Zinc in PDB 1gxd: Prommp-2/Timp-2 Complex

All present enzymatic activity of Prommp-2/Timp-2 Complex:
3.4.24.24;

The structure of Prommp-2/Timp-2 Complex, PDB code: 1gxd was solved by E.Morgunova, A.Tuuttila, U.Bergmann, K.Tryggvason, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 3.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.696, 374.575, 191.000, 90.00, 90.00, 90.00
R / Rfree (%)	27.5 / 33.3

The structure of Prommp-2/Timp-2 Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Prommp-2/Timp-2 Complex (pdb code 1gxd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Prommp-2/Timp-2 Complex, PDB code: 1gxd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Prommp-2/Timp-2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prommp-2/Timp-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1633 b:61.7 occ:1.00 OD2 A:ASP151 1.6 30.5 1.0 NE2 A:HIS149 1.8 32.8 1.0 ND1 A:HIS177 1.8 32.1 1.0 NE2 A:HIS164 1.9 26.0 1.0 CD2 A:HIS149 2.6 32.8 1.0 CG A:HIS177 2.8 33.1 1.0 CG A:ASP151 2.8 30.8 1.0 CE1 A:HIS177 2.8 32.2 1.0 CE1 A:HIS149 2.9 33.0 1.0 CE1 A:HIS164 2.9 26.6 1.0 CD2 A:HIS164 3.0 26.1 1.0 CB A:HIS177 3.1 33.9 1.0 OD1 A:ASP151 3.3 30.6 1.0 CG A:HIS149 3.8 32.0 1.0 ND1 A:HIS149 3.9 32.6 1.0 CD2 A:HIS177 3.9 32.5 1.0 NE2 A:HIS177 3.9 32.4 1.0 CB A:ASP151 4.0 30.7 1.0 ND1 A:HIS164 4.0 26.0 1.0 CG A:HIS164 4.1 26.5 1.0 CA A:HIS177 4.6 34.3 1.0 O A:TYR153 4.6 31.6 1.0 CZ A:PHE155 4.7 29.8 1.0 CE2 A:PHE166 4.7 29.9 1.0 CZ A:PHE166 4.8 29.3 1.0

Zinc binding site 2 out of 4 in the Prommp-2/Timp-2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prommp-2/Timp-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1634 b:72.9 occ:1.00 NE2 A:HIS374 1.8 26.8 1.0 NE2 A:HIS378 1.8 28.3 1.0 SG A:CYS73 1.9 31.1 1.0 NE2 A:HIS384 2.0 32.1 1.0 CE1 A:HIS374 2.5 26.9 1.0 CE1 A:HIS378 2.7 28.8 1.0 CD2 A:HIS384 2.8 32.2 1.0 CD2 A:HIS378 2.8 29.6 1.0 CB A:CYS73 2.9 31.8 1.0 CE1 A:HIS384 2.9 32.6 1.0 CD2 A:HIS374 3.0 27.1 1.0 ND2 A:ASN75 3.5 34.1 1.0 CB A:ASN75 3.6 33.7 1.0 ND1 A:HIS374 3.7 27.4 1.0 ND1 A:HIS378 3.8 29.4 1.0 CG A:HIS384 3.9 32.0 1.0 CG A:HIS378 3.9 30.4 1.0 ND1 A:HIS384 3.9 32.5 1.0 CG A:HIS374 3.9 28.0 1.0 CG A:ASN75 4.0 33.7 1.0 CA A:CYS73 4.3 32.0 1.0 N A:ASN75 4.5 33.4 1.0 CA A:ASN75 4.6 33.8 1.0 C A:CYS73 4.8 32.0 1.0 CE A:MET392 5.0 30.1 1.0

Zinc binding site 3 out of 4 in the Prommp-2/Timp-2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Prommp-2/Timp-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1633 b:50.4 occ:1.00 OD2 B:ASP151 1.5 35.5 1.0 NE2 B:HIS149 1.6 37.2 1.0 NE2 B:HIS164 1.7 30.7 1.0 ND1 B:HIS177 1.9 34.9 1.0 CE1 B:HIS164 2.2 29.9 1.0 CE1 B:HIS149 2.4 38.5 1.0 CG B:ASP151 2.4 34.6 1.0 OD1 B:ASP151 2.7 34.9 1.0 CE1 B:HIS177 2.7 35.7 1.0 CD2 B:HIS149 2.8 36.6 1.0 CG B:HIS177 3.0 34.6 1.0 CD2 B:HIS164 3.0 30.9 1.0 CB B:HIS177 3.4 35.0 1.0 ND1 B:HIS164 3.5 30.1 1.0 ND1 B:HIS149 3.6 37.2 1.0 CG B:HIS149 3.8 36.2 1.0 CB B:ASP151 3.8 34.0 1.0 CG B:HIS164 3.9 30.0 1.0 NE2 B:HIS177 3.9 35.5 1.0 CD2 B:HIS177 4.0 34.2 1.0 CZ B:PHE166 4.3 34.1 1.0 CE2 B:PHE166 4.4 32.6 1.0 O B:TYR153 4.4 33.1 1.0 CZ B:PHE155 4.8 29.4 1.0 CA B:HIS177 4.9 34.9 1.0 CE2 B:PHE155 4.9 29.4 1.0 CA B:ASP151 5.0 34.2 1.0

Zinc binding site 4 out of 4 in the Prommp-2/Timp-2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Prommp-2/Timp-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1634 b:55.8 occ:1.00 NE2 B:HIS384 1.7 36.9 1.0 NE2 B:HIS374 1.8 32.0 1.0 SG B:CYS73 1.8 31.9 1.0 NE2 B:HIS378 1.9 30.9 1.0 CD2 B:HIS384 2.7 36.6 1.0 CE1 B:HIS384 2.7 37.2 1.0 CD2 B:HIS374 2.8 32.3 1.0 CD2 B:HIS378 2.8 32.0 1.0 CE1 B:HIS374 2.8 32.4 1.0 CB B:CYS73 2.9 32.2 1.0 CE1 B:HIS378 3.0 31.5 1.0 CB B:ASN75 3.6 32.5 1.0 ND1 B:HIS384 3.8 36.5 1.0 CG B:HIS384 3.8 35.7 1.0 ND1 B:HIS374 3.9 32.3 1.0 CG B:HIS374 4.0 31.9 1.0 CG B:ASN75 4.0 33.1 1.0 CG B:HIS378 4.0 31.8 1.0 ND1 B:HIS378 4.1 31.3 1.0 OD1 B:ASN75 4.2 35.0 1.0 CA B:CYS73 4.3 32.1 1.0 N B:ASN75 4.5 32.2 1.0 ND2 B:ASN75 4.6 33.3 1.0 CA B:ASN75 4.7 32.1 1.0 C B:CYS73 4.7 32.2 1.0 CE B:MET392 4.8 33.2 1.0 O B:HIS374 4.9 32.1 1.0 N B:GLY74 4.9 31.9 1.0

E.Morgunova, A.Tuuttila, U.Bergmann, K.Tryggvason. Structural Insight Into the Complex Formation of Latent Matrix Metalloproteinase 2 with Tissue Inhibitor of Metalloproteinase 2 Proc.Natl.Acad.Sci.Usa V. 99 7414 2002.
ISSN: ISSN 0027-8424
PubMed: 12032297
DOI: 10.1073/PNAS.102185399