Zinc in PDB 7xeb: Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp

All present enzymatic activity of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp:
3.4.24.3;

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp, PDB code: 7xeb 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)	45.41 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.972, 75.549, 130.551, 90, 103.06, 90
R / Rfree (%)	20.6 / 25.5

The structure of Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Zinc atom in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp (pdb code 7xeb). 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 Complexed with Gly- Pro-Hyp, PDB code: 7xeb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:51.6 occ:1.00 OE1 A:GLU520 2.1 41.7 1.0 NE2 A:HIS496 2.3 34.9 1.0 NE2 A:HIS492 2.3 35.4 1.0 O C:HYP3 2.5 43.6 0.7 OXT C:HYP3 2.8 40.1 0.7 CD A:GLU520 2.9 31.0 1.0 C C:HYP3 2.9 43.3 0.7 OE2 A:GLU520 3.0 41.4 1.0 CD2 A:HIS496 3.0 36.4 1.0 CD2 A:HIS492 3.1 33.0 1.0 CE1 A:HIS492 3.3 37.7 1.0 CE1 A:HIS496 3.3 38.3 1.0 CE1 A:TYR564 3.9 34.1 1.0 CA D:GLY1 3.9 41.8 1.0 CG A:HIS496 4.2 41.0 1.0 CG A:HIS492 4.3 36.1 1.0 CA C:HYP3 4.3 45.1 0.7 CG A:GLU520 4.3 33.2 1.0 ND1 A:HIS496 4.3 40.5 1.0 ND1 A:HIS492 4.3 40.2 1.0 OH A:TYR564 4.3 41.0 1.0 N D:GLY1 4.4 45.7 1.0 N C:HYP3 4.5 45.6 0.7 C C:PRO2 4.5 52.7 1.0 OE2 A:GLU493 4.5 39.3 1.0 CB C:PRO2 4.5 42.9 1.0 OE1 A:GLU493 4.6 43.4 1.0 CZ A:TYR564 4.6 33.9 1.0 O C:PRO2 4.6 46.9 1.0 CB A:ALA523 4.8 32.6 1.0 CA A:GLU520 4.8 36.9 1.0 CB A:GLU520 4.9 28.6 1.0 CD1 A:TYR564 4.9 36.0 1.0 CD A:GLU493 4.9 42.6 1.0

Zinc binding site 2 out of 2 in the Collagenase From Grimontia (Vibrio) Hollisae 1706B Complexed with Gly- Pro-Hyp


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 Complexed with Gly- Pro-Hyp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:69.8 occ:1.00 OE1 B:GLU520 2.0 56.4 1.0 NE2 B:HIS496 2.3 56.5 1.0 NE2 B:HIS492 2.3 54.3 1.0 O G:HYP3 2.5 56.8 0.7 CD B:GLU520 2.8 57.1 1.0 OE2 B:GLU520 2.8 62.1 1.0 C G:HYP3 3.1 56.1 0.7 CD2 B:HIS496 3.1 52.5 1.0 OXT G:HYP3 3.2 55.7 0.7 CE1 B:HIS492 3.2 54.4 1.0 CD2 B:HIS492 3.3 50.5 1.0 CE1 B:HIS496 3.4 51.8 1.0 CA H:GLY1 3.7 53.0 1.0 CE1 B:TYR564 3.9 50.1 1.0 N H:GLY1 4.0 57.4 1.0 CG B:GLU520 4.2 54.7 1.0 CG B:HIS496 4.3 51.4 1.0 ND1 B:HIS492 4.3 52.4 1.0 CG B:HIS492 4.4 50.4 1.0 CA G:HYP3 4.4 61.5 0.7 ND1 B:HIS496 4.4 46.0 1.0 N G:HYP3 4.4 59.2 0.7 CB G:PRO2 4.5 62.8 1.0 OH B:TYR564 4.5 58.0 1.0 C G:PRO2 4.5 63.5 1.0 OE1 B:GLU493 4.6 57.4 1.0 OE2 B:GLU493 4.6 58.9 1.0 CZ B:TYR564 4.7 57.4 1.0 CD1 B:TYR564 4.8 51.8 1.0 CB B:ALA523 4.8 37.4 1.0 CA B:GLU520 4.8 47.8 1.0 O G:PRO2 4.8 54.8 1.0 CB B:GLU520 4.8 47.1 1.0 CD B:GLU493 4.9 56.9 1.0

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