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Calcium 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:

Zinc (Zn) 4 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-2 (Timp-2) (pdb code 4ilw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4ilw

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Calcium binding site 1 out of 6 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 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-2 (Timp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:18.6
occ:1.00
 OE2 D:GLU200 2.2 17.9 1.0
O D:SER179 2.2 22.5 1.0
O D:GLY177 2.3 21.6 1.0
O D:GLY175 2.3 29.5 1.0
OD2 D:ASP174 2.4 23.5 1.0
OD2 D:ASP197 2.4 20.3 1.0
C D:SER179 3.4 21.8 1.0
CD D:GLU200 3.4 18.3 1.0
CG D:ASP197 3.4 22.1 1.0
C D:GLY177 3.5 20.7 1.0
C D:GLY175 3.5 22.4 1.0
CG D:ASP174 3.6 21.0 1.0
N D:SER179 3.8 22.5 1.0
N D:GLY177 4.0 23.0 1.0
CB D:ASP197 4.0 20.1 1.0
C D:PRO176 4.1 22.9 1.0
N D:GLY175 4.1 21.6 1.0
OE1 D:GLU200 4.1 21.4 1.0
CA D:SER179 4.2 21.3 0.5
CA D:SER179 4.2 23.8 0.5
CA D:GLY177 4.2 19.6 1.0
OD1 D:ASP174 4.2 18.4 1.0
N D:ASP174 4.3 23.1 1.0
OG D:SER179 4.3 29.6 0.5
C D:ASP174 4.3 24.0 1.0
C D:HIS178 4.3 23.5 1.0
N D:LEU180 4.3 20.1 1.0
N D:PRO176 4.4 21.5 1.0
CA D:GLY175 4.4 22.9 1.0
O D:PRO176 4.4 26.7 1.0
OD1 D:ASP197 4.4 21.6 1.0
CG D:GLU200 4.5 20.3 1.0
CA D:PRO176 4.5 20.9 1.0
N D:HIS178 4.5 21.4 1.0
CA D:LEU180 4.5 19.8 1.0
CB D:HIS178 4.6 25.5 1.0
CA D:ASP174 4.7 22.3 1.0
CA D:HIS178 4.7 24.2 1.0
CB D:ASP174 4.7 21.6 1.0
CB D:SER179 4.8 19.8 0.5
O D:ASP174 4.8 23.8 1.0
CB D:SER179 4.9 24.8 0.5
O D:HIS178 5.0 26.3 1.0

Calcium binding site 2 out of 6 in 4ilw

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Calcium binding site 2 out of 6 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 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-2 (Timp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:25.2
occ:1.00
 O D:ASP157 2.2 19.2 1.0
O D:GLY189 2.3 20.8 1.0
O D:HOH410 2.3 20.7 1.0
O D:TYR191 2.4 20.2 1.0
OD1 D:ASP193 2.4 20.6 1.0
CG D:ASP193 3.4 22.6 1.0
C D:ASP157 3.4 22.4 1.0
C D:GLY189 3.5 23.1 1.0
C D:TYR191 3.5 21.1 1.0
OD2 D:ASP193 3.9 21.2 1.0
C D:LEU190 4.1 27.9 1.0
O D:ALA156 4.1 27.3 1.0
N D:ASP193 4.1 20.5 1.0
O D:LEU190 4.2 21.7 1.0
CA D:ASP157 4.2 23.2 1.0
N D:TYR191 4.2 26.2 1.0
O D:HOH406 4.2 30.6 1.0
N D:GLY189 4.3 24.4 1.0
C D:GLY192 4.4 20.4 1.0
N D:ILE158 4.4 22.0 1.0
CA D:GLY189 4.4 25.5 1.0
CA D:GLY192 4.4 22.4 1.0
N D:GLY192 4.4 23.2 1.0
O D:GLY187 4.4 31.6 1.0
N D:LEU190 4.4 25.6 1.0
CA D:TYR191 4.5 23.3 1.0
CB D:ASP193 4.5 21.1 1.0
CA D:LEU190 4.6 26.9 1.0
N D:MET159 4.6 24.3 1.0
CA D:ILE158 4.6 23.9 1.0
O D:HOH439 4.6 41.1 1.0
CA D:ASP193 4.6 21.7 1.0
C D:PRO188 4.8 28.8 1.0
CG D:MET159 4.8 29.6 1.0
CH2 D:TRP108 4.9 27.6 1.0
OE1 D:GLU155 4.9 47.7 1.0

