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Zinc in PDB 6a8z: Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans

Protein crystallography data

The structure of Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans, PDB code: 6a8z was solved by R.Agrawal, A.Kumar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.25 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.371, 57.583, 69.579, 89.74, 82.30, 67.53
R / Rfree (%) 17.5 / 22

Other elements in 6a8z:

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

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of M1 Zinc Metallopeptidase From Deinococcus Radiodurans (pdb code 6a8z). 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 From Deinococcus Radiodurans, PDB code: 6a8z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6a8z

Go back to Zinc Binding Sites List in 6a8z
Zinc binding site 1 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase 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 From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:16.6
occ:1.00
OXT A:TYR502 1.9 21.7 1.0
OE2 A:GLU345 1.9 19.0 1.0
NE2 A:HIS322 2.0 19.0 1.0
NE2 A:HIS326 2.1 18.0 1.0
C A:TYR502 2.7 23.3 1.0
CD A:GLU345 2.8 18.0 1.0
CD2 A:HIS322 2.9 16.4 1.0
O A:TYR502 2.9 25.5 1.0
CD2 A:HIS326 3.0 14.1 1.0
OE1 A:GLU345 3.0 13.9 1.0
CE1 A:HIS322 3.1 17.1 1.0
CE1 A:HIS326 3.2 15.0 1.0
CE2 A:TYR396 3.8 16.9 1.0
CA A:TYR502 3.9 22.2 1.0
N A:TYR502 4.0 16.9 1.0
CG A:HIS322 4.1 16.9 1.0
OH A:TYR396 4.1 21.6 1.0
ND1 A:HIS322 4.2 16.3 1.0
CG A:HIS326 4.2 15.7 1.0
CG A:GLU345 4.2 18.3 1.0
CB A:ALA348 4.2 15.3 1.0
ND1 A:HIS326 4.2 12.7 1.0
CZ A:TYR396 4.3 20.6 1.0
CA A:GLU345 4.4 16.1 1.0
CB A:GLU345 4.5 18.6 1.0
OE1 A:GLU303 4.5 21.8 1.0
CD2 A:TYR396 4.7 16.1 1.0
OE1 A:GLU323 4.8 21.2 1.0
OE2 A:GLU323 4.8 26.9 1.0
CB A:TYR502 4.9 24.8 1.0
OE2 A:GLU303 4.9 20.1 1.0
O A:HOH632 4.9 19.1 1.0

Zinc binding site 2 out of 2 in 6a8z

Go back to Zinc Binding Sites List in 6a8z
Zinc binding site 2 out of 2 in the Crystal Structure of M1 Zinc Metallopeptidase 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 From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:19.5
occ:1.00
OXT B:TYR502 1.8 25.1 1.0
OE2 B:GLU345 1.9 18.2 1.0
NE2 B:HIS326 2.1 19.8 1.0
NE2 B:HIS322 2.1 22.1 1.0
C B:TYR502 2.6 24.9 1.0
CD B:GLU345 2.7 20.6 1.0
O B:TYR502 2.9 29.5 1.0
OE1 B:GLU345 2.9 16.7 1.0
CD2 B:HIS326 2.9 16.1 1.0
CD2 B:HIS322 3.0 20.9 1.0
CE1 B:HIS322 3.2 23.0 1.0
CE1 B:HIS326 3.2 17.1 1.0
CE2 B:TYR396 3.9 21.5 1.0
CA B:TYR502 3.9 23.8 1.0
N B:TYR502 4.0 21.0 1.0
CG B:GLU345 4.1 21.4 1.0
CG B:HIS326 4.1 16.6 1.0
CG B:HIS322 4.2 23.5 1.0
ND1 B:HIS322 4.2 23.4 1.0
ND1 B:HIS326 4.2 15.6 1.0
CB B:ALA348 4.3 21.1 1.0
OH B:TYR396 4.3 26.0 1.0
OE1 B:GLU303 4.4 24.2 1.0
CA B:GLU345 4.5 20.2 1.0
CB B:GLU345 4.5 22.1 1.0
CZ B:TYR396 4.5 23.0 1.0
CD2 B:TYR396 4.7 20.8 1.0
OE1 B:GLU323 4.8 27.8 1.0
O B:HOH606 4.9 17.2 1.0
OE2 B:GLU303 4.9 25.7 1.0
CB B:TYR502 4.9 22.3 1.0
OE2 B:GLU323 5.0 41.4 1.0
CD B:GLU303 5.0 24.0 1.0

Reference:

R.Agrawal, V.D.Goyal, A.Kumar, N.K.Gaur, S.N.Jamdar, A.Kumar, R.D.Makde. Two-Domain Aminopeptidase of M1 Family: Structural Features For Substrate Binding and Gating in Absence of C-Terminal Domain. J.Struct.Biol. V. 208 51 2019.
ISSN: ESSN 1095-8657
PubMed: 31351924
DOI: 10.1016/J.JSB.2019.07.010
Page generated: Wed Dec 16 11:29:14 2020

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