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Zinc in PDB 3mj5: Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation

Protein crystallography data

The structure of Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation, PDB code: 3mj5 was solved by A.D.Mesecar, K.M.Ratia, S.D.Pegan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.42 / 2.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.397, 74.129, 96.895, 90.00, 103.02, 90.00
R / Rfree (%) 20.8 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation (pdb code 3mj5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation, PDB code: 3mj5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3mj5

Go back to Zinc Binding Sites List in 3mj5
Zinc binding site 1 out of 2 in the Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:61.5
occ:1.00
SG A:CYS225 2.1 59.2 1.0
SG A:CYS193 2.2 60.7 1.0
CB A:CYS227 2.2 63.3 1.0
SG A:CYS190 2.4 52.2 1.0
SG A:CYS227 2.5 63.6 1.0
CB A:CYS193 3.2 59.1 1.0
CB A:CYS225 3.2 59.4 1.0
CB A:CYS190 3.4 50.2 1.0
CA A:CYS227 3.5 63.1 1.0
N A:CYS227 3.6 62.9 1.0
N A:CYS193 3.7 58.7 1.0
CA A:CYS193 4.0 58.9 1.0
C A:CYS227 4.4 63.1 1.0
CB A:ARG229 4.4 61.2 1.0
CA A:CYS225 4.5 59.3 1.0
CB A:HIS192 4.5 57.8 1.0
C A:CYS225 4.6 60.4 1.0
ND1 A:HIS192 4.6 62.5 1.0
CD A:ARG229 4.8 60.1 1.0
C A:HIS192 4.8 58.2 1.0
CA A:CYS190 4.8 50.6 1.0
O A:CYS225 4.8 60.4 1.0
O A:CYS227 4.8 63.5 1.0
C A:VAL226 4.9 62.6 1.0
N A:VAL226 5.0 61.1 1.0
N A:ARG229 5.0 61.9 1.0

Zinc binding site 2 out of 2 in 3mj5

Go back to Zinc Binding Sites List in 3mj5
Zinc binding site 2 out of 2 in the Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:0.6
occ:1.00
SG B:CYS193 2.3 76.1 1.0
SG B:CYS225 2.5 74.6 1.0
SG B:CYS190 2.6 79.9 1.0
SG B:CYS227 3.1 80.6 1.0
CB B:CYS190 3.5 76.2 1.0
NE2 B:HIS192 3.7 83.8 1.0
CD2 B:HIS192 3.7 82.9 1.0
N B:CYS227 3.9 79.3 1.0
CB B:CYS193 3.9 76.8 1.0
CB B:VAL226 3.9 78.5 1.0
CB B:CYS227 4.0 79.7 1.0
CB B:CYS225 4.2 74.1 1.0
N B:VAL226 4.4 77.3 1.0
CA B:VAL226 4.6 78.3 1.0
CA B:CYS227 4.6 79.7 1.0
CG1 B:VAL226 4.7 78.5 1.0
CG2 B:VAL226 4.7 78.7 1.0
CE1 B:HIS192 4.7 83.2 1.0
CG B:HIS192 4.8 82.0 1.0
N B:CYS193 4.8 78.1 1.0
C B:VAL226 4.8 78.9 1.0
CA B:CYS190 4.9 75.9 1.0
C B:CYS225 5.0 75.9 1.0

Reference:

A.K.Ghosh, J.Takayama, K.V.Rao, K.Ratia, R.Chaudhuri, D.C.Mulhearn, H.Lee, D.B.Nichols, S.Baliji, S.C.Baker, M.E.Johnson, A.D.Mesecar. Severe Acute Respiratory Syndrome Coronavirus Papain-Like Novel Protease Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure and Biological Evaluation J.Med.Chem. V. 53 4968 2010.
ISSN: ISSN 0022-2623
PubMed: 20527968
DOI: 10.1021/JM1004489
Page generated: Wed Dec 16 04:35:21 2020

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