Zinc in PDB 7krx: The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER441

Protein crystallography data

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER441, PDB code: 7krx 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) 49.85 / 2.72
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.333, 114.333, 219.573, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.9

Other elements in 7krx:

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER441 also contains other interesting chemical elements:

Chlorine (Cl) 2 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_SNYDER441 (pdb code 7krx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 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_SNYDER441, PDB code: 7krx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7krx

Go back to Zinc Binding Sites List in 7krx
Zinc binding site 1 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:0.1
occ:1.00
SG A:CYS224 2.4 0.3 1.0
SG A:CYS192 2.4 0.2 1.0
SG A:CYS226 2.4 0.0 1.0
SG A:CYS189 2.4 0.7 1.0
CB A:CYS192 3.0 0.0 1.0
CB A:CYS226 3.5 0.6 1.0
CB A:CYS224 3.6 0.5 1.0
CB A:CYS189 3.6 0.1 1.0
N A:CYS226 3.8 0.0 1.0
N A:CYS192 3.9 0.7 1.0
CA A:CYS192 4.0 0.8 1.0
CA A:CYS226 4.1 0.2 1.0
C A:CYS226 4.5 0.7 1.0
N A:THR225 4.6 0.7 1.0
CA A:CYS224 4.8 0.8 1.0
C A:THR225 4.9 0.7 1.0

Zinc binding site 2 out of 4 in 7krx

Go back to Zinc Binding Sites List in 7krx
Zinc binding site 2 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:0.1
occ:1.00
NE2 A:HIS17 1.9 0.4 1.0
OE2 A:GLU67 2.0 0.9 1.0
CE1 A:HIS17 2.6 0.1 1.0
CD A:GLU67 2.9 0.7 1.0
CD2 A:HIS17 3.1 0.8 1.0
OE1 A:GLU67 3.3 0.5 1.0
CG2 A:THR63 3.6 0.7 1.0
ND1 A:HIS17 3.8 0.6 1.0
CG A:HIS17 4.1 1.0 1.0
CB A:ASN15 4.2 0.8 1.0
CG A:GLU67 4.3 0.8 1.0
CB A:THR63 4.8 0.1 1.0
CG A:ASN15 4.9 0.7 1.0
ND2 A:ASN15 4.9 0.9 1.0

Zinc binding site 3 out of 4 in 7krx

Go back to Zinc Binding Sites List in 7krx
Zinc binding site 3 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:0.1
occ:1.00
OD2 A:ASP108 2.4 86.0 1.0
ND1 A:HIS89 2.4 96.2 1.0
CG A:HIS89 3.3 90.1 1.0
CE1 A:HIS89 3.4 1.0 1.0
CG A:ASP108 3.4 86.6 1.0
CB A:HIS89 3.5 91.3 1.0
OD1 A:ASP108 3.8 92.8 1.0
CA A:HIS89 4.1 83.0 1.0
CD2 A:HIS89 4.4 94.3 1.0
NE2 A:HIS89 4.5 92.4 1.0
CG1 A:VAL159 4.7 87.9 1.0
NE1 A:TRP93 4.7 95.4 1.0
CB A:ASP108 4.8 78.5 1.0
O A:HIS89 4.9 83.7 1.0
C A:HIS89 4.9 84.6 1.0

Zinc binding site 4 out of 4 in 7krx

Go back to Zinc Binding Sites List in 7krx
Zinc binding site 4 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:0.8
occ:1.00
CL A:CL506 2.0 0.8 1.0
ND1 A:HIS73 2.3 83.5 1.0
CL A:CL507 2.5 0.2 1.0
CG A:HIS73 3.1 81.4 1.0
CB A:HIS73 3.2 79.7 1.0
CE1 A:HIS73 3.4 93.2 1.0
CB A:ASN128 4.1 0.4 1.0
CD2 A:HIS73 4.3 86.7 1.0
O A:HIS73 4.4 94.4 1.0
NE2 A:HIS73 4.5 90.0 1.0
CA A:HIS73 4.5 82.4 1.0
CG A:PRO129 4.7 79.3 1.0
ND2 A:ASN128 4.7 0.2 1.0
CD A:PRO129 4.8 85.2 1.0
CG A:ASN128 4.9 0.2 1.0
N A:PRO129 5.0 85.9 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_SNYDER441 To Be Published.
Page generated: Wed Dec 16 14:04:50 2020

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