Zinc in PDB 6iff: Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans

The structure of Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans, PDB code: 6iff was solved by R.Agrawal, A.Kumar, A.Kumar, N.K.Gaur, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.27 / 1.83
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.480, 57.658, 69.786, 89.66, 82.07, 67.54
R / Rfree (%)	18.3 / 21.5

The structure of Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans (pdb code 6iff). 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 M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans, PDB code: 6iff:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans


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 M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:12.8 occ:1.00 OXT A:TYR502 1.7 15.3 1.0 OE2 A:GLU345 1.9 10.9 1.0 NE2 A:HIS322 2.0 13.0 1.0 NE2 A:HIS326 2.0 12.6 1.0 C A:TYR502 2.6 16.8 1.0 CD A:GLU345 2.8 12.1 1.0 CD2 A:HIS322 2.8 13.3 1.0 CD2 A:HIS326 2.9 10.8 1.0 OE1 A:GLU345 3.0 12.2 1.0 O A:TYR502 3.0 15.6 1.0 CE1 A:HIS322 3.1 13.6 1.0 CE1 A:HIS326 3.1 11.5 1.0 H2 A:TYR502 3.3 21.2 1.0 H1 A:TYR502 3.6 21.2 1.0 CA A:TYR502 3.9 18.5 1.0 N A:TYR502 3.9 17.6 1.0 CE2 A:TYR396 3.9 13.3 1.0 CG A:HIS322 4.0 13.3 1.0 ND1 A:HIS322 4.1 13.4 1.0 CG A:HIS326 4.1 12.8 1.0 ND1 A:HIS326 4.2 10.7 1.0 CG A:GLU345 4.2 12.2 1.0 O A:HOH793 4.2 14.1 1.0 CB A:ALA348 4.3 12.0 1.0 OH A:TYR396 4.3 13.2 1.0 CA A:GLU345 4.4 10.9 1.0 HA A:TYR502 4.4 22.3 1.0 OE1 A:GLU303 4.5 16.2 1.0 CZ A:TYR396 4.5 14.3 1.0 CB A:GLU345 4.6 12.8 1.0 HB2 A:TYR502 4.8 25.7 1.0 H3 A:TYR502 4.8 21.2 1.0 CD2 A:TYR396 4.8 11.8 1.0 OE2 A:GLU303 4.8 16.5 1.0 O A:HOH622 4.9 13.6 1.0 CB A:TYR502 4.9 21.4 1.0 CD A:GLU303 4.9 15.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans


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 M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:16.3 occ:1.00 OXT B:TYR502 1.8 18.3 1.0 OE2 B:GLU345 1.9 15.1 1.0 NE2 B:HIS322 2.0 15.8 1.0 NE2 B:HIS326 2.1 14.9 1.0 C B:TYR502 2.6 19.5 1.0 CD B:GLU345 2.8 15.8 1.0 CD2 B:HIS322 2.9 15.7 1.0 O B:TYR502 2.9 19.3 1.0 CD2 B:HIS326 2.9 13.3 1.0 OE1 B:GLU345 3.0 15.5 1.0 CE1 B:HIS322 3.1 16.3 1.0 CE1 B:HIS326 3.1 13.3 1.0 H1 B:TYR502 3.7 25.0 1.0 CA B:TYR502 3.9 21.3 1.0 H2 B:TYR502 3.9 25.0 1.0 N B:TYR502 4.0 20.8 1.0 CE2 B:TYR396 4.0 16.5 1.0 O B:HOH744 4.1 13.6 1.0 CG B:HIS322 4.1 16.2 1.0 CG B:HIS326 4.1 13.2 1.0 ND1 B:HIS322 4.1 16.3 1.0 CG B:GLU345 4.1 15.6 1.0 ND1 B:HIS326 4.2 14.3 1.0 CB B:ALA348 4.3 15.2 1.0 CA B:GLU345 4.3 14.3 1.0 OH B:TYR396 4.4 18.8 1.0 HA B:TYR502 4.4 25.6 1.0 OE1 B:GLU303 4.4 16.9 1.0 CB B:GLU345 4.5 15.0 1.0 CZ B:TYR396 4.6 17.8 1.0 O B:HOH622 4.8 14.1 1.0 OE2 B:GLU303 4.8 15.7 1.0 HB2 B:TYR502 4.8 28.4 1.0 CD2 B:TYR396 4.8 16.4 1.0 H3 B:TYR502 4.9 25.0 1.0 CD B:GLU303 4.9 16.1 1.0 CB B:TYR502 4.9 23.7 1.0

R.Agrawal, A.Kumar, A.Kumar, R.D.Makde. Crystal Structure of Two Domain M1 Zinc Metallopeptidase E323A Mutant From Deinococcus Radiodurans To Be Published.