Zinc in PDB 2ow0: Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor

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

The structure of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor, PDB code: 2ow0 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)	19.97 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.190, 55.190, 260.361, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27.1

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

Iodine	(I)	2 atoms
Chlorine	(Cl)	6 atoms
Calcium	(Ca)	8 atoms

The binding sites of Zinc atom in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor (pdb code 2ow0). 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 Iodine-Labeled Carboxylate Inhibitor, PDB code: 2ow0:
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 Iodine-Labeled Carboxylate 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 Iodine-Labeled Carboxylate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn444 b:17.3 occ:1.00 NE2 A:HIS411 2.1 18.0 1.0 NE2 A:HIS405 2.1 15.6 1.0 NE2 A:HIS401 2.1 18.5 1.0 O A:6MR501 2.1 17.9 1.0 OXT A:6MR501 2.6 18.8 1.0 C A:6MR501 2.6 18.5 1.0 CD2 A:HIS411 2.9 17.7 1.0 CD2 A:HIS405 3.0 14.7 1.0 CD2 A:HIS401 3.1 18.2 1.0 CE1 A:HIS411 3.1 22.4 1.0 CE1 A:HIS405 3.1 16.5 1.0 CE1 A:HIS401 3.1 16.9 1.0 CE3 A:6MR501 3.9 22.7 1.0 CG A:HIS411 4.1 19.0 1.0 ND1 A:HIS411 4.1 21.0 1.0 CA A:6MR501 4.1 19.8 1.0 ND1 A:HIS405 4.2 12.0 1.0 CG A:HIS405 4.2 14.8 1.0 ND1 A:HIS401 4.2 16.2 1.0 CG A:HIS401 4.2 19.7 1.0 CZ3 A:6MR501 4.4 25.0 1.0 O A:HOH608 4.4 23.9 1.0 CAX A:6MR501 4.5 22.2 1.0 CD2 A:6MR501 4.5 24.2 1.0 CAW A:6MR501 4.5 20.9 1.0 O A:HOH503 4.6 18.8 1.0 N A:6MR501 4.7 20.3 1.0 NE2 A:GLN402 4.8 18.7 1.0 CAY A:6MR501 4.8 22.2 1.0 CE A:MET419 4.8 16.1 1.0 CB A:6MR501 4.9 20.3 1.0 CAM A:6MR501 4.9 22.3 1.0 CG A:6MR501 4.9 22.6 1.0

Zinc binding site 2 out of 4 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate 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 Iodine-Labeled Carboxylate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn445 b:19.9 occ:1.00 NE2 A:HIS175 2.0 23.1 1.0 OD2 A:ASP177 2.0 19.3 1.0 NE2 A:HIS190 2.0 18.4 1.0 ND1 A:HIS203 2.1 17.1 1.0 CD2 A:HIS175 2.7 25.0 1.0 CE1 A:HIS190 2.9 19.7 1.0 CG A:ASP177 2.9 21.9 1.0 CE1 A:HIS203 3.1 15.6 1.0 CG A:HIS203 3.1 17.6 1.0 CE1 A:HIS175 3.2 24.5 1.0 CD2 A:HIS190 3.2 18.5 1.0 OD1 A:ASP177 3.2 19.1 1.0 CB A:HIS203 3.4 16.9 1.0 CG A:HIS175 3.9 26.0 1.0 ND1 A:HIS190 4.1 17.1 1.0 ND1 A:HIS175 4.1 23.4 1.0 NE2 A:HIS203 4.2 16.2 1.0 CG A:HIS190 4.2 16.6 1.0 CD2 A:HIS203 4.2 16.9 1.0 CE1 A:PHE192 4.3 27.4 1.0 O A:TYR179 4.3 22.2 1.0 CB A:ASP177 4.3 27.2 1.0 CZ A:PHE181 4.5 19.9 1.0 CZ A:PHE192 4.5 28.2 1.0 CE2 A:PHE181 4.7 19.7 1.0 O A:HOH522 4.9 18.1 1.0 CA A:HIS203 4.9 15.4 1.0

Zinc binding site 3 out of 4 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate 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 Iodine-Labeled Carboxylate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn444 b:21.3 occ:1.00 O B:6MR502 1.9 24.3 1.0 NE2 B:HIS411 2.0 23.8 1.0 NE2 B:HIS401 2.1 22.3 1.0 NE2 B:HIS405 2.1 23.7 1.0 C B:6MR502 2.6 26.3 1.0 OXT B:6MR502 2.6 27.7 1.0 CD2 B:HIS411 2.9 23.0 1.0 CD2 B:HIS401 3.0 19.8 1.0 CE1 B:HIS411 3.0 23.0 1.0 CD2 B:HIS405 3.1 21.3 1.0 CE1 B:HIS405 3.1 24.2 1.0 CE1 B:HIS401 3.2 22.0 1.0 CE3 B:6MR502 3.8 35.2 1.0 CA B:6MR502 4.1 25.8 1.0 CG B:HIS411 4.1 25.0 1.0 ND1 B:HIS411 4.1 26.0 1.0 CG B:HIS401 4.2 21.4 1.0 ND1 B:HIS401 4.2 20.3 1.0 ND1 B:HIS405 4.2 22.7 1.0 CG B:HIS405 4.2 22.8 1.0 CZ3 B:6MR502 4.2 36.2 1.0 CAX B:6MR502 4.3 26.1 1.0 CAW B:6MR502 4.4 26.5 1.0 CD2 B:6MR502 4.5 34.7 1.0 OE1 B:GLN402 4.6 20.0 1.0 N B:6MR502 4.6 25.4 1.0 O B:HOH545 4.6 32.9 1.0 CAY B:6MR502 4.8 26.5 1.0 CB B:6MR502 4.8 29.6 1.0 CE B:MET419 4.8 17.2 1.0 CG B:6MR502 4.9 33.2 1.0 CAM B:6MR502 5.0 27.5 1.0

Zinc binding site 4 out of 4 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate 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 Iodine-Labeled Carboxylate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn445 b:20.7 occ:1.00 NE2 B:HIS190 2.0 21.1 1.0 OD2 B:ASP177 2.1 23.0 1.0 ND1 B:HIS203 2.1 16.6 1.0 CE1 B:HIS175 2.1 22.0 1.0 ND1 B:HIS175 2.8 26.1 1.0 CE1 B:HIS190 2.9 21.5 1.0 CG B:ASP177 2.9 24.5 1.0 CE1 B:HIS203 3.1 18.0 1.0 CG B:HIS203 3.1 19.6 1.0 CD2 B:HIS190 3.2 19.2 1.0 NE2 B:HIS175 3.3 25.2 1.0 OD1 B:ASP177 3.4 21.6 1.0 CB B:HIS203 3.4 16.4 1.0 CB B:ASP177 4.0 26.1 1.0 ND1 B:HIS190 4.0 20.0 1.0 O B:TYR179 4.1 21.0 1.0 CG B:HIS175 4.1 24.1 1.0 NE2 B:HIS203 4.2 20.2 1.0 CD2 B:HIS203 4.2 18.4 1.0 CG B:HIS190 4.2 19.5 1.0 CD2 B:HIS175 4.3 22.3 1.0 CZ B:PHE181 4.5 18.8 1.0 CE1 B:PHE192 4.6 26.2 1.0 CZ B:PHE192 4.6 27.9 1.0 CE2 B:PHE181 4.8 20.8 1.0 CB B:TYR179 4.9 26.4 1.0 CA B:HIS203 4.9 15.9 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