Zinc in PDB 2ovx: Mmp-9 Active Site Mutant with Barbiturate Inhibitor

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

The structure of Mmp-9 Active Site Mutant with Barbiturate Inhibitor, PDB code: 2ovx 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)	19.64 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.230, 55.230, 259.200, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.8

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

Chlorine	(Cl)	5 atoms
Calcium	(Ca)	10 atoms

The binding sites of Zinc atom in the Mmp-9 Active Site Mutant with Barbiturate Inhibitor (pdb code 2ovx). 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 Barbiturate Inhibitor, PDB code: 2ovx:
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 Barbiturate 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 Barbiturate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn444 b:21.6 occ:1.00 NE2 A:HIS405 2.0 22.6 1.0 NBA A:4MR501 2.0 21.2 1.0 NE2 A:HIS401 2.1 17.2 1.0 NE2 A:HIS411 2.2 25.4 1.0 CAZ A:4MR501 2.9 21.6 1.0 CD2 A:HIS411 2.9 21.9 1.0 CD2 A:HIS405 2.9 21.4 1.0 OAS A:4MR501 3.0 22.2 1.0 CD2 A:HIS401 3.0 19.3 1.0 CBF A:4MR501 3.0 21.1 1.0 CE1 A:HIS405 3.0 22.2 1.0 OBG A:4MR501 3.1 22.2 1.0 CE1 A:HIS401 3.2 21.0 1.0 CE1 A:HIS411 3.3 27.2 1.0 CG A:HIS405 4.1 21.4 1.0 ND1 A:HIS405 4.1 20.2 1.0 CG A:HIS411 4.1 26.5 1.0 CG A:HIS401 4.2 19.9 1.0 ND1 A:HIS401 4.2 17.3 1.0 NBE A:4MR501 4.3 23.7 1.0 CAY A:4MR501 4.3 24.5 1.0 ND1 A:HIS411 4.3 24.4 1.0 CAK A:4MR501 4.7 24.1 1.0 OE1 A:GLN402 4.7 22.6 1.0 CAL A:4MR501 4.7 23.9 1.0 CBD A:4MR501 4.8 24.6 1.0 O A:HOH521 4.8 18.4 1.0 CE A:MET419 4.9 16.7 1.0

Zinc binding site 2 out of 4 in the Mmp-9 Active Site Mutant with Barbiturate 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 Barbiturate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn445 b:23.9 occ:1.00 NE2 A:HIS175 2.0 29.9 1.0 OD2 A:ASP177 2.1 28.0 1.0 NE2 A:HIS190 2.1 23.6 1.0 ND1 A:HIS203 2.1 20.9 1.0 CE1 A:HIS190 2.9 24.0 1.0 CD2 A:HIS175 2.9 29.4 1.0 CG A:ASP177 3.0 31.4 1.0 CE1 A:HIS175 3.0 32.6 1.0 CE1 A:HIS203 3.1 21.5 1.0 CG A:HIS203 3.1 20.0 1.0 OD1 A:ASP177 3.2 25.7 1.0 CD2 A:HIS190 3.2 23.0 1.0 CB A:HIS203 3.4 18.8 1.0 ND1 A:HIS190 4.1 24.1 1.0 ND1 A:HIS175 4.1 30.8 1.0 CG A:HIS175 4.1 32.7 1.0 NE2 A:HIS203 4.2 20.9 1.0 CD2 A:HIS203 4.2 18.8 1.0 CG A:HIS190 4.2 23.2 1.0 O A:TYR179 4.3 33.1 1.0 CE1 A:PHE192 4.4 27.6 1.0 CB A:ASP177 4.4 35.7 1.0 CZ A:PHE181 4.5 27.1 1.0 CZ A:PHE192 4.5 30.0 1.0 CE2 A:PHE181 4.7 29.0 1.0 O A:HOH506 4.9 23.5 1.0 CA A:HIS203 4.9 18.1 1.0

Zinc binding site 3 out of 4 in the Mmp-9 Active Site Mutant with Barbiturate 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 Barbiturate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn444 b:23.4 occ:1.00 NBA B:4MR502 2.0 25.2 1.0 NE2 B:HIS405 2.1 26.9 1.0 NE2 B:HIS411 2.1 23.4 1.0 NE2 B:HIS401 2.1 24.5 1.0 CAZ B:4MR502 2.8 25.1 1.0 OAS B:4MR502 2.9 26.8 1.0 CBF B:4MR502 2.9 22.5 1.0 CD2 B:HIS411 3.0 26.6 1.0 CE1 B:HIS405 3.0 25.1 1.0 CD2 B:HIS401 3.1 22.6 1.0 OBG B:4MR502 3.1 19.8 1.0 CD2 B:HIS405 3.1 24.5 1.0 CE1 B:HIS401 3.1 24.2 1.0 CE1 B:HIS411 3.2 29.4 1.0 ND1 B:HIS405 4.1 23.1 1.0 CG B:HIS411 4.2 29.3 1.0 CAY B:4MR502 4.2 25.8 1.0 NBE B:4MR502 4.2 21.4 1.0 CG B:HIS401 4.2 21.3 1.0 ND1 B:HIS401 4.2 21.4 1.0 CG B:HIS405 4.2 23.8 1.0 ND1 B:HIS411 4.2 30.2 1.0 CAK B:4MR502 4.6 23.4 1.0 OE1 B:GLN402 4.6 20.2 1.0 CBD B:4MR502 4.7 20.9 1.0 CAH B:4MR502 4.8 23.1 1.0 O B:HOH541 4.9 21.3 1.0 CE B:MET419 4.9 21.6 1.0 CB B:PRO421 5.0 30.6 1.0

Zinc binding site 4 out of 4 in the Mmp-9 Active Site Mutant with Barbiturate 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 Barbiturate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn445 b:20.1 occ:1.00 NE2 B:HIS175 2.0 21.8 1.0 OD2 B:ASP177 2.0 19.0 1.0 ND1 B:HIS203 2.1 19.6 1.0 NE2 B:HIS190 2.2 22.5 1.0 CD2 B:HIS175 2.8 23.2 1.0 CE1 B:HIS190 3.0 19.9 1.0 CG B:ASP177 3.0 23.2 1.0 CE1 B:HIS203 3.0 16.7 1.0 CE1 B:HIS175 3.1 20.0 1.0 CG B:HIS203 3.1 20.3 1.0 CD2 B:HIS190 3.3 21.9 1.0 OD1 B:ASP177 3.3 16.9 1.0 CB B:HIS203 3.5 18.7 1.0 CG B:HIS175 4.0 23.9 1.0 O B:TYR179 4.1 20.5 1.0 ND1 B:HIS175 4.1 18.4 1.0 ND1 B:HIS190 4.2 19.1 1.0 NE2 B:HIS203 4.2 20.0 1.0 CD2 B:HIS203 4.2 18.5 1.0 CG B:HIS190 4.3 19.8 1.0 CB B:ASP177 4.4 24.9 1.0 CZ B:PHE181 4.5 18.3 1.0 CE2 B:PHE181 4.6 18.9 1.0 CE1 B:PHE192 4.6 28.8 1.0 CZ B:PHE192 4.7 29.5 1.0 CB B:TYR179 4.9 25.7 1.0 CA B:HIS203 5.0 17.4 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