Calcium binding site 3 out of 6 in 4ilw

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Calcium binding site 3 out of 6 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 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-2 (Timp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca305

b:29.8
occ:1.00
 OD2 D:ASP123 2.2 27.5 1.0
O D:GLU200 2.3 23.1 1.0
O D:ASP198 2.4 22.2 1.0
OD1 D:ASP198 2.5 23.0 1.0
O D:HOH425 2.5 29.6 1.0
OD1 D:ASP123 2.7 26.6 1.0
CG D:ASP123 2.8 27.1 1.0
C D:ASP198 3.4 22.3 1.0
C D:GLU200 3.5 22.0 1.0
CG D:ASP198 3.5 23.0 1.0
OG1 D:THR121 3.8 31.2 1.0
CA D:ASP198 3.9 20.1 1.0
CA D:LYS201 4.1 24.4 1.0
CB D:ASP198 4.1 22.0 1.0
N D:LYS201 4.2 21.5 1.0
CD1 D:TRP202 4.3 21.7 1.0
CB D:ASP123 4.3 26.1 1.0
N D:GLU200 4.3 23.6 1.0
N D:TRP202 4.5 24.1 1.0
N D:ASP199 4.5 22.6 1.0
OD2 D:ASP198 4.5 25.5 1.0
C D:ASP199 4.6 24.4 1.0
CA D:GLU200 4.6 21.7 1.0
CA D:ASP199 4.7 23.0 1.0
NE1 D:TRP202 4.8 19.9 1.0
C D:LYS201 4.8 21.1 1.0

Calcium binding site 4 out of 6 in 4ilw

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Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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:Ca303

b:28.9
occ:1.00
 O F:GLY175 2.1 27.1 1.0
OE2 F:GLU200 2.2 27.2 1.0
O F:GLY177 2.3 30.9 1.0
O F:SER179 2.3 23.2 1.0
OD2 F:ASP174 2.4 32.4 1.0
OD2 F:ASP197 2.4 28.8 1.0
C F:GLY175 3.3 28.9 1.0
CG F:ASP197 3.4 26.7 1.0
CD F:GLU200 3.5 25.9 1.0
C F:GLY177 3.5 29.4 1.0
C F:SER179 3.5 27.6 1.0
CG F:ASP174 3.6 31.7 1.0
N F:GLY177 3.9 34.6 1.0
N F:SER179 3.9 27.6 1.0
C F:PRO176 3.9 34.1 1.0
N F:GLY175 4.0 29.0 1.0
CB F:ASP197 4.0 28.8 1.0
OE1 F:GLU200 4.1 26.6 1.0
CA F:GLY177 4.2 29.6 1.0
N F:PRO176 4.3 28.6 1.0
C F:ASP174 4.3 30.6 1.0
CA F:SER179 4.3 28.0 0.5
O F:PRO176 4.3 31.9 1.0
CA F:SER179 4.3 27.9 0.5
OD1 F:ASP174 4.3 24.1 1.0
CA F:GLY175 4.3 27.1 1.0
CA F:PRO176 4.3 28.5 1.0
N F:ASP174 4.4 33.1 1.0
C F:HIS178 4.4 29.7 1.0
OD1 F:ASP197 4.4 23.9 1.0
OG F:SER179 4.4 32.6 0.5
N F:LEU180 4.4 24.3 1.0
CG F:GLU200 4.5 28.6 1.0
N F:HIS178 4.5 28.4 1.0
CA F:LEU180 4.6 23.9 1.0
CB F:HIS178 4.6 31.3 1.0
CA F:ASP174 4.7 31.9 1.0
O F:ASP174 4.7 28.5 1.0
CB F:ASP174 4.7 30.6 1.0
CA F:HIS178 4.8 30.0 1.0
CB F:SER179 4.8 29.9 0.5
CB F:SER179 5.0 29.5 0.5

