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Calcium in PDB 2ovz: Mmp-9 Active Site Mutant with Phosphinate Inhibitor

Enzymatic activity of Mmp-9 Active Site Mutant with Phosphinate Inhibitor

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

Protein crystallography data

The structure of Mmp-9 Active Site Mutant with Phosphinate Inhibitor, PDB code: 2ovz 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) 19.80 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.850, 55.850, 259.890, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.1

Other elements in 2ovz:

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

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor (pdb code 2ovz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor, PDB code: 2ovz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 2ovz

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Calcium binding site 1 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate 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 Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca446

b:24.3
occ:1.00
 OE1 A:GLU208 2.1 21.2 1.0
O A:GLY183 2.2 29.9 1.0
O A:ASP185 2.2 25.6 1.0
OD1 A:ASP205 2.3 22.9 1.0
O A:LEU187 2.3 22.6 1.0
OD1 A:ASP182 2.4 28.8 1.0
CD A:GLU208 3.3 19.9 1.0
C A:GLY183 3.4 31.2 1.0
C A:ASP185 3.4 25.5 1.0
C A:LEU187 3.4 23.6 1.0
CG A:ASP205 3.4 26.0 1.0
CG A:ASP182 3.6 32.1 1.0
N A:GLY183 3.8 30.9 1.0
N A:LEU187 3.8 26.2 1.0
N A:ASP185 3.9 26.6 1.0
C A:LYS184 4.1 30.1 1.0
CB A:ASP205 4.1 21.4 1.0
CA A:ASP185 4.1 27.7 1.0
CG A:GLU208 4.1 26.1 1.0
OE2 A:GLU208 4.1 18.0 1.0
CA A:GLY183 4.2 31.4 1.0
CA A:LEU187 4.2 25.0 1.0
OD2 A:ASP182 4.2 31.2 1.0
C A:GLY186 4.2 26.2 1.0
C A:ASP182 4.2 30.4 1.0
N A:ASP182 4.3 31.4 1.0
N A:GLY186 4.4 27.1 1.0
N A:LYS184 4.4 30.2 1.0
OD2 A:ASP205 4.4 24.1 1.0
N A:LEU188 4.4 23.3 1.0
O A:LYS184 4.4 30.1 1.0
CA A:GLY186 4.5 24.0 1.0
CA A:LEU188 4.6 22.9 1.0
CA A:LYS184 4.6 30.9 1.0
CA A:ASP182 4.6 31.1 1.0
CB A:LEU187 4.7 24.4 1.0
O A:HOH529 4.7 35.3 1.0
CB A:ASP182 4.7 31.7 1.0
O A:ASP182 4.8 31.3 1.0
O A:GLY186 4.8 25.0 1.0

Calcium binding site 2 out of 10 in 2ovz

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Calcium binding site 2 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate 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 Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca447

b:34.2
occ:1.00
 O A:HOH540 2.3 26.4 1.0
O A:ASP165 2.3 24.1 1.0
O A:GLN199 2.4 27.8 1.0
OD1 A:ASP201 2.5 24.6 1.0
O A:HOH502 2.6 35.0 1.0
O A:GLY197 2.6 32.3 1.0
C A:ASP165 3.5 24.2 1.0
CG A:ASP201 3.5 25.8 1.0
C A:GLN199 3.5 28.4 1.0
C A:GLY197 3.8 36.5 1.0
N A:ASP201 4.0 23.5 1.0
O A:ALA164 4.0 26.3 1.0
OD2 A:ASP201 4.1 25.4 1.0
C A:ILE198 4.1 36.3 1.0
O A:ILE198 4.1 34.4 1.0
C A:GLY200 4.2 24.5 1.0
N A:GLN199 4.2 33.5 1.0
CA A:ASP165 4.3 24.1 1.0
CA A:GLY200 4.3 24.5 1.0
N A:GLY200 4.4 27.7 1.0
N A:ILE166 4.4 22.4 1.0
O A:HOH538 4.4 37.2 1.0
O A:GLY195 4.4 36.5 1.0
CA A:GLN199 4.5 32.6 1.0
CA A:ILE166 4.5 22.5 1.0
CA A:ILE198 4.5 36.9 1.0
N A:VAL167 4.6 21.6 1.0
CB A:ASP201 4.6 23.5 1.0
CA A:ASP201 4.6 22.8 1.0
N A:ILE198 4.7 36.4 1.0
N A:GLY197 4.8 40.9 1.0
CG2 A:VAL167 4.8 24.2 1.0
CH2 A:TRP116 4.8 23.6 1.0
CA A:GLY197 4.8 37.8 1.0
C A:ALA164 5.0 28.1 1.0
O A:GLY200 5.0 24.1 1.0

