Zinc in PDB 6vyo: Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2

Protein crystallography data

The structure of Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2, PDB code: 6vyo was solved by C.Chang, K.Michalska, R.Jedrzejczak, N.Maltseva, M.Endres, A.Godzik, Y.Kim, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.05 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.238, 77.430, 114.039, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 (pdb code 6vyo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2, PDB code: 6vyo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6vyo

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Zinc binding site 1 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:16.8
occ:0.58
 ZN B:ZN201 2.2 13.7 1.0
NE2 A:HIS59 3.4 14.2 1.0
OD2 B:ASP82 3.5 12.5 1.0
NE2 B:HIS145 3.6 14.3 1.0
CE1 A:HIS59 3.6 12.2 1.0
O B:ASN77 3.6 19.5 0.5
O B:ASN77 3.7 19.9 0.5
CD2 B:HIS145 3.7 13.8 1.0
C2 A:MES203 3.8 20.1 1.0
CA B:SER78 3.9 14.8 1.0
CG1 B:ILE146 3.9 16.3 1.0
C3 A:MES203 4.0 21.5 1.0
OG1 A:THR57 4.0 16.7 1.0
CB A:THR57 4.0 14.3 1.0
CB B:SER78 4.1 15.2 1.0
CG2 A:THR57 4.1 15.2 1.0
O A:HOH307 4.1 35.1 1.0
O A:HOH340 4.1 32.6 1.0
CD1 B:ILE146 4.1 17.4 1.0
C B:ASN77 4.5 17.8 0.5
C B:ASN77 4.6 18.1 0.5
CG B:ASP82 4.6 13.1 1.0
CD2 A:HIS59 4.7 12.4 1.0
N B:SER78 4.7 16.4 1.0
N B:SER79 4.7 12.8 1.0
CE1 B:HIS145 4.8 14.9 1.0
C B:SER78 4.9 14.2 1.0
ND1 A:HIS59 4.9 13.4 1.0
O1 A:MES203 4.9 21.6 1.0
O B:HOH392 5.0 19.2 1.0

Zinc binding site 2 out of 8 in 6vyo

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Zinc binding site 2 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:12.7
occ:0.98
 OD2 A:ASP82 2.0 12.1 1.0
ND1 D:HIS59 2.0 8.5 1.0
NE2 A:HIS145 2.1 13.6 1.0
ZN A:ZN205 2.3 21.7 0.6
CG A:ASP82 2.7 12.6 1.0
OD1 A:ASP82 2.8 14.8 1.0
CE1 D:HIS59 2.8 10.2 1.0
CD2 A:HIS145 3.0 13.8 1.0
CG D:HIS59 3.1 10.4 1.0
CE1 A:HIS145 3.1 14.2 1.0
CB D:HIS59 3.6 9.8 1.0
OG A:SER79 3.7 16.0 1.0
NE2 D:HIS59 4.0 11.2 1.0
CD2 D:HIS59 4.2 12.5 1.0
CB A:ASP82 4.2 11.3 1.0
CG A:HIS145 4.2 12.9 1.0
ND1 A:HIS145 4.2 13.8 1.0
N A:SER79 4.2 13.9 1.0
CB A:SER79 4.3 14.3 1.0
O D:HOH379 4.4 24.6 1.0
CD1 A:ILE146 4.5 14.5 1.0
CA D:HIS59 4.6 12.1 1.0
CG1 A:ILE146 4.6 13.4 1.0
O A:HOH337 4.8 12.1 1.0
CA A:SER78 4.9 13.0 1.0
CA A:SER79 4.9 14.5 1.0
O D:HOH427 5.0 47.7 0.2

Zinc binding site 3 out of 8 in 6vyo

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Zinc binding site 3 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:21.7
occ:0.55
 ZN A:ZN204 2.3 12.7 1.0
OG A:SER79 2.9 16.0 1.0
OD1 A:ASP82 3.4 14.8 1.0
OD2 A:ASP82 3.5 12.1 1.0
NE2 A:HIS145 3.5 13.6 1.0
CB A:SER79 3.6 14.3 1.0
CB D:HIS59 3.6 9.8 1.0
ND1 D:HIS59 3.6 8.5 1.0
CG A:ASP82 3.7 12.6 1.0
O A:HOH424 3.8 16.1 1.0
O D:HOH379 3.9 24.6 1.0
CE1 A:HIS145 4.0 14.2 1.0
O D:HIS59 4.0 16.3 1.0
O A:HOH337 4.0 12.1 1.0
CG D:HIS59 4.1 10.4 1.0
CD2 A:HIS145 4.5 13.8 1.0
C D:HIS59 4.5 14.3 1.0
CA D:HIS59 4.5 12.1 1.0
O D:HOH465 4.6 30.9 1.0
CB A:ASP81 4.6 15.1 1.0
O A:HOH429 4.6 28.2 1.0
O D:HOH399 4.7 37.2 1.0
CE1 D:HIS59 4.8 10.2 1.0
N A:SER79 4.8 13.9 1.0
CA A:SER79 4.8 14.5 1.0
OD2 A:ASP81 4.9 22.9 1.0

