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Calcium in PDB 4h2e: Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains

Enzymatic activity of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains

All present enzymatic activity of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains, PDB code: 4h2e was solved by E.A.Stura, L.Vera, E.Cassar-Lajeunesse, E.Nuti, M.P.Catalani, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.85 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.180, 97.400, 45.690, 90.00, 111.99, 90.00
R / Rfree (%) 27.7 / 31.1

Other elements in 4h2e:

The structure of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains (pdb code 4h2e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains, PDB code: 4h2e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4h2e

Go back to Calcium Binding Sites List in 4h2e
Calcium binding site 1 out of 5 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:15.0
occ:1.00
 O A:GLN199 2.5 24.0 1.0
O A:GLY197 2.6 16.1 1.0
O A:ASP165 2.6 21.0 1.0
OD1 A:ASP201 2.7 0.0 1.0
CG A:ASP201 3.6 0.2 1.0
C A:GLY197 3.6 15.9 1.0
C A:ASP165 3.6 21.0 1.0
C A:GLN199 3.7 22.6 1.0
O A:GLY195 3.7 17.0 1.0
OD2 A:ASP201 3.9 14.9 1.0
N A:GLY197 4.0 14.3 1.0
O A:ALA164 4.0 14.6 1.0
CA A:GLY197 4.3 14.6 1.0
CA A:ASP165 4.3 20.7 1.0
CH2 A:TRP116 4.3 13.1 1.0
N A:GLN199 4.4 22.8 1.0
C A:PRO196 4.4 7.1 1.0
C A:ILE198 4.5 15.9 1.0
N A:ASP201 4.5 0.2 1.0
N A:GLY200 4.5 11.8 1.0
CA A:GLY200 4.6 11.7 1.0
N A:ILE166 4.6 8.3 1.0
C A:GLY200 4.6 12.0 1.0
CA A:GLN199 4.6 22.8 1.0
N A:ILE198 4.6 15.4 1.0
O A:ILE198 4.7 15.4 1.0
CA A:ILE166 4.7 8.1 1.0
CB A:ASP201 4.8 0.3 1.0
O A:PRO196 4.8 7.6 1.0
C A:GLY195 4.9 16.9 1.0
CA A:ILE198 4.9 15.9 1.0
CA A:PRO196 5.0 7.6 1.0

Calcium binding site 2 out of 5 in 4h2e

Go back to Calcium Binding Sites List in 4h2e
Calcium binding site 2 out of 5 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:21.4
occ:1.00
 O A:GLY183 2.1 12.7 1.0
O A:LEU187 2.2 23.2 1.0
OD2 A:ASP205 2.3 12.4 1.0
O A:ASP185 2.4 24.7 1.0
OE2 A:GLU208 2.5 30.0 1.0
OD2 A:ASP182 2.5 26.0 1.0
C A:GLY183 3.3 13.0 1.0
CG A:ASP182 3.3 25.8 1.0
C A:LEU187 3.4 23.7 1.0
CG A:ASP205 3.4 12.7 1.0
C A:ASP185 3.6 25.1 1.0
CD A:GLU208 3.6 29.0 1.0
N A:GLY183 3.7 14.1 1.0
OD1 A:ASP182 3.7 27.1 1.0
N A:ASP185 3.9 23.7 1.0
CB A:ASP205 4.0 13.2 1.0
N A:ASP182 4.1 22.5 1.0
N A:LEU187 4.1 25.6 1.0
CA A:GLY183 4.1 13.9 1.0
C A:LYS184 4.1 14.5 1.0
C A:ASP182 4.2 22.3 1.0
CA A:LEU187 4.2 26.1 1.0
CA A:ASP185 4.3 25.1 1.0
N A:LYS184 4.3 14.2 1.0
CA A:ASP182 4.4 23.0 1.0
N A:LEU188 4.4 20.0 1.0
CG A:GLU208 4.4 28.8 1.0
CB A:ASP182 4.4 23.7 1.0
OD1 A:ASP205 4.5 12.0 1.0
C A:GLY186 4.5 34.4 1.0
CA A:LYS184 4.5 14.5 1.0
OE1 A:GLU208 4.5 28.2 1.0
O A:LYS184 4.5 15.1 1.0
CA A:LEU188 4.6 19.6 1.0
N A:GLY186 4.6 35.1 1.0
CB A:LEU187 4.7 24.9 1.0
CA A:GLY186 4.9 34.2 1.0
O A:ASP182 4.9 21.9 1.0
CB A:PHE181 4.9 26.7 1.0

