Zinc in PDB 2ow2: Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor

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

The structure of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor, PDB code: 2ow2 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)	19.73 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.420, 55.420, 260.793, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 28.5

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

Fluorine	(F)	4 atoms
Chlorine	(Cl)	2 atoms
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor (pdb code 2ow2). 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 Difluoro Butanoic Acid Inhibitor, PDB code: 2ow2:
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 Difluoro Butanoic Acid 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 Difluoro Butanoic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn444 b:39.2 occ:1.00 OAJ A:8MR501 1.8 64.5 1.0 NE2 A:HIS411 1.9 36.6 1.0 NE2 A:HIS405 2.1 38.8 1.0 NE2 A:HIS401 2.3 28.5 1.0 CE1 A:HIS411 2.6 37.8 1.0 CAK A:8MR501 2.7 64.7 1.0 CD2 A:HIS405 2.9 39.9 1.0 CD2 A:HIS411 3.1 35.8 1.0 CD2 A:HIS401 3.1 29.0 1.0 CE1 A:HIS405 3.1 39.2 1.0 OAR A:8MR501 3.4 63.7 1.0 CE1 A:HIS401 3.4 28.5 1.0 CAL A:8MR501 3.7 67.0 1.0 ND1 A:HIS411 3.8 35.8 1.0 NE2 A:GLN402 3.8 44.1 1.0 O A:HOH557 3.9 29.6 1.0 CG A:HIS411 4.0 35.0 1.0 CG A:HIS405 4.0 39.0 1.0 ND1 A:HIS405 4.1 39.6 1.0 CAM A:8MR501 4.2 68.2 1.0 CG A:HIS401 4.3 30.1 1.0 CAE A:8MR501 4.3 61.9 1.0 ND1 A:HIS401 4.4 28.3 1.0 CAF A:8MR501 4.6 60.6 1.0 CAO A:8MR501 4.8 63.7 1.0 CA A:PRO421 4.9 55.7 1.0 CD A:GLN402 5.0 43.3 1.0

Zinc binding site 2 out of 4 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid 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 Difluoro Butanoic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn445 b:33.6 occ:1.00 ND1 A:HIS203 1.9 35.3 1.0 NE2 A:HIS175 1.9 33.9 1.0 OD1 A:ASP177 2.0 41.9 1.0 NE2 A:HIS190 2.0 39.0 1.0 CD2 A:HIS175 2.8 35.7 1.0 CG A:ASP177 2.8 41.8 1.0 CE1 A:HIS203 2.8 36.0 1.0 CE1 A:HIS190 3.0 37.9 1.0 CD2 A:HIS190 3.0 38.1 1.0 CG A:HIS203 3.0 34.0 1.0 CE1 A:HIS175 3.0 35.8 1.0 OD2 A:ASP177 3.1 41.5 1.0 CB A:HIS203 3.4 31.6 1.0 NE2 A:HIS203 4.0 36.3 1.0 CG A:HIS175 4.0 37.7 1.0 CD2 A:HIS203 4.1 35.0 1.0 ND1 A:HIS190 4.1 38.2 1.0 ND1 A:HIS175 4.1 36.5 1.0 CB A:ASP177 4.1 43.4 1.0 CG A:HIS190 4.1 37.4 1.0 CE1 A:PHE192 4.1 46.4 1.0 O A:TYR179 4.3 45.9 1.0 CZ A:PHE192 4.4 44.8 1.0 CZ A:PHE181 4.5 43.7 1.0 CE2 A:PHE181 4.7 44.5 1.0 O A:HOH502 4.8 8.4 1.0 CA A:HIS203 4.9 30.4 1.0

Zinc binding site 3 out of 4 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid 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 Difluoro Butanoic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn444 b:45.5 occ:1.00 OAR B:8MR502 2.0 87.9 1.0 NE2 B:HIS401 2.1 34.8 1.0 NE2 B:HIS405 2.3 45.2 1.0 NE2 B:HIS411 2.3 63.0 1.0 CAK B:8MR502 2.5 87.9 1.0 CD2 B:HIS401 2.9 33.1 1.0 CE1 B:HIS411 3.1 64.1 1.0 CAL B:8MR502 3.1 90.3 1.0 CE1 B:HIS401 3.1 35.2 1.0 CD2 B:HIS405 3.2 44.2 1.0 OAJ B:8MR502 3.2 86.9 1.0 CE1 B:HIS405 3.3 45.6 1.0 CD2 B:HIS411 3.4 63.5 1.0 CAM B:8MR502 3.8 92.8 1.0 NE2 B:GLN402 4.1 39.3 1.0 CG B:HIS401 4.1 34.2 1.0 ND1 B:HIS401 4.2 34.5 1.0 ND1 B:HIS411 4.3 64.1 1.0 CG B:HIS405 4.3 44.2 1.0 ND1 B:HIS405 4.4 45.0 1.0 CG B:HIS411 4.5 63.9 1.0 CAO B:8MR502 4.7 90.8 1.0 CAP B:8MR502 4.8 89.5 1.0 CAB B:8MR502 4.8 93.7 1.0 O B:HOH533 4.9 44.2 1.0 CAQ B:8MR502 5.0 90.0 1.0

Zinc binding site 4 out of 4 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid 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 Difluoro Butanoic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn445 b:33.3 occ:1.00 NE2 B:HIS190 2.0 34.3 1.0 CE1 B:HIS175 2.2 28.6 1.0 ND1 B:HIS203 2.4 42.5 1.0 OD2 B:ASP177 2.4 37.2 1.0 CE1 B:HIS190 2.8 34.0 1.0 ND1 B:HIS175 2.9 31.6 1.0 CG B:ASP177 3.1 38.5 1.0 CD2 B:HIS190 3.2 35.4 1.0 CG B:HIS203 3.2 41.6 1.0 NE2 B:HIS175 3.3 30.8 1.0 CE1 B:HIS203 3.3 44.0 1.0 OD1 B:ASP177 3.4 38.6 1.0 CB B:HIS203 3.5 39.8 1.0 ND1 B:HIS190 4.0 34.0 1.0 O B:TYR179 4.1 40.9 1.0 CG B:HIS175 4.2 33.7 1.0 CG B:HIS190 4.2 35.5 1.0 CB B:ASP177 4.3 39.3 1.0 CD2 B:HIS175 4.3 31.8 1.0 CD2 B:HIS203 4.4 41.8 1.0 NE2 B:HIS203 4.4 43.0 1.0 CE1 B:PHE192 4.6 47.6 1.0 CZ B:PHE181 4.6 32.4 1.0 CE2 B:PHE181 4.7 32.1 1.0 CZ B:PHE192 4.7 47.9 1.0 CB B:TYR179 4.8 41.5 1.0 CA B:HIS203 5.0 38.1 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