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Calcium in PDB 4hma: Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain

Enzymatic activity of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain

All present enzymatic activity of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4hma was solved by E.A.Stura, C.Antoni, L.Vera, E.Nuti, L.Carafa, E.Cassar-Lajeunesse, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.72 / 1.94
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.870, 98.240, 47.440, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 28.3

Other elements in 4hma:

The structure of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain 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 Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain (pdb code 4hma). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4hma:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 1 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


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 Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:30.1
occ:1.00
 O A:HOH446 2.2 23.4 1.0
O A:ASP165 2.3 23.9 1.0
OD1 A:ASP201 2.3 23.5 1.0
O A:HOH445 2.3 24.9 1.0
O A:GLY197 2.3 33.4 1.0
O A:GLN199 2.4 30.6 0.5
O A:GLN199 2.5 30.3 0.5
CG A:ASP201 3.4 29.0 1.0
C A:ASP165 3.4 24.1 1.0
C A:GLY197 3.6 34.3 1.0
C A:GLN199 3.6 30.6 0.5
C A:GLN199 3.6 30.3 0.5
O A:HOH460 3.8 41.5 1.0
OD2 A:ASP201 3.9 32.3 1.0
O A:ILE198 4.0 32.5 1.0
C A:ILE198 4.1 32.1 1.0
O A:ALA164 4.1 25.9 1.0
N A:ASP201 4.1 26.3 1.0
CA A:ASP165 4.2 24.8 1.0
N A:GLY197 4.3 33.2 1.0
C A:GLY200 4.3 28.8 1.0
CA A:GLY200 4.3 29.1 1.0
N A:ILE166 4.3 23.5 1.0
N A:GLY200 4.4 30.5 1.0
N A:GLN199 4.4 30.9 0.5
N A:GLN199 4.4 31.2 0.5
O A:GLY195 4.4 30.1 1.0
CA A:GLY197 4.4 33.1 1.0
CA A:ILE166 4.5 23.6 1.0
N A:ILE198 4.5 33.6 1.0
CB A:ASP201 4.5 25.9 1.0
CA A:GLN199 4.6 31.3 0.5
CA A:GLN199 4.6 30.8 0.5
N A:VAL167 4.6 23.4 1.0
O A:HOH447 4.6 34.1 1.0
CA A:ILE198 4.6 33.4 1.0
CA A:ASP201 4.7 26.1 1.0
CH2 A:TRP116 4.7 27.7 1.0
C A:PRO196 4.8 33.5 1.0
O A:GLY200 4.9 28.7 1.0

Calcium binding site 2 out of 6 in 4hma

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Calcium binding site 2 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


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 Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:34.1
occ:1.00
 OE1 A:GLU208 2.2 41.7 1.0
OD2 A:ASP182 2.3 42.2 1.0
O A:LEU187 2.4 32.3 1.0
O A:GLY183 2.4 43.3 1.0
O A:ASP185 2.4 39.5 1.0
OD2 A:ASP205 2.4 31.7 1.0
CD A:GLU208 3.4 36.2 1.0
C A:ASP185 3.5 40.7 1.0
C A:LEU187 3.5 31.2 1.0
CG A:ASP182 3.5 41.4 1.0
CG A:ASP205 3.6 31.3 1.0
C A:GLY183 3.6 42.4 1.0
N A:LEU187 3.7 32.6 1.0
N A:ASP185 3.9 42.6 1.0
CA A:LEU187 4.0 32.3 1.0
OD1 A:ASP182 4.1 33.0 1.0
C A:GLY186 4.1 34.5 1.0
N A:ASP182 4.2 41.9 1.0
C A:LYS184 4.2 43.4 1.0
CB A:ASP205 4.2 30.1 1.0
CG A:GLU208 4.2 32.5 1.0
CA A:ASP185 4.3 42.2 1.0
C A:ASP182 4.3 41.4 1.0
OE2 A:GLU208 4.3 37.6 1.0
CB A:LEU187 4.3 32.5 1.0
N A:GLY183 4.4 41.5 1.0
N A:GLY186 4.4 38.3 1.0
OD1 A:ASP205 4.4 26.1 1.0
N A:LYS184 4.5 41.8 1.0
CA A:LYS184 4.5 43.3 1.0
CA A:GLY186 4.6 36.6 1.0
N A:LEU188 4.6 28.1 1.0
O A:ASP182 4.6 40.9 1.0
CA A:ASP182 4.6 41.5 1.0
CA A:GLY183 4.6 40.9 1.0
CB A:ASP182 4.7 41.3 1.0
O A:GLY186 4.7 34.2 1.0
CA A:LEU188 4.7 26.7 1.0
O A:LYS184 4.8 44.7 1.0

