Zinc 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:

Sodium

(Na)

2 atoms

The binding sites of Zinc 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 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-Methionine Amino Acid, PDB code: 6kp1:
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-Methionine 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-Methionine Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.2 occ:1.00 OE2 A:GLU345 2.0 16.9 1.0 NE2 A:HIS322 2.1 18.6 1.0 OXT A:MET503 2.2 40.0 1.0 NE2 A:HIS326 2.2 17.9 1.0 N A:MET503 2.2 34.7 1.0 CD A:GLU345 2.9 17.2 1.0 C A:MET503 2.9 35.0 1.0 CD2 A:HIS326 2.9 16.2 1.0 CD2 A:HIS322 2.9 15.1 1.0 OE1 A:GLU345 3.0 16.6 1.0 CA A:MET503 3.1 28.8 1.0 CE1 A:HIS322 3.3 17.9 1.0 CE1 A:HIS326 3.4 14.0 1.0 CE2 A:TYR396 4.0 17.8 1.0 O A:MET503 4.0 39.9 1.0 O A:HOH629 4.0 17.1 1.0 OH A:TYR396 4.1 22.8 1.0 CG A:HIS326 4.1 19.6 1.0 CG A:HIS322 4.1 17.3 1.0 CB A:MET503 4.2 34.9 1.0 OE1 A:GLU303 4.3 16.0 1.0 CG A:GLU345 4.3 12.9 1.0 ND1 A:HIS322 4.3 17.9 1.0 ND1 A:HIS326 4.3 13.0 1.0 CZ A:TYR396 4.4 19.3 1.0 CB A:ALA348 4.4 14.8 1.0 CA A:GLU345 4.6 14.8 1.0 CB A:GLU345 4.7 20.6 1.0 OE2 A:GLU303 4.8 21.7 1.0 CD A:GLU303 4.9 18.1 1.0 CD2 A:TYR396 4.9 17.9 1.0

Zinc 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 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-Methionine Amino Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:19.9 occ:1.00 OE2 B:GLU345 1.9 15.1 1.0 OXT B:MET503 2.0 36.0 1.0 NE2 B:HIS322 2.1 17.8 1.0 NE2 B:HIS326 2.2 17.5 1.0 CD B:GLU345 2.8 16.4 1.0 CD2 B:HIS326 2.9 15.8 1.0 C B:MET503 2.9 34.6 1.0 OE1 B:GLU345 3.0 16.9 1.0 CD2 B:HIS322 3.0 13.1 1.0 CE1 B:HIS322 3.2 17.0 1.0 CE1 B:HIS326 3.4 15.3 1.0 O B:MET503 3.4 33.4 1.0 N B:MET503 4.0 28.7 1.0 CE2 B:TYR396 4.0 21.1 1.0 CA B:MET503 4.0 34.9 1.0 CG B:HIS326 4.1 15.8 1.0 CG B:HIS322 4.2 18.5 1.0 O B:HOH630 4.2 19.5 1.0 OH B:TYR396 4.2 23.8 1.0 CG B:GLU345 4.2 13.4 1.0 ND1 B:HIS322 4.3 25.7 1.0 OE1 B:GLU303 4.3 21.4 1.0 ND1 B:HIS326 4.3 16.5 1.0 O B:HOH611 4.4 19.0 1.0 CB B:ALA348 4.4 14.2 1.0 CZ B:TYR396 4.5 25.0 1.0 CA B:GLU345 4.5 15.0 1.0 OE2 B:GLU303 4.6 20.9 1.0 CB B:GLU345 4.6 19.7 1.0 CD B:GLU303 4.8 18.2 1.0 CD2 B:TYR396 4.9 21.7 1.0 CB B:MET503 4.9 34.8 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.