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Calcium in PDB 4h1q: Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.

Enzymatic activity of Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.

All present enzymatic activity of Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor., PDB code: 4h1q 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) 43.09 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.140, 48.660, 67.920, 90.00, 102.55, 90.00
R / Rfree (%) 17 / 21.1

Other elements in 4h1q:

The structure of Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. (pdb code 4h1q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor., PDB code: 4h1q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4h1q

Go back to Calcium Binding Sites List in 4h1q
Calcium binding site 1 out of 7 in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.


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 Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:10.6
occ:1.00
 O A:GLY197 2.3 12.4 1.0
O A:GLN199 2.3 10.7 1.0
OD1 A:ASP201 2.3 8.9 1.0
O A:HOH477 2.3 10.2 1.0
O A:ASP165 2.3 8.3 1.0
O A:HOH481 2.5 12.0 1.0
CG A:ASP201 3.3 11.3 1.0
C A:GLY197 3.5 13.5 1.0
C A:ASP165 3.5 9.8 1.0
C A:GLN199 3.5 9.0 1.0
OD2 A:ASP201 3.8 9.8 1.0
N A:ASP201 4.0 10.8 1.0
C A:ILE198 4.1 11.6 1.0
C A:GLY200 4.2 10.0 1.0
O A:ILE198 4.2 14.0 1.0
O A:ALA164 4.2 13.7 1.0
N A:GLN199 4.2 10.4 1.0
N A:GLY197 4.2 10.8 1.0
CA A:GLY200 4.2 11.1 1.0
O A:HOH424 4.3 19.6 1.0
CA A:GLY197 4.3 17.4 1.0
N A:GLY200 4.3 8.1 1.0
CA A:ASP165 4.4 7.6 1.0
O A:GLY195 4.4 9.9 1.0
O A:HOH426 4.4 23.9 1.0
N A:ILE198 4.4 14.3 1.0
N A:ILE166 4.5 8.8 1.0
CB A:ASP201 4.5 7.9 1.0
N A:VAL167 4.5 8.9 1.0
CA A:ILE198 4.5 14.9 1.0
CA A:GLN199 4.5 9.2 1.0
CA A:ILE166 4.6 7.4 1.0
CA A:ASP201 4.6 10.6 1.0
C A:PRO196 4.6 10.9 1.0
CH2 A:TRP116 4.8 10.7 1.0
O A:HOH493 4.8 13.2 1.0
CG2 A:VAL167 4.9 11.4 1.0
O A:GLY200 4.9 7.1 1.0
O A:PRO196 4.9 10.4 1.0

Calcium binding site 2 out of 7 in 4h1q

Go back to Calcium Binding Sites List in 4h1q
Calcium binding site 2 out of 7 in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.


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 Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:23.8
occ:1.00
 O A:GLU208 2.2 14.0 1.0
OD2 A:ASP131 2.3 13.1 1.0
OD1 A:ASP206 2.4 14.0 1.0
O A:ASP206 2.4 14.0 1.0
O A:HOH421 2.5 17.9 1.0
C A:ASP206 3.2 12.2 1.0
CG A:ASP131 3.3 15.8 1.0
CG A:ASP206 3.4 14.5 1.0
C A:GLU208 3.4 13.8 1.0
CA A:ASP206 3.6 11.1 1.0
OD1 A:ASP131 3.7 15.5 1.0
OG A:SER129 3.8 13.6 1.0
CD1 A:TRP210 3.9 8.9 1.0
CB A:ASP206 4.1 15.3 1.0
N A:GLU208 4.1 12.7 1.0
N A:LEU209 4.3 15.5 1.0
CA A:LEU209 4.3 14.0 1.0
N A:ASP207 4.3 14.4 1.0
OD2 A:ASP206 4.3 14.4 1.0
CA A:GLU208 4.4 11.6 1.0
C A:ASP207 4.4 14.5 1.0
O A:HOH483 4.4 17.4 1.0
N A:TRP210 4.5 10.3 1.0
NE1 A:TRP210 4.5 12.4 1.0
CB A:ASP131 4.6 10.1 1.0
CA A:ASP207 4.6 14.0 1.0
O A:ASP205 4.8 10.5 1.0
C A:LEU209 4.9 15.0 1.0
CG A:TRP210 4.9 11.9 1.0
CB A:SER129 4.9 8.8 1.0
N A:ASP206 5.0 11.8 1.0

Calcium binding site 3 out of 7 in 4h1q

Go back to Calcium Binding Sites List in 4h1q
Calcium binding site 3 out of 7 in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.


