Sodium in PDB 6a8z: Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans

The structure of Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans, PDB code: 6a8z was solved by R.Agrawal, A.Kumar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.25 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.371, 57.583, 69.579, 89.74, 82.30, 67.53
R / Rfree (%)	17.5 / 22

The structure of Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans (pdb code 6a8z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans, PDB code: 6a8z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:7.6 occ:1.00 O A:VAL53 2.2 17.5 1.0 OD1 A:ASP181 2.3 16.2 1.0 OD1 A:ASP52 2.3 24.6 1.0 O A:HOH775 2.3 15.7 1.0 O A:PRO182 2.4 17.7 1.0 O A:HOH783 2.4 20.4 1.0 C A:VAL53 3.4 17.7 1.0 CG A:ASP181 3.5 17.1 1.0 CG A:ASP52 3.5 24.4 1.0 C A:PRO182 3.6 18.5 1.0 N A:VAL53 3.9 18.0 1.0 C A:ASP181 4.0 16.8 1.0 O A:HOH660 4.1 21.4 1.0 N A:PRO182 4.1 18.4 1.0 C A:ASP52 4.1 20.4 1.0 OD2 A:ASP181 4.2 18.2 1.0 O A:ASP181 4.2 15.2 1.0 CA A:ASP181 4.2 17.7 1.0 N A:GLN54 4.2 19.9 1.0 CA A:VAL53 4.3 17.8 1.0 CA A:GLN54 4.3 20.2 1.0 CA A:ASP52 4.3 20.5 1.0 OD2 A:ASP52 4.3 22.9 1.0 CA A:PRO182 4.5 16.1 1.0 CB A:ASP181 4.5 17.2 1.0 CB A:ASP52 4.5 22.6 1.0 CD A:PRO182 4.5 18.8 1.0 N A:ALA183 4.5 19.3 1.0 CA A:ALA183 4.6 18.1 1.0 CB A:ALA183 4.6 15.4 1.0 O A:ASP52 4.7 19.2 1.0 O A:HOH767 4.7 20.7 1.0 CG A:GLN54 4.8 19.9 1.0 CG A:PRO182 5.0 16.6 1.0 CB A:VAL53 5.0 16.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:8.8 occ:1.00 OD1 B:ASP181 2.2 20.8 1.0 O B:VAL53 2.2 21.8 1.0 O B:HOH720 2.3 21.5 1.0 OD1 B:ASP52 2.3 26.2 1.0 O B:PRO182 2.4 16.3 1.0 O B:HOH723 2.4 19.2 1.0 CG B:ASP181 3.4 18.8 1.0 C B:VAL53 3.4 23.1 1.0 CG B:ASP52 3.6 24.3 1.0 C B:PRO182 3.6 18.8 1.0 C B:ASP181 4.0 16.1 1.0 N B:VAL53 4.0 22.6 1.0 OD2 B:ASP181 4.1 20.4 1.0 N B:PRO182 4.1 19.5 1.0 O B:HOH670 4.1 22.0 1.0 C B:ASP52 4.2 21.6 1.0 CA B:ASP181 4.2 17.1 1.0 N B:GLN54 4.3 24.0 1.0 O B:ASP181 4.3 16.4 1.0 CA B:GLN54 4.3 22.2 1.0 CA B:VAL53 4.3 19.9 1.0 CA B:ASP52 4.3 20.9 1.0 OD2 B:ASP52 4.4 23.7 1.0 CB B:ASP181 4.4 16.8 1.0 CD B:PRO182 4.4 20.0 1.0 CA B:PRO182 4.5 17.7 1.0 N B:ALA183 4.5 18.4 1.0 CB B:ASP52 4.5 20.5 1.0 CA B:ALA183 4.6 19.4 1.0 CB B:ALA183 4.6 19.3 1.0 O B:HOH697 4.7 18.5 1.0 O B:ASP52 4.7 22.5 1.0 CG B:GLN54 4.8 23.2 1.0 CG B:PRO182 4.9 22.1 1.0 CB B:VAL53 5.0 17.4 1.0

R.Agrawal, V.D.Goyal, A.Kumar, N.K.Gaur, S.N.Jamdar, A.Kumar, R.D.Makde. Two-Domain Aminopeptidase of M1 Family: Structural Features For Substrate Binding and Gating in Absence of C-Terminal Domain. J.Struct.Biol. V. 208 51 2019.
ISSN: ESSN 1095-8657
PubMed: 31351924
DOI: 10.1016/J.JSB.2019.07.010