Calcium binding site 3 out of 6 in 4hma

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Calcium binding site 3 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


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 Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:55.1
occ:1.00
 O A:GLU208 2.2 34.2 1.0
OD1 A:ASP131 2.2 41.2 1.0
OD1 A:ASP206 2.5 34.1 1.0
O A:ASP206 2.5 33.8 1.0
CG A:ASP131 3.1 38.8 1.0
C A:GLU208 3.4 33.8 1.0
C A:ASP206 3.4 33.3 1.0
OD2 A:ASP131 3.4 41.7 1.0
CG A:ASP206 3.5 36.3 1.0
CA A:ASP206 3.8 33.1 1.0
CD1 A:TRP210 3.9 25.5 1.0
OG A:SER129 3.9 30.8 1.0
N A:GLU208 4.1 33.9 1.0
CA A:LEU209 4.1 35.2 1.0
N A:LEU209 4.2 34.1 1.0
CB A:ASP206 4.2 33.3 1.0
CA A:GLU208 4.3 33.0 1.0
N A:TRP210 4.3 34.3 1.0
N A:ASP207 4.4 34.2 1.0
C A:ASP207 4.4 34.5 1.0
O A:HOH509 4.4 41.1 1.0
OD2 A:ASP206 4.5 37.5 1.0
NE1 A:TRP210 4.5 28.0 1.0
CB A:ASP131 4.5 36.4 1.0
CA A:ASP207 4.7 33.5 1.0
C A:LEU209 4.8 34.6 1.0
CG A:TRP210 4.9 28.5 1.0
CB A:SER129 5.0 35.8 1.0
O A:ASP205 5.0 30.6 1.0

Calcium binding site 4 out of 6 in 4hma

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Calcium binding site 4 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


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 Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:29.6
occ:1.00
 O B:GLN199 2.3 24.8 1.0
O B:ASP165 2.3 23.2 1.0
O B:HOH612 2.4 25.2 1.0
O B:HOH611 2.4 27.1 1.0
OD1 B:ASP201 2.4 25.5 1.0
O B:GLY197 2.4 28.9 1.0
CG B:ASP201 3.4 29.0 1.0
C B:ASP165 3.4 22.6 1.0
C B:GLN199 3.5 26.9 1.0
C B:GLY197 3.6 29.0 1.0
OD2 B:ASP201 3.9 30.9 1.0
N B:ASP201 4.1 26.6 1.0
O B:HOH652 4.1 33.7 1.0
O B:ALA164 4.2 26.5 1.0
CA B:GLY200 4.2 26.8 1.0
N B:GLY197 4.2 28.2 1.0
O B:GLY195 4.2 26.5 1.0
C B:ILE198 4.2 29.3 1.0
C B:GLY200 4.2 26.6 1.0
N B:GLN199 4.3 27.6 1.0
CA B:ASP165 4.3 24.6 1.0
N B:GLY200 4.3 27.0 1.0
CA B:GLY197 4.3 28.2 1.0
O B:ILE198 4.4 29.9 1.0
N B:ILE166 4.4 23.0 1.0
CA B:GLN199 4.5 27.5 1.0
CA B:ILE166 4.6 23.4 1.0
N B:ILE198 4.6 29.6 1.0
CB B:ASP201 4.6 26.0 1.0
CA B:ASP201 4.7 25.1 1.0
O B:HOH668 4.7 39.8 1.0
N B:VAL167 4.7 24.8 1.0
C B:PRO196 4.7 28.3 1.0
CH2 B:TRP116 4.8 23.1 1.0
CA B:ILE198 4.8 30.1 1.0
O B:GLY200 5.0 26.3 1.0

