Zinc in PDB 7koj: The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494

Protein crystallography data

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494, PDB code: 7koj was solved by J.Osipiuk, C.Tesar, M.Endres, V.Lisnyak, S.Maki, C.Taylor, Y.Zhang, Z.Zhou, S.A.Azizi, K.Jones, R.Kathayat, S.A.Snyder, B.C.Dickinson, 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) 45.41 / 2.02
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 113.353, 113.353, 220.106, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.3

Other elements in 7koj:

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 (pdb code 7koj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494, PDB code: 7koj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7koj

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Zinc binding site 1 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:1.0
occ:1.00
SG A:CYS224 2.3 0.6 1.0
SG A:CYS192 2.4 0.5 1.0
SG A:CYS226 2.5 0.5 1.0
CB A:CYS226 2.9 0.1 1.0
CB A:CYS192 3.0 0.1 1.0
SG A:CYS189 3.0 0.7 1.0
N A:CYS192 3.4 0.7 1.0
CB A:CYS189 3.5 0.9 1.0
CA A:CYS192 3.7 0.3 1.0
CB A:CYS224 3.9 0.2 1.0
N A:CYS226 4.0 0.5 1.0
CA A:CYS226 4.0 0.3 1.0
C A:THR191 4.5 0.9 1.0
CB A:THR191 4.6 0.3 1.0
C A:CYS192 4.9 0.6 1.0
CA A:THR191 4.9 0.0 1.0
CA A:CYS189 5.0 0.7 1.0
N A:THR191 5.0 0.2 1.0
C A:CYS226 5.0 0.9 1.0

Zinc binding site 2 out of 5 in 7koj

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Zinc binding site 2 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:98.0
occ:0.70
NE2 A:HIS17 1.6 90.9 1.0
CE1 A:HIS17 2.2 87.5 1.0
OE2 A:GLU67 2.2 67.5 1.0
CD2 A:HIS17 2.8 87.1 1.0
OE1 A:GLU67 2.9 65.2 1.0
CD A:GLU67 2.9 65.4 1.0
CG2 A:THR63 3.3 67.6 1.0
ND1 A:HIS17 3.4 90.0 1.0
CG A:HIS17 3.7 90.5 1.0
CB A:ASN15 4.0 80.3 1.0
O A:HOH603 4.2 77.0 1.0
CG A:GLU67 4.4 61.7 1.0
CD2 A:LEU64 4.6 70.8 1.0
O A:HOH653 4.7 64.7 1.0
CB A:THR63 4.7 66.7 1.0
CG A:ASN15 4.7 81.7 1.0

Zinc binding site 3 out of 5 in 7koj

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Zinc binding site 3 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:41.0
occ:0.50
ZN A:ZN504 0.0 41.0 0.5
ZN A:ZN504 1.9 63.8 0.5
OD2 A:ASP108 2.0 51.7 1.0
ND1 A:HIS89 2.0 50.3 1.0
CL A:CL508 2.2 65.0 1.0
CG A:ASP108 2.9 50.3 1.0
CE1 A:HIS89 2.9 52.9 1.0
CG A:HIS89 3.1 50.8 1.0
OD1 A:ASP108 3.2 50.3 1.0
CB A:HIS89 3.5 50.7 1.0
O A:HOH612 3.7 66.8 1.0
O A:HOH769 4.1 71.1 1.0
NE2 A:HIS89 4.1 51.3 1.0
O A:HOH733 4.1 64.0 1.0
CG1 A:VAL159 4.1 52.5 1.0
CD2 A:HIS89 4.2 49.0 1.0
CB A:ASP108 4.3 46.7 1.0
CA A:HIS89 4.4 48.7 1.0
NE1 A:TRP93 4.4 53.1 1.0

Zinc binding site 4 out of 5 in 7koj

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Zinc binding site 4 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:63.8
occ:0.50
ZN A:ZN504 0.0 63.8 0.5
ZN A:ZN504 1.9 41.0 0.5
ND1 A:HIS89 2.2 50.3 1.0
CL A:CL508 2.3 65.0 1.0
O A:HOH733 2.4 64.0 1.0
CE1 A:HIS89 2.7 52.9 1.0
CG A:HIS89 3.3 50.8 1.0
OD2 A:ASP108 3.8 51.7 1.0
CB A:HIS89 3.9 50.7 1.0
NE2 A:HIS89 3.9 51.3 1.0
CA A:HIS89 4.2 48.7 1.0
CD2 A:HIS89 4.2 49.0 1.0
O A:HOH769 4.5 71.1 1.0
O A:HOH612 4.6 66.8 1.0
CG A:ASP108 4.7 50.3 1.0
OD1 A:ASP108 4.9 50.3 1.0
CD A:LYS92 5.0 79.6 1.0

Zinc binding site 5 out of 5 in 7koj

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Zinc binding site 5 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:57.7
occ:1.00
ND1 A:HIS73 2.0 47.7 1.0
CL A:CL507 2.2 57.6 1.0
CL A:CL506 2.3 58.5 1.0
CE1 A:HIS73 3.0 50.4 1.0
CG A:HIS73 3.0 48.8 1.0
CB A:HIS73 3.3 51.0 1.0
CB A:ASN128 4.0 60.4 1.0
NE2 A:HIS73 4.1 53.0 1.0
CD2 A:HIS73 4.1 50.4 1.0
UNK A:UNX512 4.4 69.9 1.0
CA A:HIS73 4.7 50.3 1.0
ND2 A:ASN128 4.8 71.2 1.0
O A:HIS73 4.8 58.8 1.0
CG A:ASN128 4.8 64.3 1.0
UNK A:UNX516 4.8 78.5 1.0
CG A:PRO129 4.9 50.9 1.0
CD A:PRO129 4.9 52.3 1.0

Reference:

J.Osipiuk, C.Tesar, M.Endres, V.Lisnyak, S.Maki, C.Taylor, Y.Zhang, Z.Zhou, S.A.Azizi, K.Jones, R.Kathayat, S.A.Snyder, B.C.Dickinson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER494 To Be Published.
Page generated: Wed Dec 16 14:04:21 2020

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