Zinc binding site 4 out of 8 in 6vyo

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Zinc binding site 4 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:13.7
occ:1.00
 OD2 B:ASP82 1.9 12.5 1.0
NE2 A:HIS59 2.1 14.2 1.0
NE2 B:HIS145 2.1 14.3 1.0
ZN A:ZN202 2.2 16.8 0.6
CG B:ASP82 2.9 13.1 1.0
CD2 B:HIS145 3.0 13.8 1.0
CD2 A:HIS59 3.0 12.4 1.0
CE1 A:HIS59 3.1 12.2 1.0
CE1 B:HIS145 3.1 14.9 1.0
OD1 B:ASP82 3.3 13.3 1.0
CG1 B:ILE146 3.9 16.3 1.0
CD1 B:ILE146 4.0 17.4 1.0
OG B:SER79 4.1 20.6 1.0
N B:SER79 4.1 12.8 1.0
ND1 A:HIS59 4.2 13.4 1.0
CG B:HIS145 4.2 13.3 1.0
CG A:HIS59 4.2 11.3 1.0
ND1 B:HIS145 4.2 16.1 1.0
CB B:ASP82 4.2 12.7 1.0
CG2 A:THR57 4.4 15.2 1.0
CA B:SER78 4.5 14.8 1.0
CB B:SER79 4.5 16.5 1.0
CB B:SER78 4.6 15.2 1.0
C B:SER78 4.9 14.2 1.0
O A:HOH420 4.9 42.6 1.0
CA B:SER79 5.0 15.3 1.0

Zinc binding site 5 out of 8 in 6vyo

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Zinc binding site 5 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:11.1
occ:0.92
 OD2 C:ASP82 2.0 11.1 1.0
ND1 B:HIS59 2.0 10.7 1.0
NE2 C:HIS145 2.1 13.4 1.0
ZN C:ZN202 2.3 21.7 0.6
CG C:ASP82 2.7 10.7 1.0
OD1 C:ASP82 2.8 10.4 1.0
CE1 B:HIS59 2.9 11.6 1.0
CD2 C:HIS145 3.0 14.7 1.0
CE1 C:HIS145 3.1 14.2 1.0
CG B:HIS59 3.1 9.0 1.0
CB B:HIS59 3.6 9.0 1.0
OG C:SER79 3.7 13.1 1.0
NE2 B:HIS59 4.1 11.6 1.0
CG C:HIS145 4.1 14.9 1.0
O B:HOH385 4.1 21.5 1.0
ND1 C:HIS145 4.1 14.4 1.0
CB C:ASP82 4.2 9.8 1.0
CD2 B:HIS59 4.2 11.8 1.0
N C:SER79 4.3 11.5 1.0
CB C:SER79 4.3 12.5 1.0
CA B:HIS59 4.5 13.2 1.0
CD1 C:ILE146 4.5 12.8 1.0
CG1 C:ILE146 4.6 13.8 1.0
O C:HOH332 4.8 10.9 1.0
CA C:SER78 4.9 9.9 1.0
OG B:SER105 4.9 15.9 1.0
O B:HIS59 4.9 16.6 1.0
CA C:SER79 5.0 11.3 1.0

