Zinc in PDB 1jap: Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)

All present enzymatic activity of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form):
3.4.24.34;

The structure of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1jap was solved by W.Bode, P.Reinemer, R.Huber, T.Kleine, S.Schnierer, H.Tschesche, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.090, 69.370, 72.480, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / n/a

The structure of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) (pdb code 1jap). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1jap:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:13.7 occ:1.00 OD2 A:ASP149 1.8 8.1 1.0 NE2 A:HIS147 1.9 12.0 1.0 NE2 A:HIS162 2.0 11.0 1.0 ND1 A:HIS175 2.1 18.6 1.0 CG A:ASP149 2.8 14.4 1.0 CE1 A:HIS162 2.9 18.2 1.0 CD2 A:HIS147 2.9 10.6 1.0 CE1 A:HIS147 3.0 7.5 1.0 CE1 A:HIS175 3.0 18.1 1.0 CG A:HIS175 3.2 8.2 1.0 CD2 A:HIS162 3.2 15.8 1.0 OD1 A:ASP149 3.2 10.5 1.0 CB A:HIS175 3.5 6.8 1.0 ND1 A:HIS162 4.1 14.8 1.0 CG A:HIS147 4.1 17.5 1.0 CB A:ASP149 4.1 20.2 1.0 ND1 A:HIS147 4.1 10.8 1.0 NE2 A:HIS175 4.2 12.5 1.0 CG A:HIS162 4.3 15.1 1.0 CE1 A:PHE164 4.3 18.8 1.0 CD2 A:HIS175 4.3 11.2 1.0 O A:SER151 4.3 18.4 1.0 CZ A:PHE164 4.5 19.4 1.0 CZ A:PHE153 4.6 12.2 1.0 CE2 A:PHE153 4.7 15.1 1.0 O A:HOH1024 4.9 14.2 1.0 CA A:HIS175 4.9 6.4 1.0

Zinc binding site 2 out of 2 in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:16.6 occ:1.00 O I:HOA4 1.9 10.5 1.0 NE2 A:HIS197 2.0 10.8 1.0 NE2 A:HIS201 2.1 19.8 1.0 O I:GLY3 2.2 19.8 1.0 NE2 A:HIS207 2.2 12.2 1.0 N I:HOA4 2.8 10.8 1.0 C I:GLY3 2.8 18.1 1.0 CD2 A:HIS197 2.9 8.6 1.0 CE1 A:HIS207 3.1 12.9 1.0 CE1 A:HIS197 3.1 4.3 1.0 CE1 A:HIS201 3.1 11.8 1.0 CD2 A:HIS201 3.1 9.6 1.0 CD2 A:HIS207 3.2 11.9 1.0 CG A:HIS197 4.1 7.4 1.0 ND1 A:HIS197 4.2 12.8 1.0 ND1 A:HIS207 4.2 16.2 1.0 ND1 A:HIS201 4.3 9.5 1.0 CG A:HIS201 4.3 12.9 1.0 CG A:HIS207 4.3 11.1 1.0 CA I:GLY3 4.3 17.5 1.0 OE2 A:GLU198 4.4 16.6 1.0 O I:HOH25 4.6 29.2 1.0 O I:HOH23 4.6 41.3 1.0 OE1 A:GLU198 4.7 8.6 1.0 O I:LEU2 4.7 17.8 1.0 N I:GLY3 4.7 13.2 1.0 C I:LEU2 4.9 19.0 1.0 CE A:MET215 4.9 12.6 1.0 CD A:GLU198 4.9 11.6 1.0

W.Bode, P.Reinemer, R.Huber, T.Kleine, S.Schnierer, H.Tschesche. The X-Ray Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase Inhibited By A Substrate Analogue Reveals the Essentials For Catalysis and Specificity. Embo J. V. 13 1263 1994.
ISSN: ISSN 0261-4189
PubMed: 8137810