Calcium binding site 3 out of 5 in 4h2e

Go back to Calcium Binding Sites List in 4h2e
Calcium binding site 3 out of 5 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:13.6
occ:1.00
 O B:GLY197 2.4 5.3 1.0
OD1 B:ASP201 2.5 4.0 1.0
O B:GLN199 2.7 19.4 1.0
O B:ASP165 2.7 20.6 1.0
CG B:ASP201 3.3 4.4 1.0
C B:ASP165 3.6 21.2 1.0
C B:GLY197 3.6 5.2 1.0
OD2 B:ASP201 3.6 3.1 1.0
O B:ALA164 3.7 16.2 1.0
C B:GLN199 3.8 18.9 1.0
O B:GLY195 4.1 7.1 1.0
CA B:ASP165 4.2 20.8 1.0
N B:GLY197 4.3 4.2 1.0
N B:GLN199 4.3 18.5 1.0
CA B:GLY197 4.4 4.3 1.0
C B:ILE198 4.4 0.9 1.0
N B:ILE166 4.5 12.6 1.0
N B:ASP201 4.5 4.3 1.0
N B:ILE198 4.6 0.1 1.0
C B:GLY200 4.6 5.3 1.0
CB B:ASP201 4.6 4.3 1.0
O B:ILE198 4.6 0.7 1.0
N B:GLY200 4.7 5.1 1.0
CA B:GLN199 4.7 18.8 1.0
C B:ALA164 4.7 15.3 1.0
CA B:GLY200 4.7 5.4 1.0
CA B:ILE166 4.7 12.4 1.0
C B:PRO196 4.7 9.2 1.0
CA B:ILE198 4.8 0.3 1.0
N B:VAL167 4.8 14.3 1.0
CG2 B:VAL167 4.8 14.7 1.0
CH2 B:TRP116 4.9 20.1 1.0
N B:ASP165 4.9 20.9 1.0
CA B:ASP201 4.9 4.1 1.0

Calcium binding site 4 out of 5 in 4h2e

Go back to Calcium Binding Sites List in 4h2e
Calcium binding site 4 out of 5 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:25.2
occ:1.00
 O B:LEU187 2.2 24.1 1.0
O B:GLY183 2.3 17.8 1.0
OD2 B:ASP205 2.3 10.1 1.0
O B:ASP185 2.4 23.2 1.0
OE2 B:GLU208 2.7 15.8 1.0
OD2 B:ASP182 3.2 26.9 1.0
OD1 B:ASP182 3.3 27.8 1.0
C B:LEU187 3.4 24.6 1.0
CG B:ASP182 3.4 26.1 1.0
C B:GLY183 3.4 17.8 1.0
CG B:ASP205 3.5 10.4 1.0
C B:ASP185 3.6 23.9 1.0
CD B:GLU208 3.7 15.1 1.0
N B:GLY183 3.7 19.7 1.0
N B:LEU187 4.0 25.6 1.0
N B:ASP182 4.0 23.4 1.0
CG B:GLU208 4.0 14.5 1.0
N B:ASP185 4.0 22.0 1.0
CA B:GLY183 4.1 18.0 1.0
CA B:LEU187 4.2 25.5 1.0
C B:ASP182 4.2 23.7 1.0
C B:LYS184 4.2 9.2 1.0
CB B:ASP205 4.2 11.6 1.0
C B:GLY186 4.3 13.4 1.0
CA B:ASP185 4.4 24.1 1.0
N B:LEU188 4.4 6.6 1.0
CA B:ASP182 4.4 23.5 1.0
N B:LYS184 4.4 8.4 1.0
CB B:ASP182 4.4 24.9 1.0
OD1 B:ASP205 4.5 9.9 1.0
O B:LYS184 4.5 9.3 1.0
N B:GLY186 4.5 14.1 1.0
CA B:LEU188 4.6 5.8 1.0
CB B:LEU187 4.6 25.6 1.0
CB B:PHE181 4.6 23.6 1.0
CA B:LYS184 4.6 9.0 1.0
CA B:GLY186 4.7 14.1 1.0
OE1 B:GLU208 4.8 14.4 1.0
O B:ASP182 4.8 22.9 1.0
O B:GLY186 4.9 14.8 1.0
C B:PHE181 4.9 22.1 1.0

Calcium binding site 5 out of 5 in 4h2e

Go back to Calcium Binding Sites List in 4h2e
Calcium binding site 5 out of 5 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:51.9
occ:1.00
 O B:GLU208 2.4 15.9 1.0
OD1 B:ASP206 2.6 22.3 1.0
O B:ASP206 2.6 26.2 1.0
OD2 B:ASP131 2.9 25.2 1.0
OG B:SER129 3.1 19.4 1.0
CG B:ASP131 3.2 24.2 1.0
OD1 B:ASP131 3.3 25.6 1.0
C B:ASP206 3.3 23.9 1.0
C B:GLU208 3.6 16.0 1.0
CD1 B:TRP210 3.6 13.2 1.0
CA B:ASP206 3.6 22.8 1.0
CG B:ASP206 3.6 23.3 1.0
CB B:ASP206 4.2 22.5 1.0
CA B:LEU209 4.3 24.2 1.0
NE1 B:TRP210 4.3 13.0 1.0
N B:TRP210 4.3 16.3 1.0
N B:LEU209 4.4 23.8 1.0
CB B:ASP131 4.4 22.7 1.0
CB B:SER129 4.5 17.5 1.0
N B:ASP207 4.5 16.8 1.0
N B:GLU208 4.5 14.8 1.0
CG B:TRP210 4.5 13.7 1.0
O B:ASP205 4.6 11.6 1.0
C B:ASP207 4.6 18.1 1.0
CA B:GLU208 4.6 15.1 1.0
C B:LEU209 4.7 23.1 1.0
OD2 B:ASP206 4.7 24.8 1.0
N B:ASP206 4.9 21.6 1.0
CB B:TRP210 4.9 15.1 1.0
CA B:ASP207 4.9 17.6 1.0

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sun Jul 14 07:36:00 2024

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