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Calcium in PDB 2ow1: Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor

Enzymatic activity of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor

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

Protein crystallography data

The structure of Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor, PDB code: 2ow1 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) 19.79 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.720, 55.720, 260.450, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 26.7

Other elements in 2ow1:

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

Fluorine (F) 6 atoms
Chlorine (Cl) 3 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor (pdb code 2ow1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate Inhibitor, PDB code: 2ow1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 1 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca446

b:21.0
occ:1.00
 OE2 A:GLU208 2.1 20.3 1.0
O A:GLY183 2.2 41.9 1.0
O A:ASP185 2.4 39.2 1.0
OD2 A:ASP205 2.4 15.6 1.0
O A:LEU187 2.4 24.6 1.0
OD1 A:ASP182 2.5 37.0 1.0
C A:GLY183 3.3 41.2 1.0
CD A:GLU208 3.4 20.4 1.0
CG A:ASP205 3.4 16.8 1.0
CG A:ASP182 3.5 38.0 1.0
N A:GLY183 3.5 41.6 1.0
C A:LEU187 3.5 28.9 1.0
C A:ASP185 3.6 40.4 1.0
OD2 A:ASP182 3.8 38.4 1.0
N A:LEU187 3.9 34.6 1.0
CA A:GLY183 4.0 40.9 1.0
CB A:ASP205 4.0 16.8 1.0
N A:ASP185 4.1 41.7 1.0
CG A:GLU208 4.1 20.1 1.0
CA A:LEU187 4.2 32.4 1.0
C A:LYS184 4.2 41.8 1.0
C A:GLY186 4.2 36.4 1.0
OE1 A:GLU208 4.3 20.6 1.0
CA A:ASP185 4.4 41.4 1.0
OD1 A:ASP205 4.4 13.6 1.0
N A:LYS184 4.4 41.4 1.0
N A:ASP182 4.5 32.5 1.0
N A:LEU188 4.5 25.9 1.0
N A:GLY186 4.5 39.2 1.0
CB A:LEU187 4.6 36.1 1.0
O A:LYS184 4.6 41.3 1.0
C A:ASP182 4.6 39.9 1.0
CA A:GLY186 4.6 37.9 1.0
CA A:LYS184 4.7 42.4 1.0
CB A:ASP182 4.7 38.0 1.0
CA A:LEU188 4.8 22.2 1.0
O A:GLY186 4.8 37.4 1.0
CA A:ASP182 4.8 37.7 1.0

Calcium binding site 2 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 2 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca447

b:23.1
occ:1.00
 O A:HOH594 2.3 10.3 1.0
O A:GLY197 2.4 21.8 1.0
O A:GLN199 2.4 16.9 1.0
O A:ASP165 2.4 14.7 1.0
OD1 A:ASP201 2.5 14.8 1.0
O A:HOH505 2.5 11.5 1.0
CG A:ASP201 3.4 13.9 1.0
C A:GLN199 3.6 17.0 1.0
C A:GLY197 3.6 21.9 1.0
C A:ASP165 3.6 17.3 1.0
OD2 A:ASP201 3.9 12.2 1.0
O A:HOH568 4.0 26.1 1.0
O A:ALA164 4.1 20.7 1.0
C A:ILE198 4.1 20.3 1.0
N A:ASP201 4.1 12.9 1.0
N A:GLN199 4.2 19.4 1.0
O A:ILE198 4.2 19.4 1.0
CA A:ASP165 4.3 18.4 1.0
C A:GLY200 4.3 13.6 1.0
O A:GLY195 4.3 19.0 1.0
CA A:GLY200 4.4 13.8 1.0
N A:GLY200 4.4 17.0 1.0
N A:GLY197 4.5 23.6 1.0
N A:ILE198 4.5 22.0 1.0
CA A:ILE198 4.5 21.1 1.0
CA A:GLN199 4.5 19.9 1.0
CA A:GLY197 4.5 22.6 1.0
N A:ILE166 4.6 15.8 1.0
CB A:ASP201 4.6 10.7 1.0
N A:VAL167 4.7 14.6 1.0
CG2 A:VAL167 4.7 16.9 1.0
CA A:ASP201 4.7 12.4 1.0
CA A:ILE166 4.7 14.9 1.0
C A:PRO196 4.8 23.3 1.0
O A:HOH528 4.9 15.8 1.0
CH2 A:TRP116 4.9 17.4 1.0

