Zinc in PDB 1qib: Crystal Structure of Gelatinase A Catalytic Domain

All present enzymatic activity of Crystal Structure of Gelatinase A Catalytic Domain:
3.4.24.24;

The structure of Crystal Structure of Gelatinase A Catalytic Domain, PDB code: 1qib was solved by V.Dhanaraj, M.G.Williams, Q.-Z.Ye, F.Molina, L.L.Johnson, D.F.Ortwine, A.Pavlovsky, J.R.Rubin, R.W.Skeean, A.D.White, C.Humblet, D.J.Hupe, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.830, 84.830, 57.900, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.4

The structure of Crystal Structure of Gelatinase A Catalytic Domain also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Gelatinase A Catalytic Domain (pdb code 1qib). 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 Gelatinase A Catalytic Domain, PDB code: 1qib:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Gelatinase A Catalytic Domain


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 Gelatinase A Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.0 occ:1.00 NE2 A:HIS205 2.3 14.7 1.0 NE2 A:HIS211 2.3 24.7 1.0 NE2 A:HIS201 2.4 8.7 1.0 CE1 A:HIS211 3.2 22.6 1.0 CD2 A:HIS205 3.2 16.4 1.0 CE1 A:HIS201 3.3 8.0 1.0 CE1 A:HIS205 3.3 13.4 1.0 CD2 A:HIS201 3.3 10.3 1.0 CD2 A:HIS211 3.4 23.6 1.0 O A:HOH305 4.4 29.5 1.0 ND1 A:HIS201 4.4 9.0 1.0 ND1 A:HIS211 4.4 26.0 1.0 CG A:HIS205 4.4 15.7 1.0 ND1 A:HIS205 4.4 16.1 1.0 CG A:HIS201 4.4 9.7 1.0 CG A:HIS211 4.5 24.0 1.0 OE1 A:GLU202 4.5 16.4 1.0 OE2 A:GLU202 4.7 15.0 1.0 CE A:MET219 4.8 13.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Gelatinase A Catalytic Domain


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 Gelatinase A Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:14.5 occ:1.00 ND1 A:HIS179 2.3 11.8 1.0 NE2 A:HIS151 2.3 16.4 1.0 NE2 A:HIS166 2.4 14.0 1.0 OD2 A:ASP153 2.7 23.9 1.0 CG A:ASP153 3.0 23.2 1.0 CD2 A:HIS151 3.1 16.1 1.0 OD1 A:ASP153 3.1 25.4 1.0 CE1 A:HIS166 3.1 13.6 1.0 CE1 A:HIS151 3.2 19.2 1.0 CE1 A:HIS179 3.2 10.5 1.0 CG A:HIS179 3.3 10.8 1.0 CD2 A:HIS166 3.5 13.6 1.0 CB A:HIS179 3.6 10.4 1.0 CB A:ASP153 4.1 21.7 1.0 CG A:HIS151 4.2 17.8 1.0 ND1 A:HIS151 4.2 20.2 1.0 O A:TYR155 4.2 22.2 1.0 ND1 A:HIS166 4.4 15.1 1.0 NE2 A:HIS179 4.4 13.3 1.0 CE1 A:PHE168 4.4 16.7 1.0 CD2 A:HIS179 4.5 11.2 1.0 CG A:HIS166 4.6 13.4 1.0 CZ A:PHE168 4.6 19.9 1.0 CZ A:PHE157 4.7 11.0 1.0 CE2 A:PHE157 4.9 8.2 1.0

V.Dhanaraj, M.G.Williams, Q.-Z.Ye, F.Molina, L.L.Johnson, D.F.Ortwine, A.Pavlovsky, J.R.Rubin, R.W.Skeean, A.D.White, C.Humblet, D.J.Hupe, T.L.Blundell. X-Ray Structure of Gelatinase A Catalytic Domain Complexed with A Hydroxamate Inhibitor Croatica Chemica Acta V. 72 575 1999.
ISSN: ISSN 0011-1643