Calcium binding site 5 out of 6 in 4ilw

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Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca304

b:42.0
occ:1.00
 O F:ASP157 2.2 31.7 1.0
O F:GLY189 2.3 46.5 1.0
OD1 F:ASP193 2.3 28.0 1.0
O F:TYR191 2.4 41.4 1.0
CG F:ASP193 3.3 32.6 1.0
C F:ASP157 3.4 36.6 1.0
C F:GLY189 3.5 43.4 1.0
C F:TYR191 3.6 41.4 1.0
OD2 F:ASP193 3.8 35.1 1.0
C F:LEU190 4.0 47.2 1.0
O F:ALA156 4.1 42.4 1.0
N F:ASP193 4.1 31.1 1.0
O F:LEU190 4.1 41.9 1.0
CA F:ASP157 4.2 38.4 1.0
N F:TYR191 4.2 46.6 1.0
C F:GLY192 4.3 31.0 1.0
N F:ILE158 4.3 35.8 1.0
CA F:GLY192 4.4 36.9 1.0
CA F:GLY189 4.4 47.5 1.0
N F:GLY192 4.4 39.7 1.0
N F:LEU190 4.4 39.3 1.0
CB F:ASP193 4.4 31.0 1.0
N F:GLY189 4.5 49.6 1.0
N F:MET159 4.5 34.5 1.0
CA F:ILE158 4.5 37.7 1.0
CA F:TYR191 4.5 42.6 1.0
CA F:LEU190 4.5 42.9 1.0
O F:GLY187 4.6 50.8 1.0
CA F:ASP193 4.6 33.6 1.0
CG F:MET159 4.7 40.8 1.0
C F:PRO188 4.9 52.9 1.0
CH2 F:TRP108 5.0 50.9 1.0
O F:GLY192 5.0 31.8 1.0

Calcium binding site 6 out of 6 in 4ilw

Go back to Calcium Binding Sites List in 4ilw
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca305

b:31.3
occ:1.00
 O F:ASP198 2.3 23.0 1.0
O F:GLU200 2.3 31.7 1.0
OD2 F:ASP123 2.4 27.8 1.0
OD1 F:ASP198 2.5 31.4 1.0
OD1 F:ASP123 2.8 33.3 1.0
CG F:ASP123 3.0 32.0 1.0
C F:ASP198 3.3 27.1 1.0
C F:GLU200 3.5 26.8 1.0
CG F:ASP198 3.5 29.3 1.0
CA F:ASP198 3.8 26.9 1.0
OG1 F:THR121 3.9 33.9 1.0
CB F:ASP198 4.1 27.8 1.0
CA F:LYS201 4.2 29.8 1.0
N F:GLU200 4.3 28.4 1.0
N F:LYS201 4.3 27.9 1.0
O F:HOH422 4.3 47.3 1.0
N F:ASP199 4.3 26.3 1.0
CD1 F:TRP202 4.4 31.8 1.0
C F:ASP199 4.5 28.9 1.0
CB F:ASP123 4.5 35.8 1.0
OD2 F:ASP198 4.5 33.1 1.0
CA F:ASP199 4.6 27.9 1.0
N F:TRP202 4.6 32.8 1.0
CA F:GLU200 4.6 26.5 1.0
C F:LYS201 4.9 32.3 1.0
NE1 F:TRP202 5.0 27.8 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 Jul 14 08:15:48 2024

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