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Calcium in PDB 2ow2: Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor

Enzymatic activity of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor

All present enzymatic activity of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor:
3.4.24.35;

Protein crystallography data

The structure of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor, PDB code: 2ow2 was solved by A.Tochowicz, W.Bode, K.Maskos, P.Goettig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 2.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.420, 55.420, 260.793, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 28.5

Other elements in 2ow2:

The structure of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Chlorine (Cl) 2 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor (pdb code 2ow2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor, PDB code: 2ow2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2ow2

Go back to Calcium Binding Sites List in 2ow2
Calcium binding site 1 out of 6 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca446

b:38.2
occ:1.00
 O A:LEU187 2.2 40.6 1.0
OD1 A:ASP182 2.3 40.1 1.0
OD2 A:ASP205 2.3 34.9 1.0
OE2 A:GLU208 2.3 39.9 1.0
O A:GLY183 2.3 48.7 1.0
O A:ASP185 2.4 50.0 1.0
C A:LEU187 3.3 41.9 1.0
CG A:ASP205 3.4 36.3 1.0
CD A:GLU208 3.5 39.1 1.0
C A:ASP185 3.5 48.5 1.0
C A:GLY183 3.5 48.5 1.0
CG A:ASP182 3.5 42.6 1.0
N A:LEU187 3.8 44.6 1.0
C A:GLY186 3.9 45.7 1.0
N A:GLY183 3.9 47.9 1.0
C A:ASP182 4.0 47.8 1.0
CB A:ASP205 4.0 35.2 1.0
CG A:GLU208 4.0 39.0 1.0
CA A:LEU187 4.1 43.0 1.0
N A:ASP182 4.1 44.4 1.0
N A:ASP185 4.2 48.0 1.0
C A:LYS184 4.2 47.7 1.0
O A:GLY186 4.2 47.2 1.0
CA A:GLY183 4.3 48.2 1.0
O A:ASP182 4.3 49.5 1.0
CA A:ASP182 4.3 45.8 1.0
N A:LEU188 4.3 40.5 1.0
OD2 A:ASP182 4.3 43.7 1.0
N A:GLY186 4.3 47.2 1.0
CA A:ASP185 4.4 48.6 1.0
OD1 A:ASP205 4.4 37.5 1.0
CA A:GLY186 4.4 45.9 1.0
O A:LYS184 4.4 46.8 1.0
CB A:LEU187 4.4 43.2 1.0
CB A:ASP182 4.5 44.7 1.0
OE1 A:GLU208 4.5 39.0 1.0
N A:LYS184 4.5 48.6 1.0
CA A:LEU188 4.6 39.2 1.0
CA A:LYS184 4.7 48.1 1.0
CB A:PHE181 4.8 45.4 1.0
C A:PHE181 5.0 45.0 1.0

Calcium binding site 2 out of 6 in 2ow2

Go back to Calcium Binding Sites List in 2ow2
Calcium binding site 2 out of 6 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca447

b:48.7
occ:1.00
 O A:GLU208 2.4 35.3 1.0
OD2 A:ASP131 2.5 37.4 1.0
OD1 A:ASP131 2.7 37.3 1.0
O A:ASP206 2.8 33.7 1.0
O A:HOH519 2.8 30.2 1.0
CG A:ASP131 2.9 37.0 1.0
OD1 A:ASP206 3.3 35.3 1.0
C A:ASP206 3.5 34.6 1.0
C A:GLU208 3.6 34.6 1.0
CG A:ASP206 4.0 36.8 1.0
N A:GLU208 4.1 35.6 1.0
CA A:ASP206 4.1 35.9 1.0
OG A:SER129 4.2 24.1 1.0
CD1 A:TRP210 4.2 28.0 1.0
C A:ASP207 4.3 36.1 1.0
N A:ASP207 4.3 34.5 1.0
CB A:ASP131 4.3 36.4 1.0
CA A:LEU209 4.4 33.1 1.0
N A:LEU209 4.5 34.0 1.0
CA A:ASP207 4.6 35.2 1.0
CA A:GLU208 4.6 35.4 1.0
OD2 A:ASP206 4.6 38.6 1.0
N A:TRP210 4.6 29.5 1.0
CB A:ASP206 4.7 36.2 1.0
O A:HOH527 4.7 53.5 1.0
O A:ASP207 4.8 36.5 1.0
NE1 A:TRP210 4.8 28.3 1.0
N A:ASP131 4.8 36.3 1.0