Calcium binding site 3 out of 10 in 2ovz

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Calcium binding site 3 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate 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 Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca448

b:34.7
occ:1.00
 O A:ASP206 2.2 23.0 1.0
O A:GLU208 2.3 22.3 1.0
O A:HOH503 2.3 32.2 1.0
OD2 A:ASP131 2.3 22.6 1.0
OD1 A:ASP206 2.6 25.2 1.0
C A:ASP206 3.1 26.4 1.0
CG A:ASP131 3.2 25.0 1.0
CG A:ASP206 3.4 25.2 1.0
C A:GLU208 3.5 23.9 1.0
OD1 A:ASP131 3.6 21.6 1.0
CA A:ASP206 3.7 24.1 1.0
OG A:SER129 3.8 20.9 1.0
CD1 A:TRP210 3.9 16.0 1.0
N A:GLU208 4.0 25.4 1.0
CB A:ASP206 4.1 21.6 1.0
N A:ASP207 4.2 26.4 1.0
OD2 A:ASP206 4.2 26.2 1.0
C A:ASP207 4.2 28.1 1.0
CA A:GLU208 4.4 23.7 1.0
N A:LEU209 4.4 21.5 1.0
CA A:ASP207 4.5 27.1 1.0
CA A:LEU209 4.5 22.4 1.0
N A:TRP210 4.5 20.0 1.0
CB A:ASP131 4.5 18.8 1.0
NE1 A:TRP210 4.5 17.7 1.0
O A:ASP207 4.8 26.8 1.0
CG A:TRP210 4.9 16.9 1.0
O A:ASP205 4.9 21.0 1.0

Calcium binding site 4 out of 10 in 2ovz

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Calcium binding site 4 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate 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 Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca449

b:40.9
occ:1.00
 O A:HOH514 2.2 21.2 1.0
O A:LEU212 2.3 18.6 1.0
O A:LYS214 2.4 20.8 1.0
O A:HOH515 2.5 19.2 1.0
O A:GLY213 2.7 19.4 1.0
C A:LYS214 3.1 20.6 1.0
C A:LEU212 3.2 21.3 1.0
OG A:SER211 3.2 20.2 1.0
C A:GLY213 3.3 21.5 1.0
N A:GLY215 3.7 22.3 1.0
CA A:GLY215 3.7 23.4 1.0
N A:LEU212 3.8 19.6 1.0
CB A:SER211 3.9 20.2 1.0
O A:GLN391 3.9 22.1 1.0
C A:GLY215 3.9 23.9 1.0
N A:LYS214 3.9 20.1 1.0
N A:GLY213 4.0 22.0 1.0
O A:GLY215 4.0 24.1 1.0
CA A:LYS214 4.0 23.7 1.0
CA A:GLY213 4.1 23.6 1.0
CA A:LEU212 4.1 21.0 1.0
O A:HOH553 4.2 31.5 1.0
N A:GLN391 4.6 23.0 1.0
C A:SER211 4.7 20.2 1.0
O A:HOH517 4.8 20.2 1.0
C A:GLN391 4.8 23.6 1.0
CA A:SER211 4.9 17.5 1.0

Calcium binding site 5 out of 10 in 2ovz

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Calcium binding site 5 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate 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 Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca450

b:44.5
occ:1.00
 O A:THR152 2.3 24.8 1.0
O A:SER149 2.3 27.5 1.0
O A:HOH555 2.4 32.5 1.0
O A:HOH552 2.4 28.4 1.0
O A:HOH548 2.4 30.9 1.0
O A:HOH539 2.6 35.9 1.0
C A:THR152 3.4 25.5 1.0
C A:SER149 3.5 25.7 1.0
CA A:PRO153 4.1 27.9 1.0
N A:THR152 4.2 27.6 1.0
N A:PRO153 4.2 26.8 1.0
O A:LEU154 4.3 23.2 1.0
CA A:SER149 4.4 24.8 1.0
C A:ALA150 4.4 26.9 1.0
N A:ALA150 4.4 25.5 1.0
CA A:ALA150 4.5 26.2 1.0
CA A:THR152 4.5 24.8 1.0
C A:PRO153 4.5 26.6 1.0
O A:ALA150 4.6 28.7 1.0
O A:HOH511 4.7 31.5 1.0
N A:LEU154 4.7 26.8 1.0
CB A:SER149 4.8 23.9 1.0
N A:VAL151 4.8 26.1 1.0

