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Magnesium in PDB 7v3b: Crystal Structure of Np Exonuclease C409A-Pcmps Complex

Protein crystallography data

The structure of Crystal Structure of Np Exonuclease C409A-Pcmps Complex, PDB code: 7v3b 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) 29.83 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.703, 58.897, 69.188, 90, 90, 90
R / Rfree (%) 18.6 / 21.8

Other elements in 7v3b:

The structure of Crystal Structure of Np Exonuclease C409A-Pcmps Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Mercury (Hg) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Np Exonuclease C409A-Pcmps Complex (pdb code 7v3b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Np Exonuclease C409A-Pcmps Complex, PDB code: 7v3b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7v3b

Go back to Magnesium Binding Sites List in 7v3b
Magnesium binding site 1 out of 2 in the Crystal Structure of Np Exonuclease C409A-Pcmps Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Np Exonuclease C409A-Pcmps Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:37.0
occ:1.00
O A:HOH819 1.9 43.2 1.0
O A:HOH703 2.1 33.4 1.0
O A:HOH732 2.2 38.8 1.0
OD2 A:ASP389 2.2 34.5 1.0
O A:ILE390 2.4 21.1 1.0
O A:HOH815 2.5 44.2 1.0
CG A:ASP389 2.9 32.0 1.0
OD1 A:ASP389 3.2 34.2 1.0
C A:ILE390 3.4 20.8 1.0
OE2 A:GLU391 3.5 29.1 1.0
O A:HOH709 3.7 46.7 1.0
N A:ILE390 3.7 19.8 1.0
OD2 A:ASP533 3.7 26.0 1.0
O A:HOH717 3.8 48.2 1.0
O A:HOH724 3.9 40.1 1.0
CA A:ILE390 4.2 19.4 1.0
CB A:ASP389 4.2 22.7 1.0
CD A:GLU391 4.4 27.7 1.0
N A:GLU391 4.4 18.6 1.0
C A:ASP389 4.5 18.4 1.0
O A:HOH807 4.6 35.5 1.0
CA A:ASP389 4.7 19.6 1.0
CA A:GLU391 4.7 20.4 1.0
CG A:ASP533 4.8 23.1 1.0
CG A:GLU391 4.8 21.9 1.0

Magnesium binding site 2 out of 2 in 7v3b

Go back to Magnesium Binding Sites List in 7v3b
Magnesium binding site 2 out of 2 in the Crystal Structure of Np Exonuclease C409A-Pcmps Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Np Exonuclease C409A-Pcmps Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:34.7
occ:1.00
OD1 B:ASP389 2.1 31.1 1.0
O B:HOH701 2.2 35.9 1.0
O B:HOH786 2.2 35.5 1.0
O B:HOH795 2.2 35.2 1.0
O B:HOH832 2.2 35.9 1.0
O B:HOH730 2.3 34.6 1.0
CG B:ASP389 3.0 30.1 1.0
OD2 B:ASP389 3.3 36.4 1.0
OD2 B:ASP466 3.9 44.7 1.0
O B:ILE390 3.9 22.1 1.0
O B:GLN462 4.0 26.3 1.0
O B:HOH829 4.3 36.6 1.0
OD1 B:ASP466 4.3 45.8 1.0
N B:ILE390 4.4 19.8 1.0
CB B:ASP389 4.4 18.6 1.0
CG B:ASP466 4.5 42.4 1.0
O B:HOH749 4.5 36.9 1.0
O B:HOH706 4.6 34.7 1.0
CA B:ASP389 4.7 17.7 1.0
C B:ILE390 5.0 17.8 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: Thu Aug 14 16:53:08 2025

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