Sodium in PDB 6koz: Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323 Mutant Bound to L-Leucine Amino Acid

The structure of Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323 Mutant Bound to L-Leucine Amino Acid, PDB code: 6koz 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)	26.55 / 2.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.208, 57.420, 69.006, 89.97, 82.76, 67.82
R / Rfree (%)	21.8 / 27.2

The structure of Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323 Mutant Bound to L-Leucine Amino Acid 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 E323 Mutant Bound to L-Leucine Amino Acid (pdb code 6koz). 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 E323 Mutant Bound to L-Leucine Amino Acid, PDB code: 6koz:
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 E323 Mutant Bound to L-Leucine Amino Acid


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 E323 Mutant Bound to L-Leucine Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:18.4 occ:1.00 OD1 B:ASP52 2.3 27.0 1.0 OD1 B:ASP181 2.3 25.1 1.0 O B:PRO182 2.3 20.5 1.0 O B:VAL53 2.4 27.9 1.0 O B:HOH736 2.4 23.6 1.0 O B:HOH741 2.5 22.0 1.0 C B:VAL53 3.4 24.3 1.0 CG B:ASP181 3.5 22.5 1.0 C B:PRO182 3.5 18.9 1.0 CG B:ASP52 3.6 27.4 1.0 N B:VAL53 3.8 26.1 1.0 C B:ASP181 3.9 21.3 1.0 C B:ASP52 4.0 24.3 1.0 N B:PRO182 4.1 21.1 1.0 O B:HOH708 4.2 24.9 1.0 CA B:ASP52 4.2 24.5 1.0 CA B:VAL53 4.2 22.9 1.0 CA B:ASP181 4.2 19.9 1.0 O B:ASP181 4.2 19.9 1.0 OD2 B:ASP181 4.3 24.2 1.0 N B:GLN54 4.4 26.4 1.0 OD2 B:ASP52 4.4 33.1 1.0 O B:HOH726 4.4 18.4 1.0 CA B:PRO182 4.4 20.1 1.0 CB B:ASP52 4.5 24.4 1.0 N B:ALA183 4.5 19.4 1.0 CB B:ASP181 4.5 24.9 1.0 CA B:GLN54 4.5 26.6 1.0 CD B:PRO182 4.5 20.4 1.0 CA B:ALA183 4.5 21.5 1.0 O B:HOH756 4.6 22.5 1.0 CB B:ALA183 4.6 23.1 1.0 O B:ASP52 4.6 24.0 1.0 CG B:PRO182 4.9 21.7 1.0 CB B:VAL53 4.9 22.6 1.0 CG B:GLN54 5.0 28.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323 Mutant Bound to L-Leucine Amino Acid


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 E323 Mutant Bound to L-Leucine Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:10.4 occ:1.00 OD1 A:ASP52 2.3 26.1 1.0 O A:VAL53 2.3 20.1 1.0 O A:PRO182 2.4 16.0 1.0 O A:HOH788 2.4 19.9 1.0 OD1 A:ASP181 2.4 20.7 1.0 O A:HOH787 2.4 22.3 1.0 C A:VAL53 3.4 21.1 1.0 CG A:ASP52 3.5 26.1 1.0 C A:PRO182 3.6 18.9 1.0 CG A:ASP181 3.6 20.2 1.0 N A:VAL53 3.9 20.8 1.0 C A:ASP181 4.0 17.2 1.0 C A:ASP52 4.1 21.6 1.0 N A:PRO182 4.1 20.0 1.0 O A:HOH758 4.2 18.6 1.0 CA A:VAL53 4.2 17.5 1.0 N A:GLN54 4.3 24.5 1.0 CA A:ASP52 4.3 23.4 1.0 OD2 A:ASP52 4.3 28.3 1.0 CA A:ASP181 4.3 18.0 1.0 O A:ASP181 4.4 15.5 1.0 CA A:GLN54 4.4 23.7 1.0 OD2 A:ASP181 4.4 21.5 1.0 CA A:PRO182 4.5 18.4 1.0 CB A:ASP52 4.5 23.7 1.0 N A:ALA183 4.5 20.8 1.0 CA A:ALA183 4.5 20.4 1.0 CD A:PRO182 4.6 18.4 1.0 CB A:ASP181 4.6 21.5 1.0 CB A:ALA183 4.6 21.2 1.0 O A:ASP52 4.6 21.5 1.0 O A:HOH709 4.7 22.2 1.0 CG A:PRO182 4.9 18.6 1.0 CG A:GLN54 4.9 24.5 1.0 CB A:VAL53 5.0 18.7 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