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Calcium in PDB 3ma2: Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)

Enzymatic activity of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)

All present enzymatic activity of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1):
3.4.24.80;

Protein crystallography data

The structure of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1), PDB code: 3ma2 was solved by M.Grossman, D.Tworowski, O.Dym, M.-H.Lee, Y.Levy, I.Sagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.690, 63.649, 87.158, 90.00, 105.86, 90.00
R / Rfree (%) 19.6 / 24.7

Other elements in 3ma2:

The structure of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) (pdb code 3ma2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1), PDB code: 3ma2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3ma2

Go back to Calcium Binding Sites List in 3ma2
Calcium binding site 1 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-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 Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca293

b:17.2
occ:1.00
O D:ASP176 2.2 17.5 1.0
O D:GLY210 2.3 17.6 1.0
O D:ASN208 2.3 16.9 1.0
OD1 D:ASP212 2.4 13.7 1.0
O D:HOH23 2.4 16.5 1.0
O D:HOH26 2.5 16.9 1.0
C D:ASP176 3.4 16.2 1.0
CG D:ASP212 3.4 16.9 1.0
C D:GLY210 3.5 17.0 1.0
C D:ASN208 3.6 18.1 1.0
OD2 D:ASP212 3.8 11.7 1.0
C D:ILE209 4.1 18.6 1.0
N D:ASP212 4.1 14.4 1.0
O D:ILE209 4.1 20.5 1.0
O D:ALA175 4.2 15.5 1.0
N D:GLY210 4.2 17.2 1.0
CA D:ASP176 4.2 17.1 1.0
N D:ILE177 4.3 17.1 1.0
O D:HOH313 4.4 18.8 1.0
CA D:ASN208 4.4 19.0 1.0
N D:GLY211 4.4 15.6 1.0
CA D:GLY211 4.4 13.8 1.0
O D:GLY206 4.4 22.5 1.0
C D:GLY211 4.4 15.7 1.0
CA D:GLY210 4.5 17.2 1.0
N D:ASN208 4.5 20.6 1.0
N D:ILE209 4.5 18.4 1.0
CA D:ILE209 4.5 19.1 1.0
CH2 D:TRP119 4.6 21.3 1.0
CB D:ASP212 4.6 15.0 1.0
CA D:ILE177 4.6 14.7 1.0
O D:HOH47 4.6 19.0 1.0
CA D:ASP212 4.7 15.3 1.0
N D:MET178 4.8 13.9 1.0
O D:HOH65 4.8 22.6 1.0
C D:PRO207 4.9 21.4 1.0

Calcium binding site 2 out of 4 in 3ma2

Go back to Calcium Binding Sites List in 3ma2
Calcium binding site 2 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-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 Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca296

b:19.3
occ:1.00
OE2 D:GLU219 2.3 15.6 1.0
O D:GLY196 2.3 23.2 1.0
OD2 D:ASP216 2.3 18.2 1.0
O D:GLY194 2.3 19.3 1.0
OD1 D:ASP193 2.4 18.2 1.0
O D:PHE198 2.4 12.7 1.0
CG D:ASP216 3.3 15.5 1.0
CD D:GLU219 3.4 23.6 1.0
CG D:ASP193 3.5 20.7 1.0
C D:PHE198 3.5 15.3 1.0
C D:GLY194 3.5 18.4 1.0
C D:GLY196 3.6 21.6 1.0
CB D:ASP216 3.9 14.8 1.0
N D:GLY196 3.9 18.2 1.0
OD2 D:ASP193 3.9 15.1 1.0
N D:GLY194 4.0 17.6 1.0
OE1 D:GLU219 4.1 20.3 1.0
N D:PHE198 4.1 19.2 1.0
C D:GLU195 4.2 19.2 1.0
N D:ASP193 4.2 17.6 1.0
OD1 D:ASP216 4.3 16.6 1.0
C D:ASP193 4.3 18.6 1.0
N D:LEU199 4.3 14.4 1.0
CA D:LEU199 4.4 14.8 1.0
CA D:GLY194 4.4 18.1 1.0
CA D:PHE198 4.4 17.7 1.0
CA D:GLU195 4.4 17.9 1.0
CA D:GLY196 4.4 19.6 1.0
N D:GLU195 4.5 17.6 1.0
C D:GLY197 4.5 19.9 1.0
N D:GLY197 4.5 20.0 1.0
CG D:GLU219 4.5 15.5 1.0
CB D:ASP193 4.7 18.5 1.0
CA D:ASP193 4.7 19.8 1.0
O D:GLU195 4.7 16.1 1.0
O D:ASP193 4.7 13.2 1.0
CA D:GLY197 4.7 20.7 1.0
CD2 D:LEU199 4.9 17.7 1.0

