Zinc in PDB 7v38: Crystal Structure of Np Exonuclease-Pcmps Complex

Protein crystallography data

The structure of Crystal Structure of Np Exonuclease-Pcmps Complex, PDB code: 7v38 was solved by Y.Y.Hsiao, K.W.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.79 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.227, 74.012, 140.807, 90, 90, 90
R / Rfree (%) 21.3 / 26.2

Other elements in 7v38:

The structure of Crystal Structure of Np Exonuclease-Pcmps Complex also contains other interesting chemical elements:

Mercury (Hg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Np Exonuclease-Pcmps Complex (pdb code 7v38). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Np Exonuclease-Pcmps Complex, PDB code: 7v38:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7v38

Go back to Zinc Binding Sites List in 7v38
Zinc binding site 1 out of 2 in the Crystal Structure of Np Exonuclease-Pcmps Complex


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 Np Exonuclease-Pcmps Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:47.5
occ:1.00
OE2 A:GLU399 2.1 45.4 1.0
NE2 A:HIS509 2.1 45.4 1.0
SG A:CYS506 2.3 45.4 1.0
SG A:CYS529 2.4 48.4 1.0
CD2 A:HIS509 2.9 47.9 1.0
CD A:GLU399 2.9 51.1 1.0
OE1 A:GLU399 3.1 50.8 1.0
CB A:CYS529 3.2 43.7 1.0
CE1 A:HIS509 3.3 45.9 1.0
CB A:CYS506 3.4 51.9 1.0
CA A:CYS529 3.8 43.5 1.0
NE2 A:HIS412 4.0 48.4 1.0
CG A:HIS509 4.1 46.3 1.0
CE1 A:HIS412 4.2 50.8 1.0
CZ A:PHE414 4.2 51.8 1.0
ND1 A:HIS509 4.3 43.7 1.0
N A:ALA530 4.3 50.3 1.0
CG A:GLU399 4.3 51.1 1.0
CE2 A:PHE414 4.4 54.6 1.0
C A:CYS529 4.5 49.8 1.0
CA A:CYS506 4.8 60.6 1.0
N A:LEU531 4.9 38.3 1.0
CB A:MET508 4.9 54.5 1.0

Zinc binding site 2 out of 2 in 7v38

Go back to Zinc Binding Sites List in 7v38
Zinc binding site 2 out of 2 in the Crystal Structure of Np Exonuclease-Pcmps Complex


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 Np Exonuclease-Pcmps Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:45.2
occ:1.00
OE2 B:GLU399 2.1 44.1 1.0
NE2 B:HIS509 2.1 43.2 1.0
SG B:CYS506 2.2 42.4 1.0
SG B:CYS529 2.4 44.9 1.0
CD2 B:HIS509 2.9 43.0 1.0
CD B:GLU399 3.0 47.6 1.0
CE1 B:HIS509 3.2 41.3 1.0
OE1 B:GLU399 3.2 48.3 1.0
CB B:CYS529 3.3 35.4 1.0
CB B:CYS506 3.4 53.5 1.0
CA B:CYS529 3.9 35.3 1.0
NE2 B:HIS412 3.9 41.2 1.0
CE1 B:HIS412 4.1 40.7 1.0
CG B:HIS509 4.2 46.3 1.0
CZ B:PHE414 4.2 52.5 1.0
ND1 B:HIS509 4.2 44.9 1.0
N B:ALA530 4.3 46.8 1.0
CE2 B:PHE414 4.3 51.4 1.0
CG B:GLU399 4.4 46.0 1.0
C B:CYS529 4.5 42.1 1.0
CA B:CYS506 4.8 56.6 1.0
N B:LEU531 4.8 48.9 1.0

Reference:

K.W.Huang, J.W.Chen, T.Y.Hua, Y.Y.Chu, T.Y.Chiu, J.Y.Liu, C.I.Tu, K.C.Hsu, Y.T.Kao, J.W.Chu, Y.Y.Hsiao. Targeted Covalent Inhibitors Allosterically Deactivate the Deddhlassa Fever Virus Np Exonuclease From Alternative Distal Site. Jacs Au 2021.
ISSN: ESSN 2691-3704
DOI: 10.1021/JACSAU.1C00420
Page generated: Fri Dec 17 11:55:02 2021

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