Calcium binding site 3 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 3 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca448

b:46.1
occ:1.00
 O A:ASP206 2.4 16.6 1.0
O A:GLU208 2.4 20.2 1.0
OD2 A:ASP131 2.4 16.2 1.0
OD1 A:ASP206 2.8 26.2 1.0
CG A:ASP131 3.2 15.7 1.0
C A:ASP206 3.3 19.6 1.0
OD1 A:ASP131 3.4 16.2 1.0
CG A:ASP206 3.6 26.7 1.0
C A:GLU208 3.7 19.4 1.0
OG A:SER129 3.7 19.5 1.0
CA A:ASP206 3.8 19.5 1.0
CD1 A:TRP210 3.8 12.9 1.0
N A:GLU208 4.2 18.7 1.0
CB A:ASP206 4.3 22.8 1.0
OD2 A:ASP206 4.3 33.1 1.0
N A:ASP207 4.3 17.1 1.0
C A:ASP207 4.4 19.5 1.0
CB A:ASP131 4.4 15.2 1.0
N A:TRP210 4.5 15.8 1.0
NE1 A:TRP210 4.5 12.0 1.0
CA A:LEU209 4.5 18.2 1.0
N A:LEU209 4.6 19.1 1.0
CA A:GLU208 4.6 18.1 1.0
CA A:ASP207 4.6 19.3 1.0
CG A:TRP210 4.8 12.8 1.0
CB A:SER129 4.8 18.5 1.0
O A:ASP207 4.9 19.8 1.0
O A:ASP205 4.9 19.1 1.0
N A:ASP131 4.9 18.1 1.0

Calcium binding site 4 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 4 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca449

b:40.4
occ:1.00
 O A:SER149 2.3 16.1 1.0
O A:THR152 2.4 15.5 1.0
O A:HOH532 2.4 20.0 1.0
O A:HOH576 2.5 20.0 1.0
C A:SER149 3.5 18.4 1.0
C A:THR152 3.6 17.0 1.0
O A:HOH598 4.1 28.9 1.0
N A:THR152 4.1 16.8 1.0
CA A:PRO153 4.3 19.6 1.0
C A:ALA150 4.4 18.2 1.0
CA A:SER149 4.4 17.2 1.0
N A:PRO153 4.4 18.8 1.0
O A:LEU154 4.4 13.7 1.0
N A:ALA150 4.4 16.8 1.0
CA A:ALA150 4.5 17.8 1.0
O A:ALA150 4.5 18.3 1.0
CA A:THR152 4.5 17.2 1.0
O A:HOH599 4.6 32.4 1.0
CB A:SER149 4.7 17.2 1.0
C A:PRO153 4.8 19.4 1.0
N A:VAL151 4.8 17.5 1.0
N A:LEU154 4.9 17.6 1.0

Calcium binding site 5 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 5 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca446

b:20.8
occ:1.00
 O B:GLY183 2.2 19.0 1.0
OE2 B:GLU208 2.2 22.9 1.0
O B:LEU187 2.3 20.1 1.0
O B:ASP185 2.3 29.5 1.0
OD1 B:ASP182 2.3 16.6 1.0
OD2 B:ASP205 2.4 18.3 1.0
C B:GLY183 3.4 22.3 1.0
CG B:ASP205 3.4 17.6 1.0
C B:LEU187 3.4 22.8 1.0
C B:ASP185 3.4 29.4 1.0
CD B:GLU208 3.4 21.7 1.0
CG B:ASP182 3.5 21.7 1.0
N B:LEU187 3.8 26.9 1.0
N B:ASP185 3.9 28.3 1.0
N B:GLY183 3.9 22.9 1.0
CB B:ASP205 4.0 16.4 1.0
C B:LYS184 4.1 27.7 1.0
OD2 B:ASP182 4.2 24.2 1.0
C B:GLY186 4.2 27.8 1.0
CA B:LEU187 4.2 26.1 1.0
CA B:ASP185 4.2 30.2 1.0
CA B:GLY183 4.2 21.7 1.0
C B:ASP182 4.3 22.6 1.0
CG B:GLU208 4.3 22.3 1.0
OE1 B:GLU208 4.3 21.2 1.0
OD1 B:ASP205 4.4 15.0 1.0
N B:LYS184 4.4 22.7 1.0
N B:ASP182 4.4 20.4 1.0
N B:GLY186 4.4 28.1 1.0
N B:LEU188 4.4 19.8 1.0
CA B:LYS184 4.5 26.8 1.0
O B:LYS184 4.5 27.1 1.0
CA B:GLY186 4.5 27.4 1.0
CA B:LEU188 4.6 17.9 1.0
CA B:ASP182 4.6 20.7 1.0
CB B:ASP182 4.6 21.3 1.0
O B:GLY186 4.8 28.1 1.0
CB B:LEU187 4.8 29.9 1.0
O B:ASP182 4.8 21.2 1.0

