Zinc in PDB 1gkc: MMP9-Inhibitor Complex

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

The structure of MMP9-Inhibitor Complex, PDB code: 1gkc 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)	51.30 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.005, 56.005, 262.655, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

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

Calcium

(Ca)

10 atoms

The binding sites of Zinc atom in the MMP9-Inhibitor Complex (pdb code 1gkc). 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-Inhibitor Complex, PDB code: 1gkc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the MMP9-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-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1450 b:18.9 occ:1.00 ON A:NFH1448 2.1 20.4 1.0 NE2 A:HIS401 2.2 10.5 1.0 NE2 A:HIS411 2.2 21.0 1.0 NE2 A:HIS405 2.2 18.4 1.0 OM A:NFH1448 2.4 19.7 1.0 N A:NFH1448 2.8 19.5 1.0 CM A:NFH1448 2.9 20.5 1.0 CD2 A:HIS401 3.0 11.8 1.0 CD2 A:HIS405 3.1 15.4 1.0 CD2 A:HIS411 3.1 22.6 1.0 CE1 A:HIS411 3.3 24.6 1.0 CE1 A:HIS405 3.3 17.3 1.0 CE1 A:HIS401 3.3 16.3 1.0 CN A:NFH1448 4.1 21.6 1.0 CG A:HIS401 4.2 16.7 1.0 CG A:HIS411 4.3 25.7 1.0 CG A:HIS405 4.3 19.3 1.0 ND1 A:HIS411 4.3 24.5 1.0 ND1 A:HIS401 4.3 16.1 1.0 ND1 A:HIS405 4.4 18.1 1.0 O A:HOH2056 4.5 25.9 1.0 O A:HOH2038 4.5 19.3 1.0 CA A:NFH1448 4.5 20.3 1.0 CB A:NFH1448 4.6 18.4 1.0 OE1 A:GLU402 4.8 18.7 1.0 OE2 A:GLU402 4.8 17.4 1.0 CE A:MET419 4.9 13.8 1.0

Zinc binding site 2 out of 4 in the MMP9-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-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1451 b:22.1 occ:1.00 NE2 A:HIS175 2.1 15.8 1.0 OD2 A:ASP177 2.1 33.3 1.0 NE2 A:HIS190 2.1 18.9 1.0 ND1 A:HIS203 2.2 15.9 1.0 CG A:ASP177 3.0 32.0 1.0 CD2 A:HIS175 3.0 17.2 1.0 CE1 A:HIS190 3.0 17.3 1.0 CE1 A:HIS175 3.1 18.3 1.0 CE1 A:HIS203 3.2 16.2 1.0 CG A:HIS203 3.2 16.8 1.0 OD1 A:ASP177 3.2 28.2 1.0 CD2 A:HIS190 3.2 20.4 1.0 CB A:HIS203 3.5 15.5 1.0 CG A:HIS175 4.2 20.3 1.0 ND1 A:HIS175 4.2 20.1 1.0 ND1 A:HIS190 4.2 18.2 1.0 CG A:HIS190 4.3 17.3 1.0 NE2 A:HIS203 4.3 14.7 1.0 O A:TYR179 4.3 29.3 1.0 CD2 A:HIS203 4.3 14.9 1.0 CB A:ASP177 4.4 34.1 1.0 CE1 A:PHE192 4.5 27.3 1.0 CZ A:PHE181 4.6 19.1 1.0 CZ A:PHE192 4.6 28.5 1.0 CE2 A:PHE181 4.8 20.8 1.0 O A:HOH2037 5.0 18.6 1.0 O A:HOH2035 5.0 31.1 1.0 CA A:HIS203 5.0 17.6 1.0

Zinc binding site 3 out of 4 in the MMP9-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-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1451 b:30.0 occ:1.00 ON B:NFH1449 2.0 16.0 1.0 NE2 B:HIS405 2.2 25.7 1.0 NE2 B:HIS401 2.3 21.3 1.0 NE2 B:HIS411 2.3 32.0 1.0 OM B:NFH1449 2.5 27.8 1.0 N B:NFH1449 2.8 26.7 1.0 CM B:NFH1449 3.0 25.4 1.0 CD2 B:HIS405 3.0 23.3 1.0 CD2 B:HIS401 3.0 21.4 1.0 CD2 B:HIS411 3.1 27.8 1.0 CE1 B:HIS405 3.2 26.7 1.0 CE1 B:HIS411 3.4 28.1 1.0 CE1 B:HIS401 3.4 24.2 1.0 CN B:NFH1449 4.1 21.0 1.0 CG B:HIS405 4.2 26.1 1.0 CG B:HIS401 4.3 23.8 1.0 ND1 B:HIS405 4.3 25.5 1.0 CG B:HIS411 4.3 29.5 1.0 ND1 B:HIS411 4.4 28.8 1.0 ND1 B:HIS401 4.4 23.8 1.0 CA B:NFH1449 4.6 22.7 1.0 CB B:NFH1449 4.6 20.5 1.0 OE2 B:GLU402 4.7 26.5 1.0 OE1 B:GLU402 4.8 23.0 1.0 CE B:MET419 4.8 27.7 1.0

Zinc binding site 4 out of 4 in the MMP9-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-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1452 b:22.7 occ:1.00 NE2 B:HIS175 2.0 13.2 1.0 ND1 B:HIS203 2.1 18.5 1.0 OD2 B:ASP177 2.2 32.1 1.0 NE2 B:HIS190 2.3 19.4 1.0 CD2 B:HIS175 2.9 17.2 1.0 CG B:ASP177 3.1 33.7 1.0 CG B:HIS203 3.1 20.4 1.0 CE1 B:HIS175 3.1 15.0 1.0 CE1 B:HIS203 3.1 17.2 1.0 CE1 B:HIS190 3.2 20.8 1.0 OD1 B:ASP177 3.2 31.0 1.0 CD2 B:HIS190 3.3 23.0 1.0 CB B:HIS203 3.4 17.4 1.0 CG B:HIS175 4.1 19.3 1.0 ND1 B:HIS175 4.1 15.6 1.0 O B:TYR179 4.2 29.4 1.0 NE2 B:HIS203 4.2 17.1 1.0 CD2 B:HIS203 4.2 17.4 1.0 ND1 B:HIS190 4.3 20.3 1.0 CG B:HIS190 4.4 21.6 1.0 CB B:ASP177 4.5 34.6 1.0 CZ B:PHE181 4.5 16.3 1.0 CE1 B:PHE192 4.6 27.9 1.0 CE2 B:PHE181 4.7 14.8 1.0 CZ B:PHE192 4.7 29.5 1.0 CA B:HIS203 4.8 16.0 1.0 O B:HOH2036 4.9 24.6 1.0 O B:HOH2038 4.9 24.5 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