Calcium binding site 6 out of 10 in 2ovz

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Calcium binding site 6 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate 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 Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca446

b:24.2
occ:1.00
 OE2 B:GLU208 2.1 24.0 1.0
O B:GLY183 2.2 29.0 1.0
O B:LEU187 2.2 21.7 1.0
O B:ASP185 2.3 28.0 1.0
OD2 B:ASP182 2.3 28.5 1.0
OD1 B:ASP205 2.4 20.5 1.0
CD B:GLU208 3.3 22.7 1.0
C B:LEU187 3.4 21.7 1.0
C B:GLY183 3.4 28.4 1.0
CG B:ASP205 3.4 21.9 1.0
C B:ASP185 3.4 28.0 1.0
CG B:ASP182 3.5 32.0 1.0
N B:LEU187 3.8 24.6 1.0
N B:ASP185 3.9 25.7 1.0
N B:GLY183 3.9 29.0 1.0
OD1 B:ASP182 4.0 30.1 1.0
CB B:ASP205 4.1 19.9 1.0
C B:LYS184 4.1 30.8 1.0
CA B:LEU187 4.1 26.2 1.0
CG B:GLU208 4.2 24.1 1.0
C B:ASP182 4.2 32.3 1.0
C B:GLY186 4.2 26.8 1.0
CA B:ASP185 4.2 28.4 1.0
OE1 B:GLU208 4.2 21.2 1.0
CA B:GLY183 4.2 30.3 1.0
N B:LEU188 4.4 20.5 1.0
OD2 B:ASP205 4.4 19.2 1.0
N B:LYS184 4.4 29.3 1.0
N B:ASP182 4.4 29.2 1.0
O B:LYS184 4.4 26.7 1.0
N B:GLY186 4.5 28.0 1.0
CA B:LEU188 4.6 21.2 1.0
CA B:LYS184 4.6 31.1 1.0
CA B:GLY186 4.6 26.0 1.0
CB B:LEU187 4.6 29.4 1.0
O B:ASP182 4.6 35.0 1.0
CA B:ASP182 4.6 30.1 1.0
CB B:ASP182 4.6 29.8 1.0
O B:GLY186 4.7 24.8 1.0

Calcium binding site 7 out of 10 in 2ovz

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Calcium binding site 7 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca447

b:36.6
occ:1.00
 O B:ASP165 2.3 22.3 1.0
O B:GLN199 2.3 25.7 1.0
OD1 B:ASP201 2.5 20.8 1.0
O B:HOH584 2.5 24.4 1.0
O B:HOH524 2.6 28.4 1.0
O B:GLY197 2.8 26.6 1.0
C B:ASP165 3.4 21.5 1.0
C B:GLN199 3.4 26.1 1.0
CG B:ASP201 3.5 21.8 1.0
O B:ALA164 3.9 23.9 1.0
N B:ASP201 3.9 21.4 1.0
C B:GLY197 4.0 28.8 1.0
C B:ILE198 4.1 27.8 1.0
C B:GLY200 4.1 23.9 1.0
OD2 B:ASP201 4.1 20.8 1.0
CA B:GLY200 4.1 23.3 1.0
CA B:ASP165 4.1 20.3 1.0
N B:GLN199 4.2 26.8 1.0
O B:ILE198 4.2 25.8 1.0
N B:GLY200 4.2 24.5 1.0
O B:HOH567 4.3 28.0 1.0
N B:ILE166 4.3 20.4 1.0
O B:GLY195 4.4 29.8 1.0
CA B:GLN199 4.5 27.0 1.0
CA B:ILE166 4.5 19.3 1.0
CA B:ILE198 4.6 29.3 1.0
N B:VAL167 4.6 17.4 1.0
CA B:ASP201 4.6 22.3 1.0
CB B:ASP201 4.6 20.5 1.0
CH2 B:TRP116 4.6 25.6 1.0
N B:ILE198 4.8 27.9 1.0
O B:GLY200 4.8 26.4 1.0
C B:ALA164 4.8 19.8 1.0
CG2 B:VAL167 4.9 22.9 1.0
O B:HOH568 4.9 53.1 1.0
N B:ASP165 5.0 21.5 1.0