Calcium binding site 6 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 6 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca447

b:26.0
occ:1.00
 O B:GLN199 2.3 18.9 1.0
OD1 B:ASP201 2.4 13.7 1.0
O B:ASP165 2.5 17.3 1.0
O B:GLY197 2.5 21.8 1.0
O B:HOH508 2.7 11.3 1.0
CG B:ASP201 3.4 17.4 1.0
C B:GLN199 3.5 17.6 1.0
C B:ASP165 3.6 16.7 1.0
C B:GLY197 3.7 21.0 1.0
C B:ILE198 3.9 21.0 1.0
OD2 B:ASP201 3.9 14.8 1.0
N B:ASP201 4.0 16.1 1.0
O B:ILE198 4.0 19.7 1.0
N B:GLN199 4.1 19.6 1.0
O B:ALA164 4.2 18.9 1.0
C B:GLY200 4.3 16.4 1.0
CA B:ILE198 4.3 22.1 1.0
N B:GLY200 4.3 16.3 1.0
CA B:GLY200 4.3 15.8 1.0
O B:GLY195 4.4 20.1 1.0
O B:HOH581 4.4 18.3 1.0
CA B:ASP165 4.4 16.8 1.0
CA B:GLN199 4.4 18.9 1.0
N B:ILE198 4.5 21.5 1.0
N B:ILE166 4.5 15.8 1.0
CB B:ASP201 4.6 15.7 1.0
CG2 B:VAL167 4.6 10.7 1.0
N B:VAL167 4.6 12.9 1.0
CA B:ASP201 4.6 16.9 1.0
CA B:ILE166 4.7 14.1 1.0
CA B:GLY197 4.7 21.2 1.0
N B:GLY197 4.8 20.3 1.0
CH2 B:TRP116 4.8 17.7 1.0
O B:HOH582 4.9 30.3 1.0
C B:PRO196 5.0 20.2 1.0

Calcium binding site 7 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 7 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca448

b:39.0
occ:1.00
 O B:GLU208 2.3 19.5 1.0
O B:ASP206 2.4 15.0 1.0
O B:HOH568 2.4 25.4 1.0
OD2 B:ASP131 2.4 14.6 1.0
OD1 B:ASP206 2.7 13.4 1.0
C B:ASP206 3.3 15.0 1.0
CG B:ASP131 3.3 14.1 1.0
C B:GLU208 3.5 19.2 1.0
CG B:ASP206 3.6 17.0 1.0
OD1 B:ASP131 3.6 13.8 1.0
CA B:ASP206 3.8 15.1 1.0
OG B:SER129 3.9 15.1 1.0
N B:GLU208 4.0 19.1 1.0
CD1 B:TRP210 4.1 13.0 1.0
CB B:ASP206 4.2 14.9 1.0
CA B:LEU209 4.3 14.5 1.0
N B:LEU209 4.3 17.0 1.0
N B:ASP207 4.3 16.6 1.0
C B:ASP207 4.3 19.9 1.0
OD2 B:ASP206 4.4 20.4 1.0
CA B:GLU208 4.4 20.4 1.0
N B:TRP210 4.6 14.7 1.0
CA B:ASP207 4.6 18.4 1.0
NE1 B:TRP210 4.7 14.1 1.0
CB B:ASP131 4.7 14.9 1.0
O B:ASP207 4.9 20.8 1.0
C B:LEU209 4.9 15.4 1.0

Calcium binding site 8 out of 8 in 2ow1

Go back to Calcium Binding Sites List in 2ow1
Calcium binding site 8 out of 8 in the Mmp-9 Active Site Mutant with Trifluoromethyl Hydroxamate 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 Trifluoromethyl Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca449

b:45.0
occ:1.00
 O B:THR152 2.2 23.7 1.0
O B:SER149 2.3 19.6 1.0
O B:HOH543 2.5 14.6 1.0
O B:HOH583 2.5 26.8 1.0
C B:THR152 3.4 24.4 1.0
C B:SER149 3.5 19.0 1.0
CA B:PRO153 4.1 26.4 1.0
N B:THR152 4.2 24.4 1.0
N B:PRO153 4.2 26.4 1.0
O B:HOH599 4.3 44.9 1.0
O B:LEU154 4.3 21.2 1.0
O B:ALA150 4.4 22.8 1.0
CA B:SER149 4.4 18.6 1.0
CA B:THR152 4.4 24.1 1.0
C B:ALA150 4.4 22.7 1.0
N B:ALA150 4.5 19.9 1.0
C B:PRO153 4.5 24.8 1.0
CA B:ALA150 4.6 21.3 1.0
CB B:SER149 4.8 15.4 1.0
N B:LEU154 4.8 23.3 1.0
N B:VAL151 4.9 23.3 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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