Atomistry » Zinc » PDB 5lrm-5lyf » 5lrp
Atomistry »
  Zinc »
    PDB 5lrm-5lyf »
      5lrp »

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

Protein crystallography data

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

Other elements in 5lrp:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

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 5lrp

Go back to Zinc Binding Sites List in 5lrp
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 5lrp

Go back to Zinc Binding Sites List in 5lrp
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

Reference:

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
Page generated: Wed Dec 16 06:30:34 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy