Zinc in PDB 2ovz: Mmp-9 Active Site Mutant with Phosphinate Inhibitor

All present enzymatic activity of Mmp-9 Active Site Mutant with Phosphinate Inhibitor:
3.4.24.35;

The structure of Mmp-9 Active Site Mutant with Phosphinate Inhibitor, PDB code: 2ovz was solved by A.Tochowicz, W.Bode, K.Maskos, P.Goettig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.850, 55.850, 259.890, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.1

The structure of Mmp-9 Active Site Mutant with Phosphinate Inhibitor also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	10 atoms

The binding sites of Zinc atom in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor (pdb code 2ovz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor, PDB code: 2ovz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn444 b:23.4 occ:1.00 OAD A:5MR501 1.8 31.8 1.0 NE2 A:HIS405 2.0 19.6 1.0 NE2 A:HIS401 2.1 25.0 1.0 NE2 A:HIS411 2.1 28.1 1.0 PBN A:5MR501 2.7 29.8 1.0 OAE A:5MR501 2.8 29.1 1.0 CD2 A:HIS405 3.0 20.2 1.0 CD2 A:HIS411 3.0 27.1 1.0 CE1 A:HIS401 3.1 24.6 1.0 CE1 A:HIS405 3.1 21.7 1.0 CD2 A:HIS401 3.1 22.0 1.0 CE1 A:HIS411 3.1 28.8 1.0 CBG A:5MR501 3.9 35.8 1.0 CG A:HIS411 4.1 28.5 1.0 CG A:HIS405 4.1 22.1 1.0 ND1 A:HIS405 4.1 23.9 1.0 ND1 A:HIS411 4.1 28.5 1.0 ND1 A:HIS401 4.2 25.9 1.0 CAX A:5MR501 4.2 29.8 1.0 CG A:HIS401 4.2 21.4 1.0 CBL A:5MR501 4.3 25.4 1.0 CAV A:5MR501 4.4 27.0 1.0 CAP A:5MR501 4.6 40.2 1.0 CAQ A:5MR501 4.6 39.9 1.0 CE A:MET419 4.7 20.6 1.0 CAU A:5MR501 4.8 25.1 1.0 CBF A:5MR501 4.9 23.6 1.0 CA A:PRO421 4.9 26.9 1.0

Zinc binding site 2 out of 4 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn445 b:24.4 occ:1.00 OD2 A:ASP177 2.0 23.6 1.0 ND1 A:HIS203 2.0 20.1 1.0 NE2 A:HIS175 2.1 23.1 1.0 NE2 A:HIS190 2.2 34.0 1.0 CE1 A:HIS190 2.3 37.0 1.0 CD2 A:HIS175 2.7 26.6 1.0 CG A:ASP177 2.9 26.9 1.0 CE1 A:HIS203 3.0 20.7 1.0 CG A:HIS203 3.1 19.0 1.0 OD1 A:ASP177 3.2 27.6 1.0 CE1 A:HIS175 3.3 26.3 1.0 CB A:HIS203 3.4 21.1 1.0 CD2 A:HIS190 3.5 35.2 1.0 ND1 A:HIS190 3.6 37.6 1.0 CG A:HIS175 3.9 28.4 1.0 NE2 A:HIS203 4.1 17.9 1.0 ND1 A:HIS175 4.2 28.8 1.0 CD2 A:HIS203 4.2 20.0 1.0 CG A:HIS190 4.2 31.6 1.0 O A:TYR179 4.2 37.7 1.0 CB A:ASP177 4.3 32.0 1.0 CE1 A:PHE192 4.5 32.2 1.0 CZ A:PHE181 4.7 25.7 1.0 CZ A:PHE192 4.8 35.1 1.0 O A:HOH524 4.8 26.4 1.0 O A:HOH559 4.9 41.7 1.0 CA A:HIS203 4.9 20.8 1.0 CE2 A:PHE181 4.9 26.2 1.0

Zinc binding site 3 out of 4 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn444 b:24.7 occ:1.00 OAE B:5MR502 1.8 22.2 1.0 NE2 B:HIS401 2.0 23.5 1.0 NE2 B:HIS411 2.1 30.1 1.0 NE2 B:HIS405 2.1 28.5 1.0 CD2 B:HIS411 2.9 29.7 1.0 PBN B:5MR502 2.9 29.2 1.0 CD2 B:HIS401 3.0 20.2 1.0 CE1 B:HIS405 3.0 27.6 1.0 CE1 B:HIS401 3.1 20.3 1.0 CD2 B:HIS405 3.1 25.6 1.0 CE1 B:HIS411 3.1 28.4 1.0 OAD B:5MR502 3.3 25.5 1.0 CG B:HIS411 4.1 30.9 1.0 CG B:HIS401 4.1 22.7 1.0 ND1 B:HIS411 4.1 30.1 1.0 CBG B:5MR502 4.1 30.2 1.0 ND1 B:HIS405 4.1 25.7 1.0 ND1 B:HIS401 4.2 20.0 1.0 CG B:HIS405 4.2 27.6 1.0 CAX B:5MR502 4.3 26.7 1.0 CBL B:5MR502 4.4 28.6 1.0 CAQ B:5MR502 4.5 35.7 1.0 CAV B:5MR502 4.6 29.1 1.0 CE B:MET419 4.6 20.8 1.0 O B:HOH562 4.7 42.9 1.0 CA B:PRO421 4.9 31.9 1.0 CAU B:5MR502 4.9 28.0 1.0

Zinc binding site 4 out of 4 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn445 b:23.1 occ:1.00 OD2 B:ASP177 2.0 20.9 1.0 NE2 B:HIS190 2.0 23.7 1.0 ND1 B:HIS203 2.1 22.0 1.0 CE1 B:HIS175 2.1 21.1 1.0 CE1 B:HIS190 2.8 23.2 1.0 CG B:ASP177 3.0 22.5 1.0 CE1 B:HIS203 3.0 22.7 1.0 NE2 B:HIS175 3.1 25.4 1.0 CG B:HIS203 3.1 20.0 1.0 ND1 B:HIS175 3.1 26.2 1.0 CD2 B:HIS190 3.2 25.3 1.0 OD1 B:ASP177 3.3 23.9 1.0 CB B:HIS203 3.5 20.9 1.0 ND1 B:HIS190 4.0 24.7 1.0 O B:TYR179 4.1 25.9 1.0 NE2 B:HIS203 4.1 25.0 1.0 CD2 B:HIS203 4.2 19.2 1.0 CG B:HIS190 4.2 24.0 1.0 CD2 B:HIS175 4.3 22.3 1.0 CG B:HIS175 4.3 24.0 1.0 CB B:ASP177 4.3 30.3 1.0 CZ B:PHE181 4.6 23.1 1.0 CE1 B:PHE192 4.6 30.5 1.0 CZ B:PHE192 4.7 32.6 1.0 CE2 B:PHE181 4.8 22.7 1.0 O B:HOH509 4.9 26.3 1.0 CB B:TYR179 5.0 30.1 1.0 CA B:HIS203 5.0 20.7 1.0

A.Tochowicz, K.Maskos, R.Huber, R.Oltenfreiter, V.Dive, A.Yiotakis, M.Zanda, W.Bode, P.Goettig. Crystal Structures of Mmp-9 Complexes with Five Inhibitors: Contribution of the Flexible ARG424 Side-Chain to Selectivity. J.Mol.Biol. V. 371 989 2007.
ISSN: ISSN 0022-2836
PubMed: 17599356
DOI: 10.1016/J.JMB.2007.05.068