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Zinc in PDB 5eqr: Crystal Structure of A Genotype 1A/3A Chimeric Hcv NS3/4A Protease in Complex with Danoprevir

Protein crystallography data

The structure of Crystal Structure of A Genotype 1A/3A Chimeric Hcv NS3/4A Protease in Complex with Danoprevir, PDB code: 5eqr was solved by D.Soumana, N.K.Yilmaz, A.Ali, K.L.Prachanronarong, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.33 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.970, 58.494, 59.985, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20

Other elements in 5eqr:

The structure of Crystal Structure of A Genotype 1A/3A Chimeric Hcv NS3/4A Protease in Complex with Danoprevir also contains other interesting chemical elements:

Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Genotype 1A/3A Chimeric Hcv NS3/4A Protease in Complex with Danoprevir (pdb code 5eqr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of A Genotype 1A/3A Chimeric Hcv NS3/4A Protease in Complex with Danoprevir, PDB code: 5eqr:

Zinc binding site 1 out of 1 in 5eqr

Go back to Zinc Binding Sites List in 5eqr
Zinc binding site 1 out of 1 in the Crystal Structure of A Genotype 1A/3A Chimeric Hcv NS3/4A Protease in Complex with Danoprevir


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 A Genotype 1A/3A Chimeric Hcv NS3/4A Protease in Complex with Danoprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:23.2
occ:1.00
SG A:CYS1097 2.3 18.0 1.0
SG A:CYS1145 2.4 15.8 1.0
SG A:CYS1099 2.6 30.8 1.0
ND1 A:HIS1149 2.7 29.9 1.0
HB2 A:HIS1149 2.7 26.4 1.0
HB2 A:CYS1099 2.7 16.6 1.0
H A:CYS1099 3.2 19.6 1.0
HB3 A:CYS1145 3.2 15.3 1.0
CB A:CYS1099 3.2 13.8 1.0
CB A:CYS1145 3.3 12.7 1.0
HA A:CYS1097 3.3 15.9 1.0
HB2 A:CYS1145 3.4 15.3 1.0
CB A:CYS1097 3.4 14.8 1.0
HB2 A:CYS1097 3.4 17.8 1.0
CG A:HIS1149 3.4 31.9 1.0
CB A:HIS1149 3.5 22.0 1.0
HB3 A:ALA1147 3.5 19.7 1.0
H A:THR1098 3.5 20.0 1.0
CE1 A:HIS1149 3.7 34.5 1.0
CA A:CYS1097 3.8 13.3 1.0
N A:CYS1099 3.8 16.3 1.0
HB3 A:CYS1099 3.9 16.6 1.0
HB3 A:HIS1149 3.9 26.4 1.0
HE1 A:HIS1149 3.9 41.4 1.0
H A:HIS1149 4.0 18.6 1.0
N A:THR1098 4.1 16.7 1.0
CA A:CYS1099 4.2 16.2 1.0
HB3 A:CYS1097 4.2 17.8 1.0
H A:ALA1147 4.2 20.4 1.0
C A:CYS1097 4.4 18.9 1.0
CB A:ALA1147 4.5 16.4 1.0
CA A:HIS1149 4.6 12.9 1.0
CD2 A:HIS1149 4.6 38.1 1.0
CA A:CYS1145 4.7 12.2 1.0
HA A:CYS1099 4.7 19.5 1.0
N A:HIS1149 4.7 15.5 1.0
H A:CYS1145 4.7 14.4 1.0
NE2 A:HIS1149 4.8 31.9 1.0
HB2 A:ALA1147 4.8 19.7 1.0
HB3 A:SER1101 4.8 28.2 1.0
HG22 A:VAL1151 4.9 16.8 1.0
C A:THR1098 4.9 20.2 1.0
HD2 A:PRO1146 4.9 17.9 1.0
HG23 A:VAL1151 4.9 16.8 1.0
O A:HOH1330 4.9 28.5 1.0
HB1 A:ALA1147 5.0 19.7 1.0
N A:ALA1147 5.0 17.0 1.0
O A:HOH1371 5.0 34.9 1.0

Reference:

D.I.Soumana, N.Kurt Yilmaz, A.Ali, K.L.Prachanronarong, C.A.Schiffer. Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease. J.Am.Chem.Soc. V. 138 11850 2016.
ISSN: ESSN 1520-5126
PubMed: 27512818
DOI: 10.1021/JACS.6B06454
Page generated: Wed Dec 16 06:10:19 2020

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