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Zinc in PDB 4ilw: Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2)

Enzymatic activity of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2)

All present enzymatic activity of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2):
3.4.24.22;

Protein crystallography data

The structure of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2), PDB code: 4ilw was solved by J.Batra, A.S.Soares, E.S.Radisky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.58 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.687, 56.934, 82.592, 76.14, 79.84, 71.25
R / Rfree (%) 21.6 / 26.3

Other elements in 4ilw:

The structure of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2) also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2) (pdb code 4ilw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2), PDB code: 4ilw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4ilw

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Zinc binding site 1 out of 4 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:17.5
occ:1.00
 NE2 D:HIS217 2.0 15.8 1.0
N A:CYS1 2.0 16.3 1.0
NE2 D:HIS227 2.1 25.7 1.0
NE2 D:HIS221 2.2 18.1 1.0
O A:CYS1 2.2 16.5 1.0
C A:CYS1 2.8 16.8 1.0
CA A:CYS1 2.8 16.3 1.0
CD2 D:HIS227 2.9 21.7 1.0
CD2 D:HIS217 3.0 15.5 1.0
CE1 D:HIS217 3.0 14.3 1.0
CD2 D:HIS221 3.0 16.3 1.0
CE1 D:HIS227 3.1 28.6 1.0
CE1 D:HIS221 3.3 17.2 1.0
CB A:CYS1 3.5 17.6 1.0
N A:SER2 4.0 17.4 1.0
ND1 D:HIS217 4.1 15.5 1.0
CG D:HIS227 4.1 22.6 1.0
OE2 D:GLU218 4.1 18.1 1.0
CG D:HIS217 4.1 14.8 1.0
ND1 D:HIS227 4.2 24.5 1.0
OE1 D:GLU218 4.2 18.6 1.0
CG D:HIS221 4.2 17.3 1.0
O A:SER69 4.2 19.7 1.0
ND1 D:HIS221 4.3 18.1 1.0
O A:ALA70 4.5 18.6 1.0
CD D:GLU218 4.5 18.8 1.0
CA A:ALA70 4.7 20.9 1.0
CB D:PRO237 4.7 26.1 1.0
CE D:MET235 4.8 19.3 1.0
CA D:PRO237 4.8 26.3 1.0
OG A:SER2 4.8 23.7 1.0
CA A:SER2 4.9 20.9 1.0

Zinc binding site 2 out of 4 in 4ilw

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Zinc binding site 2 out of 4 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:23.7
occ:1.00
 OD2 D:ASP169 1.9 29.1 1.0
NE2 D:HIS167 1.9 35.6 1.0
ND1 D:HIS195 2.1 19.6 1.0
NE2 D:HIS182 2.2 22.1 1.0
CG D:ASP169 2.9 31.5 1.0
CD2 D:HIS167 2.9 32.9 1.0
CE1 D:HIS195 3.0 19.5 1.0
CE1 D:HIS167 3.0 32.1 1.0
CE1 D:HIS182 3.1 18.4 1.0
CG D:HIS195 3.2 19.1 1.0
OD1 D:ASP169 3.2 28.0 1.0
CD2 D:HIS182 3.2 18.1 1.0
CB D:HIS195 3.6 18.6 1.0
O D:TYR171 4.0 28.5 1.0
ND1 D:HIS167 4.0 37.3 1.0
CG D:HIS167 4.0 35.5 1.0
OH D:TYR184 4.1 18.8 1.0
NE2 D:HIS195 4.1 18.7 1.0
CB D:ASP169 4.2 33.5 1.0
ND1 D:HIS182 4.2 20.8 1.0
CD2 D:HIS195 4.2 18.2 1.0
CG D:HIS182 4.3 19.5 1.0
CE1 D:TYR184 4.6 20.6 1.0
CE1 D:PHE173 4.6 18.0 1.0
CZ D:PHE173 4.7 17.1 1.0
CZ D:TYR184 4.8 22.0 1.0
CB D:TYR171 4.9 29.7 1.0

