Zinc in PDB 7wss: Collagenase From Grimontia (Vibrio) Hollisae 1706B

All present enzymatic activity of Collagenase From Grimontia (Vibrio) Hollisae 1706B:
3.4.24.3;

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B, PDB code: 7wss was solved by T.Ikeuchi, M.Yasumoto, T.Takita, K.Mizutani, B.Mikami, K.Tanaka, S.Hattori, K.Yasukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.48 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.939, 75.12, 135.148, 90, 128.18, 90
R / Rfree (%)	18.6 / 22.7

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Zinc atom in the Collagenase From Grimontia (Vibrio) Hollisae 1706B (pdb code 7wss). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Collagenase From Grimontia (Vibrio) Hollisae 1706B, PDB code: 7wss:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:58.6 occ:1.00 OE1 A:GLU520 2.1 38.3 1.0 NE2 A:HIS496 2.3 43.7 1.0 NE2 A:HIS492 2.3 39.2 1.0 O A:HOH877 2.6 44.5 1.0 CD A:GLU520 2.8 43.1 1.0 OE2 A:GLU520 2.9 38.6 1.0 CD2 A:HIS492 3.1 39.4 1.0 CD2 A:HIS496 3.2 37.4 1.0 CE1 A:HIS496 3.3 39.1 1.0 CE1 A:HIS492 3.4 37.6 1.0 CE1 A:TYR564 3.9 46.0 1.0 OH A:TYR564 4.1 61.3 1.0 CG A:GLU520 4.3 33.9 1.0 CG A:HIS492 4.3 42.4 1.0 ND1 A:HIS496 4.4 45.8 1.0 CG A:HIS496 4.4 42.1 1.0 ND1 A:HIS492 4.4 42.8 1.0 C6 A:PGE706 4.5 61.5 1.0 OE2 A:GLU493 4.5 53.2 1.0 CZ A:TYR564 4.5 56.9 1.0 OE1 A:GLU493 4.8 45.5 1.0 O4 A:PGE706 4.9 60.2 1.0 CB A:GLU520 4.9 35.0 1.0 CA A:GLU520 4.9 42.0 1.0 CB A:ALA523 4.9 34.2 1.0 CD1 A:TYR564 4.9 47.3 1.0 CD A:GLU493 5.0 47.4 1.0

Zinc binding site 2 out of 2 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Collagenase From Grimontia (Vibrio) Hollisae 1706B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:51.2 occ:1.00 OE1 B:GLU520 2.1 40.5 1.0 NE2 B:HIS496 2.3 33.5 1.0 NE2 B:HIS492 2.3 42.6 1.0 O B:HOH988 2.6 54.4 1.0 CD B:GLU520 2.9 41.8 1.0 OE2 B:GLU520 3.1 44.2 1.0 CD2 B:HIS492 3.1 31.9 1.0 CD2 B:HIS496 3.2 35.5 1.0 CE1 B:HIS496 3.3 40.6 1.0 CE1 B:HIS492 3.4 41.8 1.0 CE1 B:TYR564 3.8 43.6 1.0 OH B:TYR564 3.8 57.9 1.0 CZ B:TYR564 4.3 48.6 1.0 O B:HOH874 4.3 45.9 1.0 CG B:HIS492 4.4 37.8 1.0 ND1 B:HIS496 4.4 35.5 1.0 CG B:GLU520 4.4 39.3 1.0 CG B:HIS496 4.4 33.1 1.0 ND1 B:HIS492 4.4 42.0 1.0 OE2 B:GLU493 4.6 45.2 1.0 O B:HOH998 4.7 49.6 1.0 CD1 B:TYR564 4.9 43.6 1.0 OE1 B:GLU493 4.9 34.5 1.0 CB B:GLU520 4.9 33.5 1.0 CA B:GLU520 5.0 40.1 1.0 C1 B:EDO712 5.0 49.2 0.5

T.Ikeuchi, M.Yasumoto, T.Takita, K.Tanaka, M.Kusubata, O.Hayashida, S.Hattori, K.Mizutani, B.Mikami, K.Yasukawa. Crystal Structure of Grimontia Hollisae Collagenase Provides Insights Into Its Novel Substrate Specificity Toward Collagen. J.Biol.Chem. V. 298 02109 2022.
ISSN: ESSN 1083-351X
PubMed: 35679897
DOI: 10.1016/J.JBC.2022.102109