Calcium binding site 3 out of 6 in 2ow2

Go back to Calcium Binding Sites List in 2ow2
Calcium binding site 3 out of 6 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca448

b:59.7
occ:1.00
 O A:HOH503 2.0 23.6 1.0
O A:HOH567 2.5 39.4 1.0
O A:LYS214 2.9 31.6 1.0
OG A:SER211 2.9 29.6 1.0
O A:GLN391 3.0 36.7 1.0
O A:LEU212 3.1 26.7 1.0
CB A:SER211 3.3 29.1 1.0
C A:GLY215 3.7 34.7 1.0
CA A:GLY215 3.7 34.7 1.0
OE1 A:GLN391 3.8 53.9 1.0
C A:LYS214 3.9 32.3 1.0
O A:GLY215 4.0 35.4 1.0
N A:LEU212 4.0 27.9 1.0
N A:GLN391 4.0 34.8 1.0
C A:GLN391 4.1 37.2 1.0
C A:LEU212 4.2 27.9 1.0
N A:GLY215 4.2 33.5 1.0
O A:GLY213 4.3 32.6 1.0
CA A:SER211 4.6 28.2 1.0
C A:SER211 4.7 28.9 1.0
CA A:GLN391 4.7 37.2 1.0
C A:GLY213 4.7 31.8 1.0
CA A:LEU212 4.7 26.9 1.0
CD A:GLN391 5.0 49.6 1.0

Calcium binding site 4 out of 6 in 2ow2

Go back to Calcium Binding Sites List in 2ow2
Calcium binding site 4 out of 6 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca446

b:28.4
occ:1.00
 O B:GLY183 2.2 37.9 1.0
OD2 B:ASP205 2.4 42.9 1.0
O B:LEU187 2.4 36.5 1.0
O B:ASP185 2.5 47.9 1.0
OD2 B:ASP182 2.7 48.0 1.0
OE2 B:GLU208 2.7 36.3 1.0
CG B:ASP182 3.0 43.8 1.0
OD1 B:ASP182 3.0 44.1 1.0
C B:GLY183 3.3 39.1 1.0
N B:GLY183 3.4 40.8 1.0
CG B:ASP205 3.5 40.8 1.0
C B:LEU187 3.5 38.8 1.0
CD B:GLU208 3.6 36.2 1.0
N B:LEU187 3.7 41.5 1.0
C B:ASP185 3.7 47.6 1.0
C B:ASP182 3.9 41.3 1.0
CA B:GLY183 4.0 39.4 1.0
N B:ASP182 4.0 40.4 1.0
CA B:LEU187 4.1 40.2 1.0
CB B:ASP182 4.1 42.7 1.0
CA B:ASP182 4.2 40.8 1.0
C B:GLY186 4.2 43.1 1.0
CB B:ASP205 4.2 39.7 1.0
C B:LYS184 4.2 44.4 1.0
OD1 B:ASP205 4.3 40.4 1.0
N B:ASP185 4.3 46.8 1.0
O B:LYS184 4.3 43.2 1.0
OE1 B:GLU208 4.4 35.7 1.0
CG B:GLU208 4.4 35.3 1.0
CB B:LEU187 4.4 40.9 1.0
N B:LYS184 4.4 40.3 1.0
CA B:GLY186 4.5 43.9 1.0
N B:GLY186 4.5 46.4 1.0
CA B:ASP185 4.6 48.4 1.0
O B:ASP182 4.6 41.7 1.0
N B:LEU188 4.7 38.5 1.0
CA B:LYS184 4.7 42.6 1.0
CB B:PHE181 4.8 36.4 1.0
O B:GLY186 4.9 44.8 1.0
C B:PHE181 5.0 38.7 1.0
CA B:LEU188 5.0 38.5 1.0

