Zinc in PDB 5lrp: Mopeia Virus Exonuclease Domain Complexed with Magnesium

The structure of Mopeia Virus Exonuclease Domain Complexed with Magnesium, PDB code: 5lrp was solved by E.L.Yekwa, J.Khourieh, B.Canard, F.Ferron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.41 / 1.94
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	45.439, 38.182, 137.093, 90.00, 91.99, 90.00
R / Rfree (%)	19.5 / 24.5

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Mopeia Virus Exonuclease Domain Complexed with Magnesium (pdb code 5lrp). 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 Magnesium, PDB code: 5lrp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mopeia Virus Exonuclease Domain Complexed with Magnesium


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 Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:21.7 occ:1.00 NE2 A:HIS510 2.0 18.2 1.0 OE2 A:GLU400 2.1 29.3 1.0 SG A:CYS530 2.3 20.2 1.0 SG A:CYS507 2.3 18.9 1.0 OE1 A:GLU400 2.6 20.5 1.0 CD A:GLU400 2.6 26.1 1.0 CD2 A:HIS510 3.0 19.6 1.0 CE1 A:HIS510 3.1 20.9 1.0 CB A:CYS530 3.1 20.0 1.0 CB A:CYS507 3.4 25.1 1.0 CA A:CYS530 3.7 29.2 1.0 NE2 A:HIS413 3.9 21.7 1.0 CE1 A:HIS413 4.1 23.7 1.0 CG A:GLU400 4.1 20.4 1.0 CG A:HIS510 4.1 23.0 1.0 ND1 A:HIS510 4.1 21.6 1.0 N A:ALA531 4.2 23.0 1.0 C A:CYS530 4.3 28.8 1.0 CE1 A:TYR415 4.5 20.0 1.0 OH A:TYR415 4.8 23.5 1.0 N A:LEU532 4.8 21.7 1.0 CA A:CYS507 4.8 26.3 1.0 CB A:MET509 4.9 23.9 1.0

Zinc binding site 2 out of 2 in the Mopeia Virus Exonuclease Domain Complexed with Magnesium


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 Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:25.3 occ:1.00 NE2 B:HIS510 2.0 28.0 1.0 OE2 B:GLU400 2.2 25.7 1.0 SG B:CYS507 2.3 24.0 1.0 SG B:CYS530 2.3 24.7 1.0 OE1 B:GLU400 2.6 25.2 1.0 CD B:GLU400 2.7 27.2 1.0 CD2 B:HIS510 2.9 29.8 1.0 CE1 B:HIS510 3.1 30.4 1.0 CB B:CYS530 3.1 24.9 1.0 CB B:CYS507 3.4 30.0 1.0 CA B:CYS530 3.6 33.0 1.0 NE2 B:HIS413 4.0 25.8 1.0 CG B:GLU400 4.1 23.4 1.0 CG B:HIS510 4.1 33.7 1.0 ND1 B:HIS510 4.2 31.3 1.0 N B:ALA531 4.2 28.3 1.0 CE1 B:HIS413 4.2 24.1 1.0 C B:CYS530 4.2 32.1 1.0 CE1 B:TYR415 4.6 26.5 1.0 N B:LEU532 4.8 22.5 1.0 CA B:CYS507 4.8 32.0 1.0 OH B:TYR415 4.9 26.9 1.0 N B:CYS530 5.0 33.2 1.0

E.Yekwa, J.Khourieh, B.Canard, N.Papageorgiou, F.Ferron. Activity Inhibition and Crystal Polymorphism Induced By Active-Site Metal Swapping. Acta Crystallogr D Struct V. 73 641 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28777079
DOI: 10.1107/S205979831700866X