Sodium in PDB 6kp1: Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Methionine Amino Acid

The structure of Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Methionine Amino Acid, PDB code: 6kp1 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)	21.45 / 2.19
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.806, 57.496, 69.444, 89.92, 82.48, 67.83
R / Rfree (%)	21.8 / 27

The structure of Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Methionine 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 E323A Mutant Bound to L-Methionine Amino Acid (pdb code 6kp1). 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-Methionine Amino Acid, PDB code: 6kp1:
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-Methionine 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 E323A Mutant Bound to L-Methionine Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:7.3 occ:1.00 OD1 A:ASP181 2.3 18.6 1.0 O A:VAL53 2.3 18.6 1.0 OD1 A:ASP52 2.3 23.8 1.0 O A:PRO182 2.4 14.7 1.0 O A:HOH751 2.4 18.0 1.0 O A:HOH768 2.5 19.9 1.0 C A:VAL53 3.5 14.9 1.0 CG A:ASP181 3.5 14.7 1.0 C A:PRO182 3.5 16.3 1.0 CG A:ASP52 3.6 21.8 1.0 C A:ASP181 3.9 15.3 1.0 N A:VAL53 3.9 16.5 1.0 N A:PRO182 4.0 16.8 1.0 CA A:ASP181 4.1 16.5 1.0 C A:ASP52 4.2 18.1 1.0 CA A:VAL53 4.3 15.1 1.0 O A:ASP181 4.3 13.6 1.0 OD2 A:ASP181 4.3 17.4 1.0 CA A:ASP52 4.3 21.2 1.0 O A:HOH748 4.3 18.6 1.0 OD2 A:ASP52 4.4 27.3 1.0 N A:GLN54 4.4 15.9 1.0 CA A:PRO182 4.4 15.2 1.0 CB A:ASP181 4.4 16.6 1.0 CD A:PRO182 4.5 16.7 1.0 CA A:GLN54 4.5 18.6 1.0 N A:ALA183 4.5 15.4 1.0 CB A:ASP52 4.5 22.2 1.0 CA A:ALA183 4.6 15.9 1.0 CB A:ALA183 4.6 16.7 1.0 O A:HOH750 4.6 16.4 1.0 O A:ASP52 4.8 13.2 1.0 CG A:PRO182 4.9 19.0 1.0 CB A:VAL53 5.0 13.1 1.0 CG A:GLN54 5.0 17.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Methionine 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 E323A Mutant Bound to L-Methionine Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:9.9 occ:1.00 OD1 B:ASP52 2.3 27.4 1.0 O B:PRO182 2.3 16.5 1.0 O B:VAL53 2.3 23.1 1.0 OD1 B:ASP181 2.3 18.4 1.0 O B:HOH740 2.4 17.7 1.0 O B:HOH747 2.5 18.0 1.0 C B:VAL53 3.5 17.6 1.0 C B:PRO182 3.5 14.8 1.0 CG B:ASP52 3.5 23.8 1.0 CG B:ASP181 3.5 11.1 1.0 N B:VAL53 3.9 21.7 1.0 C B:ASP181 4.0 14.6 1.0 N B:PRO182 4.0 19.1 1.0 C B:ASP52 4.1 19.7 1.0 O B:HOH709 4.2 17.6 1.0 CA B:ASP181 4.2 14.7 1.0 OD2 B:ASP52 4.3 28.5 1.0 CA B:VAL53 4.3 13.1 1.0 OD2 B:ASP181 4.3 17.1 1.0 CA B:ASP52 4.3 19.8 1.0 N B:GLN54 4.4 18.7 1.0 O B:ASP181 4.4 14.2 1.0 CA B:PRO182 4.4 13.0 1.0 CA B:GLN54 4.4 22.0 1.0 CD B:PRO182 4.5 16.9 1.0 O B:HOH706 4.5 10.1 1.0 N B:ALA183 4.5 14.0 1.0 CB B:ASP181 4.5 14.9 1.0 CB B:ASP52 4.5 21.4 1.0 CA B:ALA183 4.5 14.3 1.0 CB B:ALA183 4.6 16.6 1.0 O B:HOH769 4.7 22.6 1.0 O B:ASP52 4.7 18.0 1.0 CG B:PRO182 4.9 21.8 1.0

R.Agrawal, V.D.Goyal, A.Kumar, A.Kumar, R.D.Makde. Structural Basis For the Unusual Substrate Specificity of Unique Two-Domain M1 Metallopeptidase To Be Published.