Calcium binding site 3 out of 4 in 3ma2

Go back to Calcium Binding Sites List in 3ma2
Calcium binding site 3 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-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 Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca293

b:21.8
occ:1.00
O A:ASN208 2.3 19.1 1.0
O A:HOH312 2.3 26.9 1.0
O A:GLY210 2.3 19.3 1.0
OD1 A:ASP212 2.4 19.4 1.0
O A:ASP176 2.4 20.0 1.0
O A:HOH64 2.4 24.9 1.0
CG A:ASP212 3.3 17.9 1.0
C A:ASN208 3.5 21.6 1.0
C A:ASP176 3.5 21.9 1.0
C A:GLY210 3.5 22.1 1.0
OD2 A:ASP212 3.8 17.8 1.0
C A:ILE209 4.0 20.5 1.0
N A:GLY210 4.1 22.0 1.0
O A:ILE209 4.1 21.2 1.0
O A:ALA175 4.2 20.3 1.0
N A:ASP212 4.2 18.6 1.0
CA A:ASP176 4.3 21.4 1.0
O A:HOH298 4.3 18.4 1.0
N A:ILE209 4.3 19.6 1.0
CA A:ASN208 4.4 23.0 1.0
CA A:GLY210 4.4 21.5 1.0
CA A:ILE209 4.4 21.0 1.0
N A:GLY211 4.4 21.9 1.0
N A:ILE177 4.5 19.4 1.0
CA A:GLY211 4.5 20.5 1.0
CB A:ASP212 4.5 17.4 1.0
N A:ASN208 4.6 24.0 1.0
C A:GLY211 4.6 19.9 1.0
O A:GLY206 4.6 27.9 1.0
N A:MET178 4.6 18.8 1.0
CA A:ILE177 4.7 18.8 1.0
CA A:ASP212 4.7 17.4 1.0
CH2 A:TRP119 4.8 23.9 1.0
C A:PRO207 4.8 25.3 1.0
CG A:MET178 4.9 19.9 1.0

Calcium binding site 4 out of 4 in 3ma2

Go back to Calcium Binding Sites List in 3ma2
Calcium binding site 4 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca296

b:21.1
occ:1.00
OE2 A:GLU219 2.3 18.8 1.0
O A:PHE198 2.3 17.8 1.0
OD2 A:ASP216 2.3 18.1 1.0
OD1 A:ASP193 2.3 21.0 1.0
O A:GLY194 2.4 22.8 1.0
O A:GLY196 2.4 22.4 1.0
CG A:ASP216 3.3 17.9 1.0
CD A:GLU219 3.4 25.9 1.0
C A:PHE198 3.5 17.0 1.0
CG A:ASP193 3.5 24.3 1.0
C A:GLY194 3.6 23.6 1.0
C A:GLY196 3.6 22.4 1.0
CB A:ASP216 3.9 19.3 1.0
N A:GLY196 4.0 22.4 1.0
OE1 A:GLU219 4.0 19.7 1.0
OD2 A:ASP193 4.0 19.4 1.0
N A:PHE198 4.0 16.8 1.0
N A:GLY194 4.1 24.7 1.0
CA A:LEU199 4.2 17.5 1.0
C A:GLU195 4.2 23.2 1.0
N A:LEU199 4.3 16.8 1.0
OD1 A:ASP216 4.3 18.6 1.0
N A:ASP193 4.3 22.9 1.0
C A:ASP193 4.3 24.2 1.0
CA A:GLY196 4.4 20.4 1.0
CA A:PHE198 4.4 18.5 1.0
C A:GLY197 4.5 19.0 1.0
CA A:GLY194 4.5 22.7 1.0
CA A:GLU195 4.5 23.0 1.0
N A:GLU195 4.5 23.9 1.0
N A:GLY197 4.6 21.2 1.0
CG A:GLU219 4.6 18.3 1.0
CA A:GLY197 4.6 21.0 1.0
CA A:ASP193 4.7 24.0 1.0
CB A:ASP193 4.7 25.2 1.0
CD2 A:LEU199 4.8 22.2 1.0
O A:ASP193 4.8 21.6 1.0
O A:GLU195 4.8 20.7 1.0
C A:LEU199 5.0 18.1 1.0

Reference:

M.Grossman, D.Tworowski, O.Dym, M.H.Lee, Y.Levy, G.Murphy, I.Sagi. The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor Timp-1 Controls Its Binding Interface and Affects Its Function. Biochemistry V. 49 6184 2010.
ISSN: ISSN 0006-2960
PubMed: 20545310
DOI: 10.1021/BI902141X
Page generated: Sat Dec 12 04:20:36 2020

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