Zinc binding site 3 out of 4 in 4ilw

Go back to Zinc Binding Sites List in 4ilw
Zinc binding site 3 out of 4 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:29.8
occ:1.00
 NE2 F:HIS217 2.0 23.8 1.0
NE2 F:HIS227 2.1 30.6 1.0
NE2 F:HIS221 2.2 33.4 1.0
O B:CYS1 2.2 29.7 1.0
N B:CYS1 2.3 31.3 1.0
C B:CYS1 2.9 23.8 1.0
CE1 F:HIS217 3.0 24.4 1.0
CD2 F:HIS217 3.0 23.2 1.0
CA B:CYS1 3.0 26.6 1.0
CD2 F:HIS221 3.0 26.9 1.0
CD2 F:HIS227 3.0 37.5 1.0
CE1 F:HIS227 3.2 31.1 1.0
CE1 F:HIS221 3.3 34.4 1.0
CB B:CYS1 3.6 27.8 1.0
N B:SER2 4.0 23.0 1.0
ND1 F:HIS217 4.1 23.3 1.0
OE2 F:GLU218 4.1 24.4 1.0
CG F:HIS217 4.1 22.7 1.0
CG F:HIS227 4.2 34.1 1.0
OE1 F:GLU218 4.2 29.3 1.0
CG F:HIS221 4.2 28.2 1.0
ND1 F:HIS227 4.2 29.9 1.0
O B:SER69 4.3 34.0 1.0
ND1 F:HIS221 4.3 33.2 1.0
CD F:GLU218 4.5 25.5 1.0
O B:ALA70 4.6 23.8 1.0
OG B:SER2 4.7 23.8 1.0
CA B:ALA70 4.8 31.1 1.0
CE F:MET235 4.8 26.1 1.0
CB F:PRO237 4.8 34.9 1.0
CA B:SER2 4.8 22.1 1.0
CA F:PRO237 4.9 35.9 1.0

Zinc binding site 4 out of 4 in 4ilw

Go back to Zinc Binding Sites List in 4ilw
Zinc binding site 4 out of 4 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-2 (Timp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:33.9
occ:1.00
 OD2 F:ASP169 1.9 46.5 1.0
NE2 F:HIS167 2.1 36.3 1.0
NE2 F:HIS182 2.1 31.2 1.0
ND1 F:HIS195 2.1 25.9 1.0
CG F:ASP169 2.9 39.4 1.0
CE1 F:HIS195 3.0 27.8 1.0
CE1 F:HIS182 3.0 30.9 1.0
CD2 F:HIS167 3.1 39.8 1.0
CE1 F:HIS167 3.1 36.8 1.0
CD2 F:HIS182 3.1 31.0 1.0
CG F:HIS195 3.2 25.5 1.0
OD1 F:ASP169 3.2 35.8 1.0
CB F:HIS195 3.6 27.8 1.0
OH F:TYR184 4.0 36.2 1.0
O F:TYR171 4.0 42.8 1.0
NE2 F:HIS195 4.1 28.4 1.0
ND1 F:HIS182 4.2 31.1 1.0
CB F:ASP169 4.2 44.3 1.0
ND1 F:HIS167 4.2 38.1 1.0
CG F:HIS167 4.2 38.0 1.0
CG F:HIS182 4.2 30.6 1.0
CD2 F:HIS195 4.3 28.4 1.0
CE1 F:TYR184 4.5 38.5 1.0
CZ F:TYR184 4.7 37.3 1.0
CE1 F:PHE173 4.8 32.1 1.0
CZ F:PHE173 4.8 29.9 1.0
CB F:TYR171 4.9 49.5 1.0
O F:HOH424 4.9 49.4 1.0
C F:TYR171 5.0 43.1 1.0

Reference:

J.Batra, A.S.Soares, C.Mehner, E.S.Radisky. Matrix Metalloproteinase-10/Timp-2 Structure and Analyses Define Conserved Core Interactions and Diverse Exosite Interactions in Mmp/Timp Complexes. Plos One V. 8 75836 2013.
ISSN: ESSN 1932-6203
PubMed: 24073280
DOI: 10.1371/JOURNAL.PONE.0075836
Page generated: Sun Oct 27 00:47:09 2024

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