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Zinc in PDB 6sx8: Mopeia Virus Exonuclease Domain Complexed with Manganese

Protein crystallography data

The structure of Mopeia Virus Exonuclease Domain Complexed with Manganese, PDB code: 6sx8 was solved by T.H.V.Nguyen, F.Ferron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.82 / 1.80
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 45.537, 38.014, 137.23, 90, 92.94, 90
R / Rfree (%) 21.1 / 25.4

Other elements in 6sx8:

The structure of Mopeia Virus Exonuclease Domain Complexed with Manganese also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Mopeia Virus Exonuclease Domain Complexed with Manganese (pdb code 6sx8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mopeia Virus Exonuclease Domain Complexed with Manganese, PDB code: 6sx8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6sx8

Go back to Zinc Binding Sites List in 6sx8
Zinc binding site 1 out of 2 in the Mopeia Virus Exonuclease Domain Complexed with Manganese


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mopeia Virus Exonuclease Domain Complexed with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:37.1
occ:1.00
OE2 A:GLU400 1.9 37.8 1.0
NE2 A:HIS510 2.0 31.7 1.0
SG A:CYS507 2.3 40.5 1.0
SG A:CYS530 2.4 36.1 1.0
CD A:GLU400 2.9 37.4 1.0
CD2 A:HIS510 3.0 38.3 1.0
CE1 A:HIS510 3.0 34.6 1.0
OE1 A:GLU400 3.2 35.8 1.0
CB A:CYS530 3.2 38.0 1.0
CB A:CYS507 3.3 36.1 1.0
CA A:CYS530 3.8 37.4 1.0
NE2 A:HIS413 3.9 33.7 1.0
ND1 A:HIS510 4.1 32.6 1.0
CG A:HIS510 4.1 38.4 1.0
CE1 A:HIS413 4.1 36.6 1.0
CG A:GLU400 4.2 32.3 1.0
N A:ALA531 4.3 36.4 1.0
C A:CYS530 4.4 39.0 1.0
CE1 A:TYR415 4.5 35.0 1.0
CA A:CYS507 4.7 35.6 1.0
N A:LEU532 4.8 32.4 1.0
OH A:TYR415 4.8 38.1 1.0
CB A:MET509 4.8 41.4 1.0
O A:CYS507 5.0 41.0 1.0

Zinc binding site 2 out of 2 in 6sx8

Go back to Zinc Binding Sites List in 6sx8
Zinc binding site 2 out of 2 in the Mopeia Virus Exonuclease Domain Complexed with Manganese


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mopeia Virus Exonuclease Domain Complexed with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:31.2
occ:1.00
OE2 B:GLU400 2.0 31.1 1.0
NE2 B:HIS510 2.1 31.7 1.0
SG B:CYS507 2.3 30.6 1.0
SG B:CYS530 2.3 31.1 1.0
CD2 B:HIS510 2.9 34.2 1.0
CD B:GLU400 2.9 29.0 1.0
OE1 B:GLU400 3.1 30.9 1.0
CB B:CYS530 3.2 30.1 1.0
CE1 B:HIS510 3.2 33.6 1.0
CB B:CYS507 3.3 32.3 1.0
CA B:CYS530 3.7 31.1 1.0
NE2 B:HIS413 3.9 32.7 1.0
CE1 B:HIS413 4.1 31.2 1.0
CG B:HIS510 4.1 36.3 1.0
ND1 B:HIS510 4.2 33.8 1.0
N B:ALA531 4.3 30.8 1.0
CG B:GLU400 4.3 28.9 1.0
C B:CYS530 4.4 34.8 1.0
CE1 B:TYR415 4.4 28.1 1.0
CA B:CYS507 4.7 32.8 1.0
OH B:TYR415 4.7 34.1 1.0
N B:LEU532 4.9 30.1 1.0
CB B:MET509 4.9 36.0 1.0

Reference:

E.Yekwa, T.H.V.Nguyen, M.Mathieu, I.Imbert, B.Selisko, B.Canard, S.Baize, F.Ferron. Serendipity in Arenaviridae Np Exonuclease Inhibitor Discovery. To Be Published.
Page generated: Sat Aug 21 17:56:47 2021

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