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Calcium in PDB 5h0u: Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase

Enzymatic activity of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase:
3.4.24.80;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase, PDB code: 5h0u was solved by H.Ogata, E.Decaneto, W.Lubitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.54 / 2.24
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.995, 62.995, 122.620, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 25.4

Other elements in 5h0u:

The structure of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase (pdb code 5h0u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase, PDB code: 5h0u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5h0u

Go back to Calcium Binding Sites List in 5h0u
Calcium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:30.2
occ:1.00
O A:ASP176 2.3 29.6 1.0
O A:ASN208 2.3 28.6 1.0
O A:GLY210 2.3 26.9 1.0
O A:HOH429 2.4 28.6 1.0
OD1 A:ASP212 2.5 28.7 1.0
O A:HOH433 2.5 29.0 1.0
CG A:ASP212 3.4 30.1 1.0
C A:ASP176 3.5 30.7 1.0
C A:ASN208 3.5 34.0 1.0
C A:GLY210 3.5 29.2 1.0
C A:ILE209 3.9 34.3 1.0
OD2 A:ASP212 3.9 27.0 1.0
N A:GLY210 3.9 34.0 1.0
O A:ILE209 4.1 30.7 1.0
N A:ASP212 4.2 29.9 1.0
CA A:ASP176 4.2 34.6 1.0
O A:ALA175 4.2 30.5 1.0
CA A:GLY210 4.3 30.1 1.0
N A:ILE209 4.4 32.8 1.0
CA A:ILE209 4.4 34.5 1.0
CA A:ASN208 4.4 31.6 1.0
N A:ILE177 4.4 27.6 1.0
O A:GLY206 4.5 33.5 1.0
N A:ASN208 4.5 31.5 1.0
N A:GLY211 4.5 28.7 1.0
CB A:ASP212 4.6 28.5 1.0
O1 A:GOL308 4.7 41.4 0.8
CA A:GLY211 4.7 28.8 1.0
CA A:ILE177 4.7 29.4 1.0
N A:MET178 4.7 32.5 1.0
C A:GLY211 4.7 29.7 1.0
C A:PRO207 4.8 35.1 1.0
CA A:ASP212 4.8 28.7 1.0
O A:HOH434 4.8 37.6 0.9
CH2 A:TRP119 4.9 35.6 1.0
O A:PRO207 4.9 35.8 1.0
CG A:MET178 5.0 31.1 1.0

Calcium binding site 2 out of 2 in 5h0u

Go back to Calcium Binding Sites List in 5h0u
Calcium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:36.0
occ:1.00
OE2 A:GLU219 2.2 31.8 1.0
OD1 A:ASP193 2.3 36.0 1.0
O A:PHE198 2.3 31.4 1.0
O A:GLY196 2.4 37.0 1.0
O A:GLY194 2.4 40.3 1.0
OD2 A:ASP216 2.5 36.0 1.0
CG A:ASP216 3.4 35.6 1.0
CD A:GLU219 3.4 36.5 1.0
C A:PHE198 3.4 33.2 1.0
CG A:ASP193 3.5 36.7 1.0
C A:GLY196 3.6 37.0 1.0
C A:GLY194 3.6 37.8 1.0
N A:PHE198 3.9 37.8 1.0
CB A:ASP216 3.9 33.6 1.0
N A:GLY196 4.0 33.8 1.0
OD2 A:ASP193 4.1 37.4 1.0
C A:GLU195 4.1 40.0 1.0
OE1 A:GLU219 4.1 35.9 1.0
CA A:PHE198 4.2 37.7 1.0
C A:ASP193 4.2 37.8 1.0
C A:GLY197 4.2 35.0 1.0
N A:ASP193 4.3 40.3 1.0
O A:ASP193 4.3 41.9 1.0
N A:GLY194 4.4 37.4 1.0
OD1 A:ASP216 4.4 35.0 1.0
N A:LEU199 4.4 30.9 1.0
CA A:GLY196 4.4 34.7 1.0
CA A:GLU195 4.4 41.1 1.0
CG A:GLU219 4.5 34.9 1.0
N A:GLU195 4.5 36.9 1.0
CA A:LEU199 4.5 30.1 1.0
N A:GLY197 4.5 39.2 1.0
O A:GLU195 4.5 39.1 1.0
CA A:GLY197 4.6 36.1 1.0
CA A:GLY194 4.6 37.5 1.0
CA A:ASP193 4.6 38.8 1.0
CB A:ASP193 4.7 35.0 1.0
O A:GLY197 4.8 36.5 1.0
CB A:PHE198 4.8 35.5 1.0

Reference:

E.Decaneto, T.Vasilevskaya, Y.Kutin, H.Ogata, M.Grossman, I.Sagi, M.Havenith, W.Lubitz, W.Thiel, N.Cox. Solvent Water Interactions Within the Active Site of the Membrane Type I Matrix Metalloproteinase. Phys Chem Chem Phys V. 19 30316 2017.
ISSN: ESSN 1463-9084
PubMed: 28951896
DOI: 10.1039/C7CP05572B
Page generated: Sat Dec 12 05:27:39 2020

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