Sodium in PDB 6kp0: Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine

The structure of Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine, PDB code: 6kp0 was solved by R.Agrawal, A.Kumar, A.Kumar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.39 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.632, 57.204, 67.049, 89.86, 85.08, 68.57
R / Rfree (%)	23.1 / 26.4

The structure of Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine (pdb code 6kp0). 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 Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine, PDB code: 6kp0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine


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 Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:13.7 occ:1.00 O A:PRO182 2.3 14.2 1.0 O A:VAL53 2.4 20.2 1.0 O A:HOH656 2.4 13.8 1.0 OD1 A:ASP181 2.4 13.8 1.0 OD1 A:ASP52 2.5 24.8 1.0 C A:VAL53 3.4 19.9 1.0 C A:PRO182 3.5 15.6 1.0 CG A:ASP181 3.6 13.0 1.0 CG A:ASP52 3.7 24.5 1.0 C A:ASP181 3.9 14.3 1.0 N A:VAL53 3.9 19.1 1.0 N A:PRO182 4.1 14.8 1.0 C A:ASP52 4.1 20.1 1.0 O A:ASP181 4.1 12.7 1.0 CA A:ASP181 4.2 14.2 1.0 CA A:VAL53 4.3 18.2 1.0 N A:GLN54 4.3 21.8 1.0 OD2 A:ASP181 4.3 13.0 1.0 CA A:ASP52 4.3 19.4 1.0 CA A:GLN54 4.4 24.0 1.0 O A:HOH637 4.4 27.4 1.0 CA A:PRO182 4.4 14.8 1.0 N A:ALA183 4.4 17.5 1.0 CA A:ALA183 4.5 17.2 1.0 CB A:ALA183 4.5 16.4 1.0 OD2 A:ASP52 4.5 26.1 1.0 CB A:ASP181 4.5 14.4 1.0 CD A:PRO182 4.5 15.7 1.0 O A:ASP52 4.6 19.1 1.0 CB A:ASP52 4.6 21.7 1.0 CG A:PRO182 4.9 14.7 1.0 CB A:VAL53 5.0 17.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine


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 Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Arginine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:13.2 occ:1.00 O B:PRO182 2.3 16.5 1.0 OD1 B:ASP181 2.3 14.9 1.0 O B:VAL53 2.4 23.1 1.0 OD1 B:ASP52 2.4 21.7 1.0 C B:VAL53 3.4 22.1 1.0 CG B:ASP181 3.5 13.7 1.0 C B:PRO182 3.5 18.0 1.0 CG B:ASP52 3.7 23.6 1.0 C B:ASP181 3.9 17.1 1.0 N B:VAL53 3.9 20.7 1.0 N B:PRO182 4.1 18.4 1.0 O B:ASP181 4.1 17.9 1.0 C B:ASP52 4.1 21.9 1.0 CA B:ASP181 4.2 17.2 1.0 OD2 B:ASP181 4.2 13.9 1.0 CA B:VAL53 4.3 21.5 1.0 N B:GLN54 4.3 22.3 1.0 CA B:ASP52 4.4 21.6 1.0 CA B:GLN54 4.4 24.5 1.0 CA B:PRO182 4.4 18.0 1.0 CB B:ASP181 4.5 18.4 1.0 N B:ALA183 4.5 18.1 1.0 OD2 B:ASP52 4.5 23.8 1.0 CA B:ALA183 4.5 18.5 1.0 CB B:ALA183 4.5 18.4 1.0 CD B:PRO182 4.5 17.6 1.0 O B:ASP52 4.6 22.7 1.0 CB B:ASP52 4.6 22.4 1.0 CG B:PRO182 4.9 15.5 1.0 NH2 B:ARG81 4.9 31.0 1.0 CB B:VAL53 5.0 20.4 1.0

R.Agrawal, V.D.Goyal, R.Singh, A.Kumar, S.N.Jamdar, A.Kumar, R.D.Makde. Structural Basis For the Unusual Substrate Specificity of Unique Two-Domain M1 Metallopeptidase. Int.J.Biol.Macromol. 2020.
ISSN: ISSN 0141-8130
PubMed: 31923495
DOI: 10.1016/J.IJBIOMAC.2019.12.239