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

The structure of Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Tryptophan Amino Acid, PDB code: 6koy 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)	41.91 / 2.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.833, 57.457, 69.492, 89.75, 82.64, 67.93
R / Rfree (%)	16.6 / 22.2

The binding sites of Zinc atom in the Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Tryptophan Amino Acid (pdb code 6koy). 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 E323A Mutant Bound to L-Tryptophan Amino Acid, PDB code: 6koy:
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 E323A Mutant Bound to L-Tryptophan 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 E323A Mutant Bound to L-Tryptophan Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:18.5 occ:1.00 OXT A:TRP501 2.0 16.8 1.0 OE1 A:GLU345 2.0 15.0 1.0 NE2 A:HIS326 2.1 20.1 1.0 NE2 A:HIS322 2.1 17.6 1.0 C A:TRP501 2.7 19.0 1.0 CD2 A:HIS326 2.9 11.9 1.0 CD2 A:HIS322 2.9 16.0 1.0 CD A:GLU345 2.9 16.4 1.0 O A:TRP501 3.1 14.5 1.0 CE1 A:HIS322 3.2 15.3 1.0 OE2 A:GLU345 3.2 18.9 1.0 CE1 A:HIS326 3.2 15.7 1.0 N A:TRP501 3.8 12.2 1.0 CA A:TRP501 3.9 13.8 1.0 CE2 A:TYR396 3.9 15.9 1.0 CG A:HIS326 4.1 18.5 1.0 CG A:HIS322 4.1 16.6 1.0 O A:HOH672 4.1 11.6 1.0 ND1 A:HIS322 4.2 14.4 1.0 ND1 A:HIS326 4.2 14.6 1.0 OH A:TYR396 4.2 17.4 1.0 OE1 A:GLU303 4.3 13.0 1.0 CG A:GLU345 4.3 14.9 1.0 CA A:GLU345 4.4 14.2 1.0 CB A:ALA348 4.4 10.6 1.0 CZ A:TYR396 4.5 18.8 1.0 CB A:GLU345 4.6 17.6 1.0 OE2 A:GLU303 4.8 16.6 1.0 CD2 A:TYR396 4.8 16.7 1.0 CD A:GLU303 4.8 19.6 1.0 CB A:TRP501 4.9 13.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant Bound to L-Tryptophan 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 E323A Mutant Bound to L-Tryptophan Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:21.4 occ:1.00 OE2 B:GLU345 1.9 14.3 1.0 OXT B:TRP501 2.0 14.5 1.0 NE2 B:HIS322 2.1 20.3 1.0 NE2 B:HIS326 2.2 17.3 1.0 C B:TRP501 2.7 16.4 1.0 CD B:GLU345 2.8 21.2 1.0 CD2 B:HIS322 2.9 11.5 1.0 CD2 B:HIS326 2.9 14.9 1.0 OE1 B:GLU345 3.0 18.3 1.0 O B:TRP501 3.1 20.6 1.0 CE1 B:HIS322 3.2 10.7 1.0 CE1 B:HIS326 3.4 17.3 1.0 N B:TRP501 3.9 17.6 1.0 CA B:TRP501 3.9 16.3 1.0 CE2 B:TYR396 4.0 16.1 1.0 CG B:HIS322 4.1 16.9 1.0 CG B:HIS326 4.1 17.8 1.0 ND1 B:HIS322 4.2 15.1 1.0 CG B:GLU345 4.2 14.9 1.0 O B:HOH690 4.3 9.4 1.0 CB B:ALA348 4.3 14.2 1.0 OE1 B:GLU303 4.3 13.8 1.0 ND1 B:HIS326 4.3 19.7 1.0 CA B:GLU345 4.4 12.4 1.0 OH B:TYR396 4.4 17.8 1.0 CZ B:TYR396 4.6 19.9 1.0 CB B:GLU345 4.6 17.8 1.0 OE2 B:GLU303 4.8 21.8 1.0 CD2 B:TYR396 4.8 14.0 1.0 CD B:GLU303 4.8 20.7 1.0 CB B:TRP501 4.9 17.7 1.0 O B:HOH615 5.0 17.1 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