Calcium binding site 8 out of 10 in 2ovz

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Calcium binding site 8 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca448

b:32.4
occ:1.00
 O B:GLU208 2.3 20.6 1.0
OD2 B:ASP131 2.3 18.4 1.0
O B:ASP206 2.4 19.5 1.0
OD1 B:ASP206 2.4 20.2 1.0
O B:HOH503 2.6 49.6 1.0
O B:HOH564 3.1 38.2 1.0
C B:ASP206 3.2 21.4 1.0
CG B:ASP131 3.2 20.8 1.0
CG B:ASP206 3.4 22.5 1.0
C B:GLU208 3.5 23.0 1.0
OD1 B:ASP131 3.6 18.1 1.0
CA B:ASP206 3.7 21.1 1.0
O B:HOH559 3.9 36.3 1.0
OG B:SER129 3.9 20.4 1.0
CD1 B:TRP210 3.9 17.8 1.0
N B:GLU208 4.0 22.2 1.0
CB B:ASP206 4.1 20.4 1.0
OD2 B:ASP206 4.2 23.1 1.0
N B:ASP207 4.2 23.6 1.0
CA B:LEU209 4.3 22.2 1.0
N B:LEU209 4.3 20.7 1.0
C B:ASP207 4.3 23.9 1.0
N B:TRP210 4.4 20.8 1.0
CA B:GLU208 4.4 22.7 1.0
CB B:ASP131 4.5 20.8 1.0
NE1 B:TRP210 4.5 18.2 1.0
O B:HOH546 4.6 32.3 1.0
CA B:ASP207 4.6 24.1 1.0
C B:LEU209 4.8 21.3 1.0
CG B:TRP210 4.8 17.6 1.0
O B:ASP207 4.9 24.1 1.0
O B:ASP205 4.9 19.7 1.0

Calcium binding site 9 out of 10 in 2ovz

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Calcium binding site 9 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca449

b:38.0
occ:1.00
 O B:LEU212 2.2 20.1 1.0
O B:HOH532 2.3 20.0 1.0
O B:LYS214 2.4 23.1 1.0
O B:HOH525 2.5 20.9 1.0
O B:GLY213 3.0 19.5 1.0
OG B:SER211 3.0 18.9 1.0
C B:LYS214 3.2 23.0 1.0
C B:LEU212 3.2 19.3 1.0
C B:GLY213 3.4 22.8 1.0
N B:LEU212 3.7 17.9 1.0
CB B:SER211 3.8 17.9 1.0
CA B:GLY215 3.8 24.2 1.0
N B:GLY215 3.8 23.4 1.0
O B:GLN391 4.0 19.5 1.0
N B:LYS214 4.0 21.9 1.0
C B:GLY215 4.0 23.4 1.0
N B:GLY213 4.0 20.6 1.0
O B:GLY215 4.1 23.0 1.0
CA B:LEU212 4.1 20.2 1.0
CA B:GLY213 4.1 19.9 1.0
CA B:LYS214 4.2 24.8 1.0
O B:HOH533 4.4 23.7 1.0
C B:SER211 4.6 18.2 1.0
N B:GLN391 4.6 22.9 1.0
CA B:SER211 4.8 17.6 1.0
C B:GLN391 4.9 22.1 1.0

Calcium binding site 10 out of 10 in 2ovz

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Calcium binding site 10 out of 10 in the Mmp-9 Active Site Mutant with Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Mmp-9 Active Site Mutant with Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca450

b:50.7
occ:1.00
 O B:SER149 2.3 28.0 1.0
O B:THR152 2.3 31.7 1.0
O B:HOH522 2.3 27.8 1.0
O B:HOH542 2.5 28.9 1.0
C B:THR152 3.5 31.3 1.0
C B:SER149 3.5 29.0 1.0
N B:THR152 4.1 30.2 1.0
O B:HOH583 4.2 40.9 1.0
CA B:PRO153 4.3 32.9 1.0
N B:PRO153 4.3 33.5 1.0
O B:LEU154 4.3 23.7 1.0
C B:ALA150 4.3 31.2 1.0
CA B:SER149 4.4 28.9 1.0
CA B:ALA150 4.4 29.5 1.0
N B:ALA150 4.4 29.9 1.0
CA B:THR152 4.4 32.3 1.0
O B:ALA150 4.5 31.8 1.0
C B:PRO153 4.6 32.2 1.0
CB B:SER149 4.7 27.9 1.0
N B:VAL151 4.7 28.3 1.0
N B:LEU154 4.9 29.7 1.0

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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