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Calcium in PDB 5d2b: Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470

Enzymatic activity of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470

All present enzymatic activity of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470, PDB code: 5d2b was solved by C.Rouanet-Mehouas, L.Devel, V.Dive, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.45 / 1.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.900, 63.100, 36.790, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 17.5

Other elements in 5d2b:

The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 (pdb code 5d2b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470, PDB code: 5d2b:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5d2b

Go back to Calcium Binding Sites List in 5d2b
Calcium binding site 1 out of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470


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 A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:14.2
occ:1.00
 O A:GLY190 2.3 16.4 1.0
O A:GLY192 2.3 13.7 1.0
O A:HOH441 2.3 16.4 1.0
O A:ASP158 2.3 11.9 1.0
O A:HOH456 2.4 16.3 1.0
OD2 A:ASP194 2.4 12.9 1.0
CG A:ASP194 3.4 13.0 1.0
C A:ASP158 3.5 11.5 1.0
C A:GLY190 3.5 16.4 1.0
C A:GLY192 3.5 13.3 1.0
OD1 A:ASP194 3.8 14.2 1.0
C A:ILE191 3.9 14.7 0.6
C A:ILE191 4.0 15.2 0.4
N A:GLY192 4.0 14.6 1.0
O A:ILE191 4.2 15.1 0.4
O A:ILE191 4.2 14.0 0.6
N A:ASP194 4.3 11.5 1.0
O A:ALA157 4.3 15.1 1.0
CA A:ASP158 4.3 12.0 1.0
CA A:GLY192 4.3 14.2 1.0
CA A:ILE191 4.3 16.2 0.6
N A:ILE191 4.3 16.4 0.6
N A:ILE191 4.4 16.4 0.4
O A:GLY188 4.4 18.0 1.0
CA A:GLY190 4.4 17.7 1.0
N A:ILE159 4.4 11.0 1.0
CA A:ILE191 4.4 16.4 0.4
N A:GLY190 4.4 18.6 1.0
N A:GLY193 4.4 13.0 1.0
O A:HOH644 4.5 28.5 1.0
CA A:ILE159 4.5 11.0 1.0
CA A:GLY193 4.5 12.6 1.0
N A:LEU160 4.6 11.2 0.4
C A:GLY193 4.6 11.5 1.0
N A:LEU160 4.6 11.2 0.6
CB A:ASP194 4.6 12.4 1.0
O A:HOH437 4.7 26.4 1.0
C A:SER189 4.8 18.9 1.0
CA A:ASP194 4.8 11.5 1.0
O A:HOH450 4.8 16.9 1.0
CH2 A:TRP109 4.9 14.8 1.0
CE A:MET156 4.9 25.7 0.3
CG A:LEU160 5.0 12.7 0.4

Calcium binding site 2 out of 3 in 5d2b

Go back to Calcium Binding Sites List in 5d2b
Calcium binding site 2 out of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470


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 A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:14.8
occ:1.00
 OE2 A:GLU199 2.3 14.1 1.0
O A:GLU199 2.4 13.9 1.0
OD2 A:ASP124 2.4 14.9 1.0
O A:HOH552 2.4 19.3 1.0
O A:GLU201 2.4 14.6 1.0
O A:HOH588 2.4 18.3 1.0
OD1 A:ASP124 2.6 16.4 1.0
CG A:ASP124 2.8 15.3 1.0
CD A:GLU199 3.4 14.1 1.0
C A:GLU199 3.5 12.6 1.0
C A:GLU201 3.6 13.8 1.0
CG A:GLU199 3.9 13.8 1.0
OG1 A:THR122 4.1 13.7 1.0
CA A:GLU199 4.2 12.4 1.0
CA A:PHE202 4.2 14.8 1.0
CD1 A:TRP203 4.3 12.8 1.0
N A:PHE202 4.4 13.6 1.0
CB A:ASP124 4.4 15.5 1.0
O A:HOH648 4.4 35.6 1.0
N A:GLU201 4.4 13.4 1.0
C A:ASP200 4.5 14.5 1.0
OE1 A:GLU199 4.5 14.4 1.0
N A:ASP200 4.5 12.2 1.0
O A:HOH428 4.6 26.9 1.0
CB A:GLU199 4.6 13.2 1.0
O A:HOH445 4.6 25.9 1.0
CA A:GLU201 4.7 13.6 1.0
CA A:ASP200 4.7 13.7 1.0
N A:TRP203 4.8 13.2 1.0
NE1 A:TRP203 4.8 12.4 1.0
O A:HOH677 4.9 21.7 1.0
O A:ASP200 4.9 16.0 1.0
CD1 A:PHE202 5.0 19.4 1.0

Calcium binding site 3 out of 3 in 5d2b

Go back to Calcium Binding Sites List in 5d2b
Calcium binding site 3 out of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470


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 A Mutated Catalytic Domain of Human MMP12 in Complex with An Hydroxamate Analogue of RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:13.0
occ:1.00
 OE2 A:GLU201 2.3 16.6 1.0
O A:ILE180 2.3 13.3 1.0
O A:GLY178 2.3 15.1 1.0
O A:GLY176 2.3 14.9 1.0
OD2 A:ASP175 2.3 13.8 1.0
OD1 A:ASP198 2.3 12.5 1.0
CG A:ASP198 3.4 11.7 1.0
C A:ILE180 3.5 12.4 1.0
CD A:GLU201 3.5 15.8 1.0
C A:GLY178 3.5 15.2 1.0
CG A:ASP175 3.5 14.4 1.0
C A:GLY176 3.5 14.7 1.0
N A:GLY178 3.9 15.9 1.0
N A:ILE180 3.9 14.0 1.0
CB A:ASP198 4.0 11.3 1.0
N A:GLY176 4.1 15.0 1.0
OD1 A:ASP175 4.1 14.9 1.0
OE1 A:GLU201 4.1 16.7 1.0
C A:LYS177 4.2 16.8 1.0
C A:GLY179 4.2 14.4 1.0
CA A:ILE180 4.3 14.1 1.0
N A:ASP175 4.3 13.8 1.0
C A:ASP175 4.3 14.7 1.0
CA A:GLY178 4.3 16.1 1.0
OD2 A:ASP198 4.3 12.0 1.0
CA A:GLY176 4.4 15.2 1.0
N A:LEU181 4.4 12.0 1.0
CA A:LYS177 4.4 16.9 1.0
N A:LYS177 4.5 15.8 1.0
CG2 A:ILE180 4.5 17.9 1.0
N A:GLY179 4.5 15.5 1.0
CG A:GLU201 4.5 14.2 1.0
CA A:LEU181 4.6 11.9 1.0
CA A:ASP175 4.6 14.7 1.0
CA A:GLY179 4.6 14.7 1.0
CB A:ASP175 4.6 14.8 1.0
O A:ASP175 4.7 15.5 1.0
O A:HOH513 4.7 28.3 1.0
O A:GLY179 4.8 15.2 1.0
O A:LYS177 4.8 18.3 1.0

Reference:

C.Rouanet-Mehouas, B.Czarny, F.Beau, E.Cassar-Lajeunesse, E.A.Stura, V.Dive, L.Devel. Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played By the Zinc-Binding Group on Potency and Selectivity. J. Med. Chem. V. 60 403 2017.
ISSN: ISSN 1520-4804
PubMed: 27996256
DOI: 10.1021/ACS.JMEDCHEM.6B01420
Page generated: Wed Jul 9 04:59:20 2025

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