Calcium binding site 5 out of 6 in 2ow2

Go back to Calcium Binding Sites List in 2ow2
Calcium binding site 5 out of 6 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca447

b:53.0
occ:1.00
 O B:LEU212 2.6 38.4 1.0
O B:HOH534 2.7 21.1 1.0
O B:LYS214 2.8 45.4 1.0
O B:GLY213 3.3 41.9 1.0
C B:LYS214 3.4 44.0 1.0
OG B:SER211 3.4 29.9 1.0
O B:GLN391 3.5 41.6 1.0
CA B:GLY215 3.5 43.3 1.0
N B:GLY215 3.7 43.9 1.0
C B:LEU212 3.7 36.5 1.0
C B:GLY215 3.7 43.2 1.0
CB B:SER211 3.8 29.8 1.0
C B:GLY213 3.8 41.0 1.0
N B:LEU212 4.0 33.0 1.0
O B:GLY215 4.1 42.2 1.0
N B:GLN391 4.2 43.6 1.0
N B:LYS214 4.4 41.6 1.0
CA B:LYS214 4.4 43.8 1.0
CA B:LEU212 4.5 33.9 1.0
C B:GLN391 4.5 43.4 1.0
N B:GLY213 4.6 37.3 1.0
CA B:GLY213 4.6 39.3 1.0
C B:SER211 4.9 33.2 1.0
CA B:GLN391 5.0 44.8 1.0
CA B:SER211 5.0 32.2 1.0

Calcium binding site 6 out of 6 in 2ow2

Go back to Calcium Binding Sites List in 2ow2
Calcium binding site 6 out of 6 in the Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mmp-9 Active Site Mutant with Difluoro Butanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca448

b:65.9
occ:1.00
 O B:GLU208 2.4 38.2 1.0
OD2 B:ASP131 2.5 36.5 1.0
O B:ASP206 2.8 40.3 1.0
OD1 B:ASP206 2.8 42.4 1.0
CG B:ASP131 3.2 35.1 1.0
OD1 B:ASP131 3.3 34.6 1.0
C B:GLU208 3.4 36.5 1.0
C B:ASP206 3.5 39.9 1.0
CG B:ASP206 3.8 42.8 1.0
CD1 B:TRP210 3.8 29.6 1.0
N B:GLU208 3.9 38.8 1.0
CA B:ASP206 3.9 41.0 1.0
OG B:SER129 4.0 31.8 1.0
CA B:LEU209 4.1 32.0 1.0
N B:LEU209 4.1 34.1 1.0
CA B:GLU208 4.3 37.3 1.0
N B:TRP210 4.3 30.5 1.0
NE1 B:TRP210 4.3 30.4 1.0
N B:ASP207 4.4 39.6 1.0
CB B:ASP206 4.4 42.1 1.0
C B:ASP207 4.5 38.6 1.0
OD2 B:ASP206 4.6 42.5 1.0
CB B:ASP131 4.6 33.4 1.0
C B:LEU209 4.6 31.3 1.0
CA B:ASP207 4.7 39.4 1.0
CG B:TRP210 4.8 29.2 1.0
CG B:GLU130 4.9 36.4 0.0
OE1 B:GLU130 4.9 37.2 0.0

Reference:

A.Tochowicz, K.Maskos, R.Huber, R.Oltenfreiter, V.Dive, A.Yiotakis, M.Zanda, W.Bode, P.Goettig. Crystal Structures of Mmp-9 Complexes with Five Inhibitors: Contribution of the Flexible ARG424 Side-Chain to Selectivity. J.Mol.Biol. V. 371 989 2007.
ISSN: ISSN 0022-2836
PubMed: 17599356
DOI: 10.1016/J.JMB.2007.05.068
Page generated: Fri Jul 12 14:47:20 2024

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