Zinc in PDB 4ar8: Crystal Structure of the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution.

The structure of Crystal Structure of the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution., PDB code: 4ar8 was solved by U.Eckhard, H.Brandstetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.75 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.420, 102.080, 102.480, 90.00, 90.00, 90.00
R / Rfree (%)	21.765 / 26.793

The structure of Crystal Structure of the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution. also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution. (pdb code 4ar8). 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 the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution., PDB code: 4ar8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution.


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 the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1731 b:34.0 occ:1.00 OE1 A:GLU499 2.0 28.2 1.0 O2 C:IP80 2.0 42.5 1.0 NE2 A:HIS469 2.0 29.5 1.0 NE2 A:HIS465 2.0 32.4 1.0 O C:IP80 2.2 34.5 1.0 P1 C:IP80 2.8 40.5 1.0 CE1 A:HIS465 3.0 28.2 1.0 CD A:GLU499 3.0 27.4 1.0 CE1 A:HIS469 3.0 25.5 1.0 CD2 A:HIS469 3.0 24.3 1.0 CD2 A:HIS465 3.1 27.5 1.0 OE2 A:GLU499 3.3 30.8 1.0 N C:GLY1 3.9 43.4 1.0 CE2 A:TYR548 4.0 31.2 1.0 C C:GLY1 4.1 44.6 1.0 O1 C:IP80 4.1 43.7 1.0 ND1 A:HIS465 4.1 27.0 1.0 ND1 A:HIS469 4.1 24.1 1.0 CG A:HIS469 4.2 23.1 1.0 CG A:HIS465 4.2 27.5 1.0 OH A:TYR548 4.2 35.0 1.0 OE2 A:GLU466 4.3 34.6 1.0 CG A:GLU499 4.4 25.4 1.0 C1 C:IP80 4.5 46.0 1.0 CB A:ALA502 4.6 21.0 1.0 CZ A:TYR548 4.6 31.2 1.0 O A:HOH2051 4.6 32.5 1.0 CB A:GLU499 4.8 24.4 1.0 CA A:GLU499 4.8 23.3 1.0 CD A:GLU466 4.9 30.1 1.0 O A:HOH2062 5.0 53.2 1.0 CD2 A:TYR548 5.0 31.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution.


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 the Peptidase Domain of Collagenase T From Clostridium Tetani Complexed with the Peptidic Inhibitor Isoamyl- Phosphonyl-Gly-Pro-Ala at 2.05 Angstrom Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1731 b:38.1 occ:1.00 OE1 B:GLU499 2.0 34.2 1.0 NE2 B:HIS469 2.0 33.7 1.0 O2 D:IP80 2.0 54.7 1.0 NE2 B:HIS465 2.0 34.0 1.0 O D:IP80 2.2 58.4 1.0 P1 D:IP80 2.7 53.0 1.0 CE1 B:HIS465 3.0 28.9 1.0 CE1 B:HIS469 3.0 29.8 1.0 CD B:GLU499 3.0 32.0 1.0 CD2 B:HIS469 3.0 29.4 1.0 CD2 B:HIS465 3.1 29.8 1.0 OE2 B:GLU499 3.3 35.0 1.0 N D:GLY1 3.9 54.5 1.0 O1 D:IP80 3.9 55.5 1.0 C D:GLY1 3.9 56.0 1.0 C2 D:IP80 4.0 52.2 1.0 CE2 B:TYR548 4.1 32.3 1.0 ND1 B:HIS469 4.1 28.5 1.0 ND1 B:HIS465 4.1 25.3 1.0 CG B:HIS469 4.2 27.4 1.0 CG B:HIS465 4.2 27.5 1.0 OH B:TYR548 4.3 40.6 1.0 CG B:GLU499 4.4 31.4 1.0 OE2 B:GLU466 4.4 37.4 1.0 C1 D:IP80 4.5 52.1 1.0 CB B:ALA502 4.6 17.8 1.0 CZ B:TYR548 4.7 34.3 1.0 CA B:GLU499 4.7 28.3 1.0 CB B:GLU499 4.8 29.6 1.0 CD B:GLU466 5.0 32.0 1.0

U.Eckhard, E.Schonauer, H.Brandstetter. Structural Basis For Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T. J.Biol.Chem. V. 288 20184 2013.
ISSN: ISSN 0021-9258
PubMed: 23703618
DOI: 10.1074/JBC.M112.448548