Magnesium in PDB 7v3a: Crystal Structure of Apo-Np Exonuclease C409A

Protein crystallography data

The structure of Crystal Structure of Apo-Np Exonuclease C409A, PDB code: 7v3a 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) 29.79 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.324, 59.431, 71.533, 90, 90, 90
R / Rfree (%) 20.3 / 24

Other elements in 7v3a:

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

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Apo-Np Exonuclease C409A (pdb code 7v3a). 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 Apo-Np Exonuclease C409A, PDB code: 7v3a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7v3a

Go back to Magnesium Binding Sites List in 7v3a
Magnesium binding site 1 out of 2 in the Crystal Structure of Apo-Np Exonuclease C409A


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 Apo-Np Exonuclease C409A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:33.8
occ:1.00
OD1 A:ASP389 2.1 35.3 1.0
O A:HOH757 2.1 32.2 1.0
O A:HOH771 2.1 36.9 1.0
O A:HOH701 2.2 34.6 1.0
O A:HOH804 2.2 32.0 1.0
O A:HOH848 2.2 34.1 1.0
CG A:ASP389 3.1 32.6 1.0
OD2 A:ASP389 3.4 33.7 1.0
O A:GLN462 3.9 31.0 1.0
OD2 A:ASP466 3.9 42.1 1.0
O A:HOH851 4.0 40.8 1.0
O A:ILE390 4.0 26.6 1.0
O A:HOH744 4.1 32.5 1.0
O A:HOH856 4.1 59.2 1.0
CB A:ASP389 4.4 26.5 1.0
OD1 A:ASP466 4.5 40.9 1.0
N A:ILE390 4.5 24.2 1.0
O A:HOH837 4.5 46.3 1.0
CG A:ASP466 4.6 40.9 1.0
CA A:ASP389 4.8 26.0 1.0
O A:HOH709 4.8 33.9 1.0
O A:GLY463 4.9 35.5 1.0
O A:HOH784 5.0 29.9 1.0

Magnesium binding site 2 out of 2 in 7v3a

Go back to Magnesium Binding Sites List in 7v3a
Magnesium binding site 2 out of 2 in the Crystal Structure of Apo-Np Exonuclease C409A


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 Apo-Np Exonuclease C409A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:40.1
occ:1.00
OD1 B:ASP389 2.0 38.2 1.0
O B:HOH702 2.0 35.3 1.0
O B:HOH729 2.1 36.4 1.0
O B:HOH736 2.1 38.2 1.0
O B:HOH851 2.2 47.4 1.0
O B:HOH751 2.3 35.7 1.0
CG B:ASP389 3.0 35.0 1.0
OD2 B:ASP389 3.4 36.0 1.0
O B:GLN462 3.8 38.5 1.0
OD2 B:ASP466 3.9 52.2 1.0
O B:ILE390 4.0 33.1 1.0
O B:HOH711 4.2 33.9 1.0
OD1 B:ASP466 4.2 51.4 1.0
O B:HOH852 4.3 37.1 1.0
N B:ILE390 4.3 25.3 1.0
CB B:ASP389 4.3 31.1 1.0
CG B:ASP466 4.5 50.2 1.0
O B:HOH832 4.6 51.6 1.0
CA B:ASP389 4.6 29.1 1.0
O B:HOH756 4.7 33.3 1.0
O B:GLY463 4.8 42.7 1.0
O B:HOH725 5.0 37.8 1.0
C B:ILE390 5.0 30.2 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
Page generated: Fri Dec 17 10:56:03 2021

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