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 Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:14.9
occ:1.00
 OE2 A:GLU208 2.2 18.0 1.0
O A:LEU187 2.2 17.4 1.0
O A:GLY183 2.2 21.0 1.0
O A:ASP185 2.3 20.6 1.0
OD1 A:ASP182 2.3 18.0 1.0
OD2 A:ASP205 2.4 15.5 1.0
C A:LEU187 3.4 18.0 1.0
CD A:GLU208 3.4 15.0 1.0
C A:ASP185 3.4 21.2 1.0
CG A:ASP205 3.5 15.4 1.0
C A:GLY183 3.5 21.5 1.0
CG A:ASP182 3.5 21.3 1.0
N A:ASP185 3.8 20.0 1.0
N A:LEU187 3.9 14.4 1.0
C A:LYS184 4.0 27.5 1.0
OD2 A:ASP182 4.0 20.1 1.0
CA A:LEU187 4.1 12.1 1.0
CB A:ASP205 4.1 10.8 1.0
CA A:ASP185 4.2 23.1 1.0
N A:GLY183 4.2 16.6 1.0
C A:GLY186 4.2 17.2 1.0
OE1 A:GLU208 4.3 20.1 1.0
C A:ASP182 4.3 21.0 1.0
N A:ASP182 4.3 21.2 1.0
CG A:GLU208 4.3 13.9 1.0
O A:LYS184 4.4 30.3 1.0
N A:LYS184 4.4 18.1 1.0
OD1 A:ASP205 4.4 11.6 1.0
CA A:LYS184 4.4 22.2 1.0
CA A:GLY183 4.4 16.5 1.0
N A:GLY186 4.4 21.7 1.0
CB A:LEU187 4.5 20.8 1.0
N A:LEU188 4.5 12.0 1.0
CA A:GLY186 4.6 13.3 1.0
O A:ASP182 4.6 26.5 1.0
CA A:ASP182 4.6 19.8 1.0
CB A:ASP182 4.7 21.9 1.0
O A:GLY186 4.7 17.5 1.0
CA A:LEU188 4.7 8.6 1.0

Calcium binding site 4 out of 7 in 4h1q

Go back to Calcium Binding Sites List in 4h1q
Calcium binding site 4 out of 7 in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.


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 Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:29.6
occ:1.00
 O A:LEU154 2.2 11.6 1.0
O A:SER149 2.4 8.9 0.4
O A:SER149 2.4 8.8 0.6
O A:HOH496 2.5 25.3 1.0
O A:THR152 2.6 13.1 1.0
OG A:SER149 2.9 12.8 0.6
C A:SER149 3.2 12.0 0.4
C A:SER149 3.2 12.0 0.6
C A:LEU154 3.4 12.9 1.0
CB A:SER149 3.5 12.5 0.4
CA A:SER149 3.5 12.9 0.4
CA A:SER149 3.6 13.0 0.6
C A:THR152 3.7 8.3 1.0
CB A:SER149 3.8 10.7 0.6
C A:PRO153 3.9 18.7 1.0
N A:LEU154 3.9 13.3 1.0
O A:PRO153 4.0 18.4 1.0
CG2 A:THR152 4.1 18.9 1.0
CA A:LEU154 4.2 14.6 1.0
OG A:SER149 4.3 11.7 0.4
N A:THR155 4.3 11.5 1.0
CA A:PRO153 4.4 9.3 1.0
N A:ALA150 4.4 11.3 1.0
CA A:THR155 4.5 12.0 1.0
N A:PRO153 4.5 11.0 1.0
CG2 A:THR155 4.6 13.2 1.0
N A:THR152 4.7 14.5 1.0
CA A:THR152 4.7 17.3 1.0
N A:SER149 4.9 12.6 0.4
N A:SER149 5.0 12.6 0.6
CA A:ALA150 5.0 10.1 1.0

Calcium binding site 5 out of 7 in 4h1q

Go back to Calcium Binding Sites List in 4h1q
Calcium binding site 5 out of 7 in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.


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 Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:9.3
occ:1.00
 O B:GLY197 2.3 10.6 1.0
O B:HOH487 2.3 9.0 1.0
O B:ASP165 2.3 10.1 1.0
O B:GLN199 2.3 8.4 1.0
OD1 B:ASP201 2.3 8.3 1.0
O B:HOH489 2.4 10.4 1.0
CG B:ASP201 3.3 9.6 1.0
C B:GLY197 3.5 11.6 1.0
C B:ASP165 3.5 9.8 1.0
C B:GLN199 3.5 8.6 1.0
OD2 B:ASP201 3.8 9.9 1.0
N B:ASP201 4.1 8.9 1.0
C B:ILE198 4.1 9.6 1.0
O B:ILE198 4.2 11.5 1.0
O B:ALA164 4.2 12.9 1.0
C B:GLY200 4.2 7.9 1.0
CA B:GLY200 4.2 10.5 1.0
O B:HOH421 4.2 19.4 1.0
N B:GLY197 4.2 9.8 1.0
N B:GLN199 4.3 11.0 1.0
CA B:GLY197 4.3 12.8 1.0
CA B:ASP165 4.3 9.1 1.0
N B:GLY200 4.3 8.5 1.0
O B:GLY195 4.4 10.7 1.0
N B:ILE166 4.4 8.9 1.0
N B:ILE198 4.5 13.2 1.0
CB B:ASP201 4.5 8.4 1.0
N B:VAL167 4.5 10.7 1.0
CA B:GLN199 4.5 8.5 1.0
CA B:ILE198 4.6 13.8 1.0
CA B:ILE166 4.6 7.7 1.0
CA B:ASP201 4.6 8.4 1.0
O B:HOH560 4.6 28.6 1.0
C B:PRO196 4.6 10.4 1.0
CH2 B:TRP116 4.7 9.9 1.0
O B:HOH496 4.8 14.2 1.0
CG2 B:VAL167 4.9 11.8 1.0
O B:GLY200 4.9 9.7 1.0
O B:PRO196 5.0 9.6 1.0