Zinc binding site 6 out of 8 in 6vyo

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Zinc binding site 6 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:21.7
occ:0.60
 ZN C:ZN201 2.3 11.1 0.9
OG C:SER79 2.9 13.1 1.0
OD1 C:ASP82 3.3 10.4 1.0
OD2 C:ASP82 3.4 11.1 1.0
NE2 C:HIS145 3.5 13.4 1.0
CB B:HIS59 3.6 9.0 1.0
ND1 B:HIS59 3.6 10.7 1.0
O B:HOH385 3.7 21.5 1.0
CG C:ASP82 3.7 10.7 1.0
CB C:SER79 3.7 12.5 1.0
O C:HOH426 3.7 45.4 1.0
O C:HOH414 3.9 16.1 1.0
CE1 C:HIS145 3.9 14.2 1.0
O B:HIS59 3.9 16.6 1.0
O C:HOH332 4.1 10.9 1.0
CG B:HIS59 4.1 9.0 1.0
O B:HOH449 4.3 34.1 1.0
C B:HIS59 4.4 15.8 1.0
CD2 C:HIS145 4.4 14.7 1.0
CA B:HIS59 4.4 13.2 1.0
O C:HOH428 4.6 28.9 1.0
O B:HOH364 4.6 30.2 1.0
CB C:ASP81 4.6 14.4 1.0
CE1 B:HIS59 4.8 11.6 1.0
N C:SER79 4.9 11.5 1.0
CA C:SER79 4.9 11.3 1.0
ND1 C:HIS145 4.9 14.4 1.0

Zinc binding site 7 out of 8 in 6vyo

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Zinc binding site 7 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:11.7
occ:1.00
 OD2 D:ASP82 2.0 11.5 1.0
NE2 D:HIS145 2.0 11.8 1.0
NE2 C:HIS59 2.1 11.0 1.0
ZN D:ZN202 2.2 17.9 0.6
CG D:ASP82 2.9 11.3 1.0
CD2 D:HIS145 3.0 11.7 1.0
CE1 C:HIS59 3.0 12.7 1.0
CD2 C:HIS59 3.1 10.6 1.0
CE1 D:HIS145 3.1 12.4 1.0
OD1 D:ASP82 3.2 12.7 1.0
CD1 D:ILE146 4.0 11.6 1.0
CG1 D:ILE146 4.0 13.0 1.0
N D:SER79 4.1 16.5 1.0
OG D:SER79 4.1 19.7 1.0
CG D:HIS145 4.1 10.8 1.0
ND1 C:HIS59 4.2 13.3 1.0
ND1 D:HIS145 4.2 13.0 1.0
CG C:HIS59 4.2 11.1 1.0
CB D:ASP82 4.2 8.8 1.0
CA D:SER78 4.4 14.9 1.0
CG2 C:THR57 4.5 14.1 1.0
CB D:SER79 4.5 16.3 1.0
CB D:SER78 4.5 14.3 1.0
C D:SER78 4.8 15.9 1.0
CA D:SER79 5.0 15.4 1.0
CB C:THR57 5.0 13.0 1.0

Zinc binding site 8 out of 8 in 6vyo

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Zinc binding site 8 out of 8 in the Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2


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 Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:17.9
occ:0.63
 ZN D:ZN201 2.2 11.7 1.0
NE2 C:HIS59 3.4 11.0 1.0
OD2 D:ASP82 3.4 11.5 1.0
NE2 D:HIS145 3.5 11.8 1.0
CE1 C:HIS59 3.5 12.7 1.0
O D:ASN77 3.7 22.1 1.0
CD2 D:HIS145 3.7 11.7 1.0
C6 C:MES204 3.7 20.5 1.0
CG1 D:ILE146 3.8 13.0 1.0
CA D:SER78 3.8 14.9 1.0
OG1 C:THR57 4.0 14.6 1.0
CB C:THR57 4.0 13.0 1.0
CD1 D:ILE146 4.0 11.6 1.0
CB D:SER78 4.0 14.3 1.0
C5 C:MES204 4.0 22.3 1.0
O C:HOH322 4.1 21.6 1.0
CG2 C:THR57 4.2 14.1 1.0
O C:HOH317 4.2 32.9 1.0
C D:ASN77 4.5 17.9 1.0
CG D:ASP82 4.6 11.3 1.0
N D:SER78 4.6 15.3 1.0
CD2 C:HIS59 4.7 10.6 1.0
N D:SER79 4.7 16.5 1.0
CE1 D:HIS145 4.7 12.4 1.0
C D:SER78 4.8 15.9 1.0
ND1 C:HIS59 4.8 13.3 1.0
O D:HOH339 4.9 24.7 1.0
O1 C:MES204 5.0 23.4 1.0
CG D:HIS145 5.0 10.8 1.0

Reference:

C.Chang, K.Michalska, R.Jedrzejczak, N.Maltseva, M.Endres, A.Godzik, Y.Kim, A.Joachimiak. Crystal Structure of Rna Binding Domain of Nucleocapsid Phosphoprotein From Sars Coronavirus 2 To Be Published.
Page generated: Wed Dec 16 13:03:20 2020

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