Zinc in PDB 2ow1: Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor

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

The structure of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor, PDB code: 2ow1 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)	19.79 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.720, 55.720, 260.450, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.7

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

Fluorine	(F)	6 atoms
Chlorine	(Cl)	3 atoms
Calcium	(Ca)	8 atoms

The binding sites of Zinc atom in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor (pdb code 2ow1). 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 Trifluoromethyl Hydroxamate Inhibitor, PDB code: 2ow1:
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 Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn444 b:17.9 occ:1.00 NE2 A:HIS411 2.1 22.1 1.0 NE2 A:HIS401 2.1 12.3 1.0 OAA A:7MR501 2.1 22.1 1.0 NE2 A:HIS405 2.2 13.0 1.0 OAB A:7MR501 2.2 23.5 1.0 CAE A:7MR501 2.8 23.1 1.0 NAD A:7MR501 2.9 22.5 1.0 CD2 A:HIS411 3.0 21.8 1.0 CD2 A:HIS401 3.0 13.5 1.0 CE1 A:HIS401 3.1 11.4 1.0 CE1 A:HIS411 3.1 23.6 1.0 CD2 A:HIS405 3.1 13.9 1.0 CE1 A:HIS405 3.2 15.2 1.0 O A:HOH551 4.1 13.1 1.0 CG A:HIS411 4.1 22.4 1.0 ND1 A:HIS411 4.2 24.0 1.0 ND1 A:HIS401 4.2 11.8 1.0 CG A:HIS401 4.2 11.9 1.0 ND1 A:HIS405 4.3 15.4 1.0 CG A:HIS405 4.3 15.4 1.0 NE2 A:GLN402 4.3 18.2 1.0 CAO A:7MR501 4.3 23.8 1.0 FBA A:7MR501 4.5 25.6 1.0 FAF A:7MR501 4.7 24.5 1.0 CAX A:7MR501 4.8 19.4 1.0 CAP A:7MR501 4.8 24.4 1.0 CAW A:7MR501 4.9 19.1 1.0

Zinc binding site 2 out of 4 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn445 b:16.8 occ:1.00 OD2 A:ASP177 1.9 16.5 1.0 NE2 A:HIS175 1.9 16.1 1.0 NE2 A:HIS190 2.0 16.9 1.0 ND1 A:HIS203 2.1 9.1 1.0 CD2 A:HIS175 2.8 16.6 1.0 CE1 A:HIS190 2.9 19.4 1.0 CG A:ASP177 2.9 19.2 1.0 CE1 A:HIS175 3.0 19.0 1.0 CG A:HIS203 3.1 11.4 1.0 CE1 A:HIS203 3.1 10.8 1.0 CD2 A:HIS190 3.1 19.4 1.0 OD1 A:ASP177 3.3 18.1 1.0 CB A:HIS203 3.4 11.3 1.0 CG A:HIS175 4.0 17.1 1.0 ND1 A:HIS190 4.0 18.3 1.0 ND1 A:HIS175 4.0 16.7 1.0 NE2 A:HIS203 4.2 9.7 1.0 CG A:HIS190 4.2 16.7 1.0 CD2 A:HIS203 4.2 9.9 1.0 CB A:ASP177 4.3 20.3 1.0 CE1 A:PHE192 4.3 21.9 1.0 O A:TYR179 4.3 21.8 1.0 CZ A:PHE192 4.6 22.0 1.0 CZ A:PHE181 4.6 20.0 1.0 CE2 A:PHE181 4.8 19.8 1.0 CA A:HIS203 4.9 11.6 1.0 O A:HOH535 4.9 26.9 1.0

Zinc binding site 3 out of 4 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn444 b:22.6 occ:1.00 NE2 B:HIS401 2.0 17.6 1.0 NE2 B:HIS411 2.0 29.6 1.0 OAA B:7MR502 2.1 30.3 1.0 NE2 B:HIS405 2.2 22.6 1.0 OAB B:7MR502 2.3 33.3 1.0 CD2 B:HIS401 2.9 17.3 1.0 NAD B:7MR502 2.9 32.6 1.0 CAE B:7MR502 2.9 33.7 1.0 CD2 B:HIS411 3.0 27.6 1.0 CE1 B:HIS411 3.0 28.8 1.0 CE1 B:HIS401 3.1 18.0 1.0 CD2 B:HIS405 3.1 20.1 1.0 CE1 B:HIS405 3.3 22.4 1.0 CG B:HIS401 4.1 17.5 1.0 ND1 B:HIS411 4.1 29.7 1.0 CG B:HIS411 4.1 28.8 1.0 ND1 B:HIS401 4.1 16.5 1.0 NE2 B:GLN402 4.2 23.9 1.0 O B:HOH532 4.3 15.3 1.0 CG B:HIS405 4.3 20.4 1.0 ND1 B:HIS405 4.4 21.2 1.0 CAO B:7MR502 4.4 33.8 1.0 FAF B:7MR502 4.6 36.1 1.0 FBA B:7MR502 4.8 36.3 1.0 CAK B:7MR502 4.8 26.7 1.0 CE B:MET419 4.9 12.9 1.0 CAP B:7MR502 4.9 36.1 1.0 CAJ B:7MR502 4.9 25.9 1.0

Zinc binding site 4 out of 4 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn445 b:17.6 occ:1.00 NE2 B:HIS190 2.0 14.2 1.0 OD2 B:ASP177 2.0 17.1 1.0 ND1 B:HIS203 2.1 11.7 1.0 CE1 B:HIS175 2.1 19.6 1.0 CE1 B:HIS190 2.8 15.9 1.0 ND1 B:HIS175 2.9 21.7 1.0 CG B:ASP177 3.0 21.7 1.0 CE1 B:HIS203 3.0 14.3 1.0 CG B:HIS203 3.1 13.3 1.0 NE2 B:HIS175 3.1 22.0 1.0 CD2 B:HIS190 3.2 16.1 1.0 OD1 B:ASP177 3.3 21.2 1.0 CB B:HIS203 3.4 11.9 1.0 ND1 B:HIS190 4.0 15.2 1.0 O B:TYR179 4.1 20.0 1.0 CG B:HIS175 4.1 20.3 1.0 NE2 B:HIS203 4.1 15.5 1.0 CD2 B:HIS203 4.2 14.3 1.0 CG B:HIS190 4.2 16.6 1.0 CB B:ASP177 4.2 23.7 1.0 CD2 B:HIS175 4.2 17.6 1.0 CZ B:PHE181 4.5 18.7 1.0 CE1 B:PHE192 4.6 24.6 1.0 CZ B:PHE192 4.7 25.8 1.0 CE2 B:PHE181 4.8 16.1 1.0 CB B:TYR179 4.8 23.8 1.0 CA B:HIS203 4.9 14.4 1.0 O B:HOH601 5.0 31.0 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