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Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mopeia Virus Exonuclease Domain Complexed with Magnesium (pdb code 5lrp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mopeia Virus Exonuclease Domain Complexed with Magnesium, PDB code: 5lrp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5lrp

Go back to Magnesium Binding Sites List in 5lrp
Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of Mopeia Virus Exonuclease Domain Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:36.2
occ:1.00
OD2 A:ASP390 2.1 30.4 1.0
O A:HOH719 2.1 43.0 1.0
OE2 A:GLU392 2.1 34.8 1.0
OD2 A:ASP534 2.1 32.3 1.0
OD1 A:ASP390 2.1 38.4 1.0
CG A:ASP390 2.5 31.1 1.0
CG A:ASP534 3.2 28.0 1.0
CD A:GLU392 3.4 33.5 1.0
CB A:ASP534 3.7 21.4 1.0
O A:ILE391 3.8 22.4 1.0
CB A:ASP390 4.0 20.9 1.0
OE1 A:GLU392 4.2 32.5 1.0
CG A:GLU392 4.3 23.6 1.0
OD1 A:ASP534 4.3 29.5 1.0
O A:HOH814 4.3 32.1 1.0
CA A:ALA531 4.4 19.6 1.0
O A:CYS530 4.4 29.1 1.0
C A:ILE391 4.5 26.7 1.0
CB A:HIS529 4.6 24.9 1.0
N A:ILE391 4.7 19.9 1.0
N A:ALA531 4.7 23.0 1.0
C A:CYS530 4.7 28.8 1.0
O A:HOH767 4.7 43.4 1.0
CD2 A:HIS529 5.0 36.6 1.0
CA A:ASP390 5.0 22.4 1.0

Magnesium binding site 2 out of 2 in 5lrp

Go back to Magnesium Binding Sites List in 5lrp
Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of Mopeia Virus Exonuclease Domain Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:41.0
occ:1.00
O B:HOH790 2.1 47.9 1.0
OD2 B:ASP534 2.1 37.6 1.0
OD1 B:ASP390 2.2 39.2 1.0
OD2 B:ASP390 2.3 39.5 1.0
CG B:ASP390 2.5 34.2 1.0
OE2 B:GLU392 2.7 47.0 1.0
CG B:ASP534 3.1 35.1 1.0
CB B:ASP534 3.5 30.8 1.0
O B:ILE391 3.6 33.1 1.0
CD B:GLU392 3.8 41.1 1.0
CB B:ASP390 4.0 23.7 1.0
O B:HOH788 4.2 36.1 1.0
OD1 B:ASP534 4.3 34.4 1.0
C B:ILE391 4.4 31.2 1.0
CA B:ALA531 4.4 27.1 1.0
O B:HOH728 4.5 41.6 1.0
CG B:GLU392 4.5 32.1 1.0
N B:ILE391 4.5 26.2 1.0
O B:CYS530 4.6 32.3 1.0
OE1 B:GLU392 4.7 48.5 1.0
N B:ALA531 4.8 28.3 1.0
C B:ASP390 4.8 25.5 1.0
CA B:ASP390 4.9 24.5 1.0
C B:CYS530 4.9 32.1 1.0
CE2 B:PHE538 4.9 31.3 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: Mon Dec 14 20:49:04 2020

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