS83 4.2 0.5 1.0
CA A:CYS90 4.2 0.4 1.0
ND1 A:HIS83 4.2 0.5 1.0
C A:TYR76 4.4 0.3 1.0
CB A:TYR76 4.5 0.0 1.0
CA A:CYS74 4.9 0.1 1.0
CA A:TYR76 4.9 0.3 1.0
CB A:LYS93 4.9 96.2 1.0
O A:CYS74 4.9 0.4 1.0
C A:CYS90 5.0 0.5 1.0
N A:LYS93 5.0 0.6 1.0

Zinc binding site 2 out of 10 in 5c8t

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Zinc binding site 2 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:0.5
occ:1.00
 SG A:CYS120 2.2 0.1 1.0
SG A:CYS130 2.3 0.6 1.0
SG A:CYS117 2.3 0.8 1.0
SG A:CYS128 2.3 0.3 1.0
CB A:CYS130 3.0 0.4 1.0
CB A:CYS117 3.4 0.3 1.0
CB A:CYS120 3.6 0.3 1.0
N A:CYS120 3.7 0.6 1.0
N A:CYS130 4.1 0.0 1.0
CB A:CYS128 4.1 0.2 1.0
CA A:CYS130 4.2 0.2 1.0
CA A:CYS120 4.2 0.1 1.0
CB A:VAL119 4.3 0.0 1.0
CG2 A:VAL119 4.3 0.1 1.0
C A:VAL119 4.7 0.4 1.0
CA A:CYS117 4.8 0.8 1.0
N A:VAL119 4.8 0.1 1.0
CA A:VAL119 4.8 0.2 1.0
CA A:CYS128 4.9 0.9 1.0
N A:SER129 4.9 1.0 1.0
O A:CYS117 4.9 0.0 1.0
C A:CYS117 4.9 0.8 1.0

Zinc binding site 3 out of 10 in 5c8t

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Zinc binding site 3 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:0.4
occ:1.00
 CD2 B:HIS229 2.1 0.2 1.0
SG B:CYS210 2.1 0.1 1.0
CG B:HIS229 2.1 0.7 1.0
NE2 B:HIS229 2.1 0.6 1.0
ND1 B:HIS229 2.2 0.3 1.0
CE1 B:HIS229 2.3 0.8 1.0
SG B:CYS226 2.5 0.9 1.0
CB B:CYS210 2.6 0.9 1.0
SG B:CYS207 2.8 0.5 1.0
CB B:HIS229 3.2 0.1 1.0
CB B:CYS226 3.2 0.1 1.0
CA B:CYS210 4.1 0.9 1.0
N B:HIS229 4.2 0.0 1.0
CA B:HIS229 4.3 0.2 1.0
CB B:CYS207 4.3 0.5 1.0
CA B:CYS226 4.7 0.5 1.0
O B:LEU209 4.9 0.3 1.0
N B:CYS210 4.9 0.0 1.0
O B:CYS208 4.9 0.9 1.0
CG B:LYS212 4.9 0.7 1.0

Zinc binding site 4 out of 10 in 5c8t

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Zinc binding site 4 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:0.5
occ:1.00
 ND1 B:HIS264 1.9 0.3 1.0
CE1 B:HIS257 2.2 0.3 1.0
SG B:CYS261 2.2 93.9 1.0
NE2 B:HIS257 2.3 0.8 1.0
SG B:CYS279 2.4 60.0 1.0
CE1 B:HIS264 2.6 95.3 1.0
CG B:HIS264 2.8 94.0 1.0
CB B:CYS261 3.3 0.1 1.0
CB B:HIS264 3.4 0.9 1.0
ND1 B:HIS257 3.5 0.3 1.0
NE2 B:HIS264 3.6 62.4 1.0
CD2 B:HIS257 3.6 84.9 1.0
CB B:CYS279 3.7 49.4 1.0
CD2 B:HIS264 3.7 99.5 1.0
N B:HIS264 3.8 95.4 1.0
O B:CYS261 4.2 0.7 1.0
CG B:HIS257 4.2 89.6 1.0
CA B:HIS264 4.2 0.2 1.0
C B:CYS261 4.5 96.3 1.0
CA B:CYS261 4.5 0.1 1.0
CB B:CYS414 4.8 0.6 1.0
C B:VAL263 4.8 0.5 1.0
N B:VAL263 4.8 95.3 1.0
O B:HIS264 4.9 0.1 1.0

Zinc binding site 5 out of 10 in 5c8t

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Zinc binding site 5 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:0.5
occ:1.00
 CE1 B:HIS487 1.5 90.7 1.0
CB B:CYS484 2.2 0.9 1.0
ND1 B:HIS487 2.2 0.8 1.0
SG B:CYS484 2.3 0.8 1.0
SG B:CYS452 2.3 0.9 1.0
SG B:CYS477 2.3 0.1 1.0
NE2 B:HIS487 2.5 0.7 1.0
CG B:HIS487 3.2 0.5 1.0
CB B:CYS452 3.2 0.4 1.0
CD2 B:HIS487 3.3 0.7 1.0
CB B:CYS477 3.5 1.0 1.0
N B:CYS477 3.7 95.2 1.0
CA B:CYS484 3.7 0.8 1.0
CB B:ARG476 4.0 0.4 1.0
CA B:CYS477 4.2 98.2 1.0
C B:ARG476 4.3 0.3 1.0
CA B:CYS452 4.4 96.4 1.0
N B:CYS484 4.4 0.5 1.0
C B:CYS484 4.4 0.1 1.0
CB B:HIS487 4.5 0.7 1.0
O B:CYS484 4.5 0.7 1.0
CA B:ARG476 4.6 0.0 1.0
O B:CYS477 4.7 0.6 1.0
OG1 B:THR475 4.8 0.9 1.0
N B:ARG476 4.8 0.1 1.0
CD B:ARG476 4.9 92.8 1.0

Zinc binding site 6 out of 10 in 5c8t

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Zinc binding site 6 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:0.4
occ:1.00
 CE1 C:HIS83 1.8 0.9 1.0
NE2 C:HIS83 2.2 0.8 1.0
SG C:CYS77 2.2 98.1 1.0
SG C:CYS90 2.3 72.9 1.0
SG C:CYS74 2.6 67.7 1.0
CB C:CYS90 2.7 0.7 1.0
ND1 C:HIS83 2.9 91.8 1.0
CD2 C:HIS83 3.3 1.0 1.0
CB C:CYS77 3.4 72.0 1.0
CB C:CYS74 3.6 59.8 1.0
CG C:HIS83 3.7 0.3 1.0
N C:CYS77 3.7 98.5 1.0
CA C:CYS77 3.9 85.8 1.0
CA C:CYS90 4.1 95.7 1.0
O D:ASN129 4.4 0.2 1.0
C C:TYR76 4.4 87.2 1.0
CB C:TYR76 4.6 87.2 1.0
CB C:LYS93 4.7 0.6 1.0
N C:CYS90 4.9 95.4 1.0

Zinc binding site 7 out of 10 in 5c8t

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Zinc binding site 7 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:0.1
occ:1.00
 SG C:CYS128 2.3 0.9 1.0
SG C:CYS130 2.3 0.5 1.0
SG C:CYS117 2.3 0.2 1.0
SG C:CYS120 2.4 0.6 1.0
CB C:CYS130 3.0 0.2 1.0
CB C:CYS117 3.3 0.2 1.0
CB C:VAL119 3.7 0.3 1.0
CB C:CYS128 3.7 0.4 1.0
CB C:CYS120 4.1 0.8 1.0
N C:CYS120 4.1 0.7 1.0
CG2 C:VAL119 4.3 0.9 1.0
CG1 C:VAL119 4.3 0.9 1.0
CA C:CYS130 4.4 0.0 1.0
CA C:CYS128 4.6 0.7 1.0
O C:SER129 4.7 0.1 1.0
CA C:CYS117 4.7 0.3 1.0
CA C:CYS120 4.7 0.9 1.0
CA C:VAL119 4.8 0.6 1.0
N C:CYS130 4.8 0.4 1.0
O C:CYS117 4.8 0.3 1.0
C C:SER129 4.8 0.6 1.0
C C:CYS128 4.8 0.1 1.0
C C:CYS117 4.9 0.4 1.0
C C:VAL119 4.9 0.2 1.0
N C:VAL119 5.0 0.8 1.0
O C:MET122 5.0 0.9 1.0
N C:SER129 5.0 0.3 1.0