Calcium binding site 5 out of 6 in 4hma

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Calcium binding site 5 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


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 Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:29.5
occ:1.00
 OE1 B:GLU208 2.1 29.8 1.0
OD2 B:ASP205 2.2 28.5 1.0
O B:GLY183 2.2 37.2 1.0
O B:ASP185 2.3 37.4 1.0
O B:LEU187 2.4 29.4 1.0
OD1 B:ASP182 2.4 39.0 1.0
CD B:GLU208 3.4 30.2 1.0
CG B:ASP205 3.4 29.4 1.0
C B:ASP185 3.5 36.8 1.0
C B:GLY183 3.5 37.8 1.0
C B:LEU187 3.5 29.6 1.0
CG B:ASP182 3.6 39.1 1.0
N B:LEU187 3.8 32.2 1.0
N B:ASP185 3.9 36.7 1.0
C B:LYS184 4.1 37.6 1.0
CB B:ASP205 4.1 26.4 1.0
CA B:LEU187 4.2 31.1 1.0
N B:GLY183 4.2 38.1 1.0
OD2 B:ASP182 4.2 38.8 1.0
OE2 B:GLU208 4.2 33.6 1.0
CA B:ASP185 4.2 38.1 1.0
CG B:GLU208 4.2 29.1 1.0
C B:GLY186 4.3 34.4 1.0
C B:ASP182 4.3 37.6 1.0
OD1 B:ASP205 4.3 26.8 1.0
N B:LYS184 4.3 37.2 1.0
N B:ASP182 4.4 37.9 1.0
CA B:LYS184 4.4 37.3 1.0
CA B:GLY183 4.4 37.2 1.0
N B:GLY186 4.5 35.9 1.0
CB B:LEU187 4.5 31.1 1.0
O B:LYS184 4.6 37.0 1.0
N B:LEU188 4.6 27.0 1.0
O B:ASP182 4.6 37.7 1.0
CA B:GLY186 4.7 35.2 1.0
CA B:ASP182 4.7 38.0 1.0
CB B:ASP182 4.8 38.1 1.0
CA B:LEU188 4.8 26.4 1.0
O B:GLY186 4.8 34.3 1.0

Calcium binding site 6 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 6 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


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 An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:55.8
occ:1.00
 O B:GLU208 2.2 28.0 1.0
OD2 B:ASP131 2.3 31.8 1.0
O B:HOH681 2.5 42.2 1.0
OD1 B:ASP206 2.6 32.9 1.0
O B:ASP206 2.6 31.5 1.0
CG B:ASP131 3.1 35.3 1.0
OD1 B:ASP131 3.3 38.9 1.0
C B:GLU208 3.4 28.7 1.0
C B:ASP206 3.5 31.2 1.0
CG B:ASP206 3.5 34.0 1.0
CA B:ASP206 4.0 30.6 1.0
CA B:LEU209 4.0 28.1 1.0
N B:LEU209 4.1 28.0 1.0
OG B:SER129 4.2 31.2 1.0
CD1 B:TRP210 4.2 26.3 1.0
N B:GLU208 4.2 31.4 1.0
OD2 B:ASP206 4.2 35.2 1.0
CB B:ASP206 4.3 30.6 1.0
CA B:GLU208 4.4 29.5 1.0
C B:ASP207 4.4 32.4 1.0
N B:TRP210 4.5 26.9 1.0
N B:ASP207 4.5 32.7 1.0
CB B:ASP131 4.6 30.7 1.0
C B:LEU209 4.8 27.6 1.0
CA B:ASP207 4.8 32.9 1.0
NE1 B:TRP210 4.8 26.1 1.0
O B:ASP207 5.0 32.7 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 07:49:18 2024

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