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Calcium in PDB 3v96: Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)

Enzymatic activity of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)

All present enzymatic activity of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1):
3.4.24.22;

Protein crystallography data

The structure of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1), PDB code: 3v96 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) 35.00 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 231.720, 37.682, 39.523, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 26.6

Other elements in 3v96:

The structure of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) (pdb code 3v96). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1), PDB code: 3v96:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3v96

Go back to Calcium Binding Sites List in 3v96
Calcium binding site 1 out of 3 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:33.9
occ:1.00
 O B:SER179 2.2 27.9 1.0
OE2 B:GLU200 2.3 36.7 1.0
O B:GLY175 2.3 39.0 1.0
OD2 B:ASP174 2.4 37.1 1.0
O B:GLY177 2.4 31.6 1.0
OD2 B:ASP197 2.5 36.2 1.0
CG B:ASP197 3.3 39.3 1.0
C B:SER179 3.4 25.8 1.0
CD B:GLU200 3.5 34.1 1.0
C B:GLY175 3.5 39.9 1.0
C B:GLY177 3.6 32.8 1.0
CG B:ASP174 3.6 36.2 1.0
N B:GLY177 3.8 35.6 1.0
CB B:ASP197 3.9 35.7 1.0
N B:GLY175 4.0 40.1 1.0
N B:SER179 4.0 26.6 1.0
OE1 B:GLU200 4.1 34.8 1.0
C B:PRO176 4.1 37.4 1.0
C B:ASP174 4.2 40.1 1.0
CA B:SER179 4.2 25.1 0.5
CA B:SER179 4.2 25.4 0.5
OD1 B:ASP197 4.2 40.7 1.0
OD1 B:ASP174 4.3 34.6 1.0
CA B:GLY177 4.3 34.3 1.0
N B:LEU180 4.3 25.5 1.0
N B:ASP174 4.3 37.6 1.0
OG B:SER179 4.3 24.9 0.5
CA B:GLY175 4.4 41.1 1.0
N B:PRO176 4.4 40.4 1.0
CA B:PRO176 4.4 39.3 1.0
CA B:LEU180 4.5 27.0 1.0
C B:HIS178 4.5 28.4 1.0
CG B:GLU200 4.6 35.6 1.0
O B:ASP174 4.6 39.8 1.0
O B:PRO176 4.6 38.1 1.0
N B:HIS178 4.6 31.0 1.0
CA B:ASP174 4.7 39.1 1.0
CB B:ASP174 4.7 37.2 1.0
CB B:HIS178 4.8 32.1 1.0
CD2 B:LEU180 4.9 25.4 1.0
CA B:HIS178 4.9 29.4 1.0
CB B:SER179 4.9 25.6 0.5
CB B:SER179 5.0 25.6 0.5

Calcium binding site 2 out of 3 in 3v96

Go back to Calcium Binding Sites List in 3v96
Calcium binding site 2 out of 3 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:49.2
occ:1.00
 O B:HOH449 2.2 53.3 1.0
O B:ASP157 2.3 48.9 1.0
O B:HOH447 2.3 56.1 1.0
O B:GLY189 2.4 52.2 1.0
O B:TYR191 2.5 43.2 1.0
OD1 B:ASP193 2.6 45.4 1.0
CG B:ASP193 3.4 42.8 1.0
C B:ASP157 3.5 48.8 1.0
C B:TYR191 3.6 42.2 1.0
C B:GLY189 3.6 54.0 1.0
OD2 B:ASP193 3.7 48.1 1.0
O B:LEU190 3.9 46.7 1.0
O B:ALA156 3.9 56.4 1.0
C B:LEU190 4.0 47.9 1.0
N B:ASP193 4.2 37.5 1.0
CA B:ASP157 4.2 51.3 1.0
CA B:GLY192 4.3 37.1 1.0
N B:TYR191 4.3 47.2 1.0
OE1 B:GLU155 4.4 70.4 1.0
O B:GLY187 4.4 44.7 1.0
N B:GLY192 4.4 38.7 1.0
C B:GLY192 4.4 36.5 1.0
N B:ILE158 4.5 47.9 1.0
O B:HOH437 4.5 57.5 1.0
N B:LEU190 4.5 54.5 1.0
CA B:LEU190 4.6 52.0 1.0
CA B:GLY189 4.6 57.5 1.0
CA B:TYR191 4.6 44.3 1.0
CB B:ASP193 4.6 41.1 1.0
N B:GLY189 4.6 55.4 1.0
N B:MET159 4.6 47.4 1.0
C B:PRO188 4.7 52.7 1.0
CG B:MET159 4.7 57.3 1.0
CA B:ASP193 4.8 37.7 1.0
CA B:ILE158 4.8 44.3 1.0
C B:ALA156 4.9 57.4 1.0
O B:HOH427 4.9 60.5 1.0
O B:PRO188 5.0 48.5 1.0

Calcium binding site 3 out of 3 in 3v96

Go back to Calcium Binding Sites List in 3v96
Calcium binding site 3 out of 3 in the Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Matrix Metalloproteinase-10 Catalytic Domain (Mmp-10CD) with Tissue Inhibitor of Metalloproteinases-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:56.4
occ:1.00
 OD1 B:ASP198 2.3 50.2 1.0
O B:GLU200 2.3 45.1 1.0
O B:ASP198 2.3 44.0 1.0
OD2 B:ASP123 2.5 47.8 1.0
C B:ASP198 3.1 43.4 1.0
OD1 B:ASP123 3.1 55.7 1.0
CG B:ASP123 3.2 48.6 1.0
CG B:ASP198 3.2 49.3 1.0
C B:GLU200 3.5 43.0 1.0
CA B:ASP198 3.5 42.8 1.0
CB B:ASP198 3.8 45.5 1.0
OG1 B:THR121 4.0 51.5 1.0
OD2 B:ASP198 4.2 59.5 1.0
N B:GLU200 4.2 39.8 1.0
CD1 B:TRP202 4.2 43.5 1.0
N B:ASP199 4.2 43.1 1.0
CA B:LYS201 4.2 46.3 1.0
N B:LYS201 4.3 44.3 1.0
C B:ASP199 4.4 42.1 1.0
CA B:GLU200 4.5 40.2 1.0
CA B:ASP199 4.5 43.6 1.0
CB B:ASP123 4.6 52.1 1.0
NE1 B:TRP202 4.6 41.4 1.0
N B:TRP202 4.8 45.3 1.0
O B:ASP197 4.8 38.5 1.0
N B:ASP198 4.9 40.2 1.0
O B:HOH439 5.0 66.6 1.0
O B:ASP199 5.0 42.1 1.0

Reference:

J.Batra, J.Robinson, A.S.Soares, A.P.Fields, D.C.Radisky, E.S.Radisky. Matrix Metalloproteinase-10 (Mmp-10) Interaction with Tissue Inhibitors of Metalloproteinases Timp-1 and Timp-2: Binding Studies and Crystal Structure. J.Biol.Chem. V. 287 15935 2012.
ISSN: ISSN 0021-9258
PubMed: 22427646
DOI: 10.1074/JBC.M112.341156
Page generated: Sat Dec 12 04:34:03 2020

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