Zinc binding site 8 out of 10 in 5c8t

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Zinc binding site 8 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:0.5
occ:1.00
 CD2 D:HIS229 1.6 93.1 1.0
NE2 D:HIS229 2.2 91.9 1.0
SG D:CYS210 2.3 88.3 1.0
SG D:CYS226 2.4 0.4 1.0
SG D:CYS207 2.4 97.0 1.0
CG D:HIS229 2.8 94.8 1.0
CB D:CYS210 3.0 87.3 1.0
CB D:CYS207 3.3 76.6 1.0
CE1 D:HIS229 3.4 70.2 1.0
N D:CYS210 3.6 61.0 1.0
CB D:CYS226 3.7 0.8 1.0
ND1 D:HIS229 3.7 77.7 1.0
CB D:HIS229 3.8 90.2 1.0
CA D:CYS210 3.9 64.6 1.0
N D:CYS226 4.2 88.6 1.0
N D:HIS229 4.4 91.0 1.0
C D:CYS210 4.5 80.0 1.0
C D:LEU209 4.6 86.2 1.0
CA D:CYS226 4.6 90.7 1.0
CB D:LEU209 4.6 51.8 1.0
CA D:HIS229 4.8 0.4 1.0
CA D:CYS207 4.8 75.1 1.0
O D:CYS210 4.8 93.0 1.0
CA D:LEU209 4.9 73.1 1.0
CB D:ASN228 4.9 69.4 1.0
N D:LEU209 5.0 75.2 1.0

Zinc binding site 9 out of 10 in 5c8t

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Zinc binding site 9 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:0.2
occ:1.00
 NE2 D:HIS257 1.6 0.5 1.0
CE1 D:HIS264 1.7 0.5 1.0
NE2 D:HIS264 1.8 0.1 1.0
CE1 D:HIS257 2.1 0.6 1.0
SG D:CYS261 2.3 0.1 1.0
SG D:CYS279 2.4 83.4 1.0
ND1 D:HIS264 2.4 0.5 1.0
CD2 D:HIS264 2.6 80.6 1.0
CG D:HIS264 2.9 0.1 1.0
CD2 D:HIS257 2.9 0.7 1.0
CB D:CYS261 3.1 0.9 1.0
ND1 D:HIS257 3.4 0.6 1.0
CB D:CYS279 3.4 92.6 1.0
CG D:HIS257 3.7 0.2 1.0
O D:HIS264 4.0 0.5 1.0
N D:HIS264 4.2 0.9 1.0
CB D:HIS264 4.2 0.7 1.0
O D:CYS261 4.3 0.5 1.0
CA D:CYS261 4.4 0.5 1.0
CA D:HIS264 4.5 0.8 1.0
C D:CYS261 4.6 0.2 1.0
C D:HIS264 4.7 0.6 1.0
O D:ASP415 4.9 0.8 1.0
CA D:CYS279 4.9 87.6 1.0
CA D:MET276 5.0 83.1 1.0

Zinc binding site 10 out of 10 in 5c8t

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Zinc binding site 10 out of 10 in the Crystal Structure of the Sars Coronavirus NSP14-NSP10 Complex with Functional Ligand Sam


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 NSP14-NSP10 Complex with Functional Ligand Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:0.7
occ:1.00
 CD2 D:HIS487 1.4 0.8 1.0
CG D:HIS487 1.8 0.8 1.0
SG D:CYS484 2.0 0.3 1.0
SG D:CYS477 2.3 0.7 1.0
SG D:CYS452 2.3 0.2 1.0
NE2 D:HIS487 2.4 0.7 1.0
CB D:HIS487 2.5 0.7 1.0
ND1 D:HIS487 2.8 81.6 1.0
CE1 D:HIS487 3.1 0.3 1.0
CB D:CYS484 3.1 0.2 1.0
CB D:CYS477 3.3 92.3 1.0
CB D:CYS452 3.3 81.0 1.0
O D:CYS484 3.8 0.0 1.0
CA D:HIS487 3.9 86.4 1.0
CG2 D:THR475 4.0 83.3 1.0
N D:HIS487 4.1 94.6 1.0
CB D:THR475 4.2 78.7 1.0
CA D:CYS452 4.3 0.2 1.0
CA D:CYS484 4.4 64.8 1.0
C D:CYS484 4.5 85.2 1.0
CA D:CYS477 4.6 92.5 1.0
OG1 D:THR475 4.6 79.6 1.0
N D:CYS477 4.7 90.6 1.0
N D:CYS484 4.8 95.2 1.0
N D:CYS452 4.9 0.2 1.0
C D:HIS487 5.0 1.0 1.0

Reference:

Y.Y.Ma, L.J.Wu, N.Shaw, Y.Gao, J.Wang, Y.N.Sun, Z.Y.Lou, L.M.Yan, R.G.Zhang, Z.H.Rao. Structural Basis and Functional Analysis of the Sars Coronavirus NSP14-NSP10 Complex Proc.Natl.Acad.Sci.Usa V. 112 9436 2015.
ISSN: ESSN 1091-6490
PubMed: 26159422
DOI: 10.1073/PNAS.1508686112
Page generated: Sun Oct 27 13:57:35 2024

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