Zinc 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:

Sodium

(Na)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:22.5 occ:1.00 OE2 B:GLU345 2.0 18.1 1.0 NE2 B:HIS326 2.1 21.6 1.0 NE2 B:HIS322 2.2 20.5 1.0 CD B:GLU345 2.8 24.9 1.0 CD2 B:HIS326 2.8 20.8 1.0 OE1 B:GLU345 2.9 21.2 1.0 OXT B:LEU502 2.9 29.1 1.0 CD2 B:HIS322 2.9 18.9 1.0 C B:LEU502 3.0 22.4 1.0 O B:LEU502 3.2 22.1 1.0 CE1 B:HIS322 3.3 19.5 1.0 CE1 B:HIS326 3.3 22.6 1.0 N B:LEU502 3.3 18.6 1.0 CA B:LEU502 3.8 22.3 1.0 O B:HOH681 3.9 18.0 1.0 CG B:HIS326 4.0 21.9 1.0 CE1 B:TYR396 4.1 22.3 1.0 CG B:HIS322 4.2 23.5 1.0 CG B:GLU345 4.2 20.7 1.0 ND1 B:HIS326 4.3 23.5 1.0 OE1 B:GLU303 4.3 19.2 1.0 ND1 B:HIS322 4.3 26.0 1.0 CB B:ALA348 4.3 22.4 1.0 OH B:TYR396 4.3 23.1 1.0 O B:HOH662 4.5 21.4 1.0 CA B:GLU345 4.6 24.2 1.0 CZ B:TYR396 4.6 23.2 1.0 CB B:GLU345 4.7 24.4 1.0 CB B:LEU502 4.9 25.7 1.0 CD B:GLU303 4.9 23.2 1.0 CD1 B:TYR396 4.9 22.8 1.0 OE2 B:GLU303 5.0 20.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:18.9 occ:1.00 OE2 A:GLU345 2.0 17.2 1.0 NE2 A:HIS322 2.1 20.2 1.0 NE2 A:HIS326 2.2 18.9 1.0 OXT A:LEU502 2.4 26.7 1.0 CD A:GLU345 2.8 20.4 1.0 CD2 A:HIS322 2.8 18.3 1.0 CD2 A:HIS326 2.9 18.2 1.0 OE1 A:GLU345 3.0 17.6 1.0 C A:LEU502 3.0 24.2 1.0 CE1 A:HIS322 3.3 19.4 1.0 CE1 A:HIS326 3.4 19.3 1.0 N A:LEU502 3.5 22.3 1.0 O A:LEU502 3.5 29.8 1.0 CA A:LEU502 3.8 25.2 1.0 O A:HOH664 4.0 17.0 1.0 CE2 A:TYR396 4.0 20.1 1.0 CG A:HIS322 4.1 20.9 1.0 CG A:HIS326 4.2 21.2 1.0 OE1 A:GLU303 4.2 17.4 1.0 ND1 A:HIS322 4.3 20.0 1.0 OH A:TYR396 4.3 22.7 1.0 CG A:GLU345 4.3 17.6 1.0 ND1 A:HIS326 4.4 18.5 1.0 CB A:ALA348 4.5 16.8 1.0 CZ A:TYR396 4.5 23.8 1.0 CA A:GLU345 4.6 19.9 1.0 O A:HOH726 4.7 22.2 1.0 CB A:GLU345 4.7 21.1 1.0 CD A:GLU303 4.8 20.9 1.0 OE2 A:GLU303 4.9 21.7 1.0 CD2 A:TYR396 4.9 18.8 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