Calcium binding site 6 out of 7 in 4h1q

Go back to Calcium Binding Sites List in 4h1q
Calcium binding site 6 out of 7 in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:14.0
occ:1.00
 O B:ASP206 2.3 12.1 1.0
O B:HOH518 2.3 15.3 1.0
OD1 B:ASP206 2.4 12.7 1.0
O B:GLU208 2.4 12.2 1.0
O B:HOH517 2.4 19.0 1.0
OD2 B:ASP131 2.5 13.3 1.0
OD1 B:ASP131 2.7 15.4 1.0
CG B:ASP131 2.9 18.9 1.0
C B:ASP206 3.3 11.8 1.0
CG B:ASP206 3.4 11.6 1.0
C B:GLU208 3.6 13.3 1.0
CA B:ASP206 3.8 10.4 1.0
OG B:SER129 4.0 12.9 1.0
CB B:ASP206 4.1 10.7 1.0
OD2 B:ASP206 4.2 14.2 1.0
CA B:LEU209 4.3 11.7 1.0
N B:ASP207 4.4 13.3 1.0
N B:LEU209 4.4 12.6 1.0
N B:GLU208 4.4 11.9 1.0
O B:HOH440 4.4 17.0 1.0
CB B:ASP131 4.4 11.0 1.0
CD1 B:TRP210 4.5 11.9 1.0
C B:ASP207 4.5 14.2 1.0
O B:HOH437 4.5 17.1 1.0
CA B:GLU208 4.6 10.5 1.0
CA B:ASP207 4.6 14.2 1.0
O B:HOH419 4.7 13.8 1.0
N B:TRP210 4.8 15.0 1.0
O B:HOH473 4.8 13.9 1.0

Calcium binding site 7 out of 7 in 4h1q

Go back to Calcium Binding Sites List in 4h1q
Calcium binding site 7 out of 7 in the Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Mutant Mmp-9 Catalytic Domain in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:11.7
occ:1.00
 O B:LEU187 2.3 12.5 1.0
OE2 B:GLU208 2.3 16.9 1.0
OD2 B:ASP205 2.3 12.7 1.0
O B:GLY183 2.3 16.5 1.0
O B:ASP185 2.4 16.4 1.0
OD1 B:ASP182 2.4 17.8 1.0
CG B:ASP205 3.4 14.2 1.0
C B:LEU187 3.4 15.6 1.0
C B:ASP185 3.5 19.2 1.0
CD B:GLU208 3.5 10.1 1.0
CG B:ASP182 3.5 15.4 1.0
C B:GLY183 3.6 19.6 1.0
N B:LEU187 3.8 12.7 1.0
N B:ASP185 3.9 21.0 1.0
OD2 B:ASP182 4.0 17.2 1.0
C B:LYS184 4.0 18.3 1.0
CA B:LEU187 4.1 14.8 1.0
CB B:ASP205 4.1 9.3 1.0
CA B:ASP185 4.2 27.1 1.0
N B:GLY183 4.2 17.7 1.0
C B:GLY186 4.2 13.3 1.0
N B:ASP182 4.3 16.4 1.0
OD1 B:ASP205 4.3 15.1 1.0
CG B:GLU208 4.3 13.5 1.0
C B:ASP182 4.4 15.5 1.0
OE1 B:GLU208 4.4 13.9 1.0
CB B:LEU187 4.4 20.2 1.0
CA B:LYS184 4.4 16.5 1.0
N B:LYS184 4.5 16.3 1.0
O B:LYS184 4.5 17.6 1.0
N B:LEU188 4.5 11.6 1.0
CA B:GLY183 4.5 13.2 1.0
N B:GLY186 4.5 20.5 1.0
CA B:ASP182 4.7 18.7 1.0
CB B:ASP182 4.7 16.2 1.0
CA B:GLY186 4.7 18.9 1.0
O B:GLY186 4.7 16.4 1.0
CA B:LEU188 4.7 10.7 1.0
O B:HOH498 4.8 32.8 1.0
O B:ASP182 4.8 19.4 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 07:33:13 2024

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