Sodium in PDB 6iff: Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans

The structure of Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans, PDB code: 6iff was solved by R.Agrawal, A.Kumar, A.Kumar, N.K.Gaur, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.27 / 1.83
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.480, 57.658, 69.786, 89.66, 82.07, 67.54
R / Rfree (%)	18.3 / 21.5

The structure of Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant 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 E323A Mutant From Deinococcus Radiodurans (pdb code 6iff). 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 E323A Mutant From Deinococcus Radiodurans, PDB code: 6iff:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant 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 E323A Mutant From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:11.3 occ:1.00 OD1 A:ASP52 2.3 16.3 1.0 O A:VAL53 2.4 12.3 1.0 O A:HOH817 2.4 11.5 1.0 O A:PRO182 2.4 12.5 1.0 OD1 A:ASP181 2.4 14.3 1.0 O A:HOH821 2.4 15.4 1.0 C A:VAL53 3.4 12.7 1.0 CG A:ASP181 3.6 13.6 1.0 CG A:ASP52 3.6 16.4 1.0 C A:PRO182 3.6 12.1 1.0 N A:VAL53 4.0 13.8 1.0 C A:ASP181 4.0 12.6 1.0 C A:ASP52 4.1 14.5 1.0 O A:HOH714 4.1 16.1 1.0 N A:PRO182 4.2 13.1 1.0 CA A:GLN54 4.2 15.2 1.0 N A:GLN54 4.2 13.5 1.0 O A:ASP181 4.3 12.3 1.0 OD2 A:ASP181 4.3 14.7 1.0 CA A:VAL53 4.3 12.8 1.0 CA A:ASP181 4.3 13.3 1.0 CA A:ASP52 4.3 14.5 1.0 OD2 A:ASP52 4.4 16.6 1.0 O A:HOH746 4.5 21.7 1.0 CA A:ALA183 4.5 12.4 1.0 N A:ALA183 4.5 12.1 1.0 CA A:PRO182 4.5 11.9 1.0 CB A:ASP52 4.5 15.6 1.0 CB A:ASP181 4.6 12.7 1.0 CB A:ALA183 4.6 11.7 1.0 CD A:PRO182 4.7 13.0 1.0 O A:ASP52 4.7 15.2 1.0 NH2 A:ARG81 4.7 37.9 1.0 CG A:GLN54 4.8 18.0 1.0 CG A:PRO182 5.0 11.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant 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 E323A Mutant From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:12.1 occ:1.00 OD1 B:ASP181 2.3 15.1 1.0 O B:VAL53 2.3 16.6 1.0 O B:HOH757 2.3 15.2 1.0 OD1 B:ASP52 2.3 16.8 1.0 O B:PRO182 2.4 12.2 1.0 O B:HOH756 2.4 17.2 1.0 C B:VAL53 3.4 15.3 1.0 CG B:ASP181 3.5 15.4 1.0 C B:PRO182 3.6 16.3 1.0 CG B:ASP52 3.6 16.8 1.0 N B:VAL53 4.0 15.8 1.0 C B:ASP181 4.0 14.4 1.0 C B:ASP52 4.1 16.9 1.0 N B:PRO182 4.1 15.2 1.0 OD2 B:ASP181 4.1 15.3 1.0 O B:HOH662 4.2 18.4 1.0 N B:GLN54 4.2 15.2 1.0 CA B:ASP181 4.2 14.8 1.0 O B:ASP181 4.2 15.4 1.0 CA B:GLN54 4.3 15.4 1.0 CA B:VAL53 4.3 14.4 1.0 CA B:ASP52 4.4 16.3 1.0 OD2 B:ASP52 4.4 16.2 1.0 CB B:ASP181 4.5 15.8 1.0 CA B:PRO182 4.5 15.7 1.0 N B:ALA183 4.5 15.1 1.0 CA B:ALA183 4.6 14.3 1.0 CB B:ASP52 4.6 16.1 1.0 O B:HOH700 4.6 18.0 1.0 CB B:ALA183 4.6 12.4 1.0 CD B:PRO182 4.6 15.3 1.0 O B:ASP52 4.6 17.9 1.0 CG B:GLN54 4.8 17.7 1.0 NH2 B:ARG81 4.9 40.4 1.0 CG B:PRO182 5.0 15.1 1.0 CB B:VAL53 5.0 13.7 1.0

R.Agrawal, A.Kumar, A.Kumar, R.D.Makde. Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans To Be Published.