Zinc in PDB 1gkd: MMP9 Active Site Mutant-Inhibitor Complex

All present enzymatic activity of MMP9 Active Site Mutant-Inhibitor Complex:
3.4.24.35;

The structure of MMP9 Active Site Mutant-Inhibitor Complex, PDB code: 1gkd was solved by S.Rowsell, R.A.Pauptit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.30 / 2.1
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.523, 56.523, 263.761, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of MMP9 Active Site Mutant-Inhibitor Complex also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Zinc atom in the MMP9 Active Site Mutant-Inhibitor Complex (pdb code 1gkd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the MMP9 Active Site Mutant-Inhibitor Complex, PDB code: 1gkd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the MMP9 Active Site Mutant-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MMP9 Active Site Mutant-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1450 b:14.7 occ:1.00 ON A:STN1448 2.2 16.2 1.0 NE2 A:HIS401 2.2 10.6 1.0 NE2 A:HIS405 2.3 20.2 1.0 NE2 A:HIS411 2.3 24.6 1.0 OM A:STN1448 2.4 15.6 1.0 N A:STN1448 2.9 16.4 1.0 CM A:STN1448 2.9 16.2 1.0 CD2 A:HIS401 3.1 9.9 1.0 CD2 A:HIS405 3.1 18.6 1.0 CD2 A:HIS411 3.1 24.6 1.0 CE1 A:HIS401 3.2 10.9 1.0 CE1 A:HIS411 3.4 24.0 1.0 CE1 A:HIS405 3.5 20.0 1.0 CN A:STN1448 4.2 15.3 1.0 CG A:HIS401 4.3 10.0 1.0 ND1 A:HIS401 4.3 9.9 1.0 CG A:HIS405 4.3 18.9 1.0 CG A:HIS411 4.4 24.4 1.0 ND1 A:HIS411 4.5 25.1 1.0 ND1 A:HIS405 4.5 19.8 1.0 O A:HOH2051 4.6 17.4 1.0 CA A:STN1448 4.7 13.6 1.0 O A:HOH2098 4.7 29.2 1.0 CB A:STN1448 4.7 12.4 1.0 OE1 A:GLN402 4.9 18.9 1.0 CE A:MET419 5.0 19.9 1.0

Zinc binding site 2 out of 4 in the MMP9 Active Site Mutant-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MMP9 Active Site Mutant-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1451 b:14.3 occ:1.00 NE2 A:HIS190 2.2 17.5 1.0 ND1 A:HIS203 2.2 11.3 1.0 OD2 A:ASP177 2.2 22.4 1.0 NE2 A:HIS175 2.2 21.4 1.0 CE1 A:HIS190 3.0 18.4 1.0 CG A:ASP177 3.0 24.4 1.0 CE1 A:HIS203 3.1 11.0 1.0 OD1 A:ASP177 3.1 23.1 1.0 CD2 A:HIS175 3.1 21.8 1.0 CE1 A:HIS175 3.2 22.2 1.0 CG A:HIS203 3.2 12.5 1.0 CD2 A:HIS190 3.3 17.8 1.0 CB A:HIS203 3.6 11.4 1.0 ND1 A:HIS190 4.2 16.9 1.0 NE2 A:HIS203 4.2 12.7 1.0 ND1 A:HIS175 4.3 22.6 1.0 O A:TYR179 4.3 26.1 1.0 CG A:HIS175 4.3 23.2 1.0 CD2 A:HIS203 4.3 13.3 1.0 CG A:HIS190 4.3 17.0 1.0 CZ A:PHE192 4.4 20.6 1.0 CB A:ASP177 4.4 25.7 1.0 CE1 A:PHE192 4.5 20.4 1.0 CZ A:PHE181 4.6 21.4 1.0 O A:HOH2046 4.9 14.7 1.0 CE2 A:PHE181 5.0 20.3 1.0

Zinc binding site 3 out of 4 in the MMP9 Active Site Mutant-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of MMP9 Active Site Mutant-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1450 b:22.9 occ:1.00 NE2 B:HIS401 2.2 13.2 1.0 ON B:STN1448 2.2 21.0 1.0 NE2 B:HIS405 2.3 23.4 1.0 NE2 B:HIS411 2.3 26.5 1.0 OM B:STN1448 2.5 22.3 1.0 N B:STN1448 2.9 21.4 1.0 CM B:STN1448 2.9 20.9 1.0 CD2 B:HIS405 3.1 21.8 1.0 CD2 B:HIS411 3.1 26.6 1.0 CD2 B:HIS401 3.1 14.5 1.0 CE1 B:HIS401 3.2 12.8 1.0 CE1 B:HIS405 3.4 22.4 1.0 CE1 B:HIS411 3.4 26.9 1.0 CN B:STN1448 4.2 20.0 1.0 CG B:HIS405 4.3 21.4 1.0 CG B:HIS401 4.3 13.4 1.0 ND1 B:HIS401 4.3 13.4 1.0 CG B:HIS411 4.3 27.4 1.0 ND1 B:HIS405 4.4 22.1 1.0 ND1 B:HIS411 4.4 27.7 1.0 CB B:STN1448 4.6 20.8 1.0 CA B:STN1448 4.6 22.0 1.0 O B:HOH2086 4.7 28.0 1.0 CE B:MET419 4.9 23.0 1.0 OE1 B:GLN402 4.9 19.9 1.0

Zinc binding site 4 out of 4 in the MMP9 Active Site Mutant-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of MMP9 Active Site Mutant-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1451 b:15.3 occ:1.00 NE2 B:HIS175 2.1 20.4 1.0 OD2 B:ASP177 2.2 23.6 1.0 ND1 B:HIS203 2.2 11.7 1.0 NE2 B:HIS190 2.3 16.0 1.0 CD2 B:HIS175 3.0 20.6 1.0 CG B:ASP177 3.0 25.0 1.0 CE1 B:HIS190 3.1 16.1 1.0 CE1 B:HIS175 3.1 21.2 1.0 CE1 B:HIS203 3.1 12.0 1.0 OD1 B:ASP177 3.2 22.7 1.0 CG B:HIS203 3.3 12.1 1.0 CD2 B:HIS190 3.4 17.4 1.0 CB B:HIS203 3.6 11.2 1.0 O B:TYR179 4.0 25.5 1.0 CG B:HIS175 4.1 22.2 1.0 ND1 B:HIS175 4.1 21.4 1.0 NE2 B:HIS203 4.3 12.5 1.0 ND1 B:HIS190 4.3 17.7 1.0 CD2 B:HIS203 4.4 12.7 1.0 CB B:ASP177 4.5 25.6 1.0 CG B:HIS190 4.5 17.4 1.0 CZ B:PHE192 4.5 20.8 1.0 CZ B:PHE181 4.5 20.6 1.0 CE1 B:PHE192 4.7 21.1 1.0 CE2 B:PHE181 4.8 20.1 1.0 CB B:TYR179 4.9 29.5 1.0 O B:HOH2045 5.0 17.5 1.0

S.Rowsell, P.Hawtin, C.A.Minshull, H.Jepson, S.Brockbank, D.Barratt, A.M.Slater, W.Mcpheat, D.Waterson, A.Henney, R.A.Pauptit. Crystal Structure of MMP9 in Complex with A Reverse Hydroxamate Inhibitor J.Mol.Biol. V. 319 173 2002.
ISSN: ISSN 0022-2836
PubMed: 12051944
DOI: 10.1016/S0022-2836(02)00262-0