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Calcium in PDB 5l7f: Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.

Enzymatic activity of Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.

All present enzymatic activity of Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21., PDB code: 5l7f was solved by L.Tepshi, T.Bordenave, 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) 47.34 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.920, 70.370, 52.220, 90.00, 104.61, 90.00
R / Rfree (%) 17.6 / 19.5

Other elements in 5l7f:

The structure of Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Bromine (Br) 3 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. (pdb code 5l7f). 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 MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21., PDB code: 5l7f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5l7f

Go back to Calcium Binding Sites List in 5l7f
Calcium binding site 1 out of 6 in the Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.


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 MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:15.1
occ:1.00
 O A:ILE180 2.3 14.7 1.0
OE2 A:GLU201 2.3 17.4 1.0
OD1 A:ASP175 2.3 13.3 1.0
OD2 A:ASP198 2.3 13.4 1.0
O A:GLY176 2.3 15.7 1.0
O A:GLY178 2.4 14.8 1.0
C A:ILE180 3.4 14.8 1.0
CG A:ASP198 3.5 11.7 1.0
CD A:GLU201 3.5 16.2 1.0
CG A:ASP175 3.5 16.1 1.0
C A:GLY178 3.6 16.0 1.0
C A:GLY176 3.6 16.1 1.0
N A:ILE180 3.9 13.2 1.0
N A:GLY178 3.9 16.4 1.0
N A:GLY176 4.0 12.2 1.0
CB A:ASP198 4.1 11.3 1.0
OD2 A:ASP175 4.2 13.4 1.0
CA A:ILE180 4.2 14.2 1.0
OE1 A:GLU201 4.2 16.1 1.0
N A:ASP175 4.2 10.8 1.0
C A:LYS177 4.2 20.5 1.0
C A:ASP175 4.3 12.3 1.0
C A:GLY179 4.3 15.1 1.0
CA A:GLY178 4.3 17.4 1.0
N A:LEU181 4.3 14.3 1.0
CA A:GLY176 4.4 13.7 1.0
OD1 A:ASP198 4.4 10.2 1.0
N A:LYS177 4.5 15.0 1.0
CA A:LYS177 4.5 21.3 1.0
CA A:LEU181 4.5 11.2 1.0
N A:GLY179 4.6 13.8 1.0
CG A:GLU201 4.6 15.0 1.0
CA A:ASP175 4.6 11.6 1.0
CA A:GLY179 4.7 14.6 1.0
CB A:ASP175 4.7 12.9 1.0
O A:ASP175 4.7 14.9 1.0
CB A:ILE180 4.8 13.9 1.0
O A:LYS177 4.9 21.9 1.0
O A:GLY179 4.9 14.0 1.0

Calcium binding site 2 out of 6 in 5l7f

Go back to Calcium Binding Sites List in 5l7f
Calcium binding site 2 out of 6 in the Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.


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 MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:15.1
occ:1.00
 O A:ASP158 2.3 10.6 1.0
O A:GLY192 2.3 14.6 1.0
O A:GLY190 2.3 13.9 1.0
O A:HOH446 2.3 12.3 1.0
O A:HOH436 2.4 13.2 1.0
OD1 A:ASP194 2.5 12.5 1.0
CG A:ASP194 3.3 12.4 1.0
C A:ASP158 3.4 10.4 1.0
C A:GLY192 3.5 14.8 1.0
C A:GLY190 3.5 16.4 1.0
OD2 A:ASP194 3.8 15.6 1.0
C A:ILE191 3.9 14.1 1.0
N A:GLY192 4.0 10.3 1.0
O A:ILE191 4.1 12.7 1.0
CA A:GLY192 4.3 13.1 1.0
CA A:ASP158 4.3 13.2 1.0
O A:GLY188 4.3 15.6 1.0
N A:GLY190 4.3 17.1 1.0
N A:ILE191 4.4 16.3 1.0
CA A:ILE191 4.4 16.0 1.0
N A:ASP194 4.4 13.1 1.0
N A:ILE159 4.4 11.5 1.0
O A:ALA157 4.4 14.4 1.0
CA A:GLY190 4.4 17.2 1.0
N A:GLY193 4.5 14.6 1.0
CA A:ILE159 4.5 12.6 1.0
CB A:ASP194 4.6 11.5 1.0
CA A:GLY193 4.6 13.2 1.0
N A:LEU160 4.7 13.8 0.6
N A:LEU160 4.7 13.8 0.4
C A:SER189 4.7 16.5 1.0
O A:HOH418 4.7 19.4 1.0
C A:GLY193 4.7 13.2 1.0
CA A:ASP194 4.8 11.9 1.0
CH2 A:TRP109 4.8 15.9 1.0
CG A:LEU160 4.8 12.1 0.4
O A:SER189 4.9 17.7 1.0

Calcium binding site 3 out of 6 in 5l7f

Go back to Calcium Binding Sites List in 5l7f
Calcium binding site 3 out of 6 in the Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.


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 MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:16.7
occ:1.00
 O A:GLU199 2.3 13.6 1.0
OE2 A:GLU199 2.4 15.2 1.0
OD2 A:ASP124 2.4 16.9 1.0
O A:GLU201 2.4 12.9 1.0
O A:HOH532 2.4 17.4 1.0
O A:HOH533 2.5 14.0 1.0
OD1 A:ASP124 2.7 15.8 1.0
CG A:ASP124 2.9 19.6 1.0
C A:GLU199 3.4 14.7 1.0
CD A:GLU199 3.4 15.6 1.0
C A:GLU201 3.6 14.9 1.0
CG A:GLU199 3.8 15.5 1.0
CA A:GLU199 4.1 12.3 1.0
OG1 A:THR122 4.2 15.1 1.0
CA A:PHE202 4.2 18.2 1.0
N A:PHE202 4.3 15.2 1.0
O A:HOH424 4.3 29.2 1.0
CD1 A:TRP203 4.4 16.3 1.0
CB A:ASP124 4.4 18.9 1.0
N A:ASP200 4.5 16.7 1.0
N A:GLU201 4.5 14.6 1.0
O A:HOH460 4.5 21.9 1.0
C A:ASP200 4.5 14.6 1.0
CB A:GLU199 4.5 14.7 1.0
OE1 A:GLU199 4.6 16.8 1.0
CA A:ASP200 4.7 15.6 1.0
CA A:GLU201 4.7 13.8 1.0
O A:HOH562 4.7 29.3 1.0
N A:TRP203 4.8 14.7 1.0
NE1 A:TRP203 4.8 14.8 1.0
O A:HOH407 4.8 22.9 1.0
CD1 A:PHE202 4.9 18.2 1.0
O A:ASP200 5.0 16.1 1.0

Calcium binding site 4 out of 6 in 5l7f

Go back to Calcium Binding Sites List in 5l7f
Calcium binding site 4 out of 6 in the Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.


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 MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:14.8
occ:1.00
 OE2 B:GLU201 2.3 19.0 1.0
OD1 B:ASP175 2.3 10.7 1.0
O B:GLY176 2.3 14.1 1.0
O B:ILE180 2.3 13.3 1.0
OD2 B:ASP198 2.3 12.9 1.0
O B:GLY178 2.4 13.6 1.0
CG B:ASP198 3.4 13.8 1.0
C B:ILE180 3.4 13.2 1.0
CG B:ASP175 3.5 12.5 1.0
CD B:GLU201 3.5 17.5 1.0
C B:GLY176 3.5 15.0 1.0
C B:GLY178 3.6 14.6 1.0
N B:GLY178 3.9 14.9 1.0
N B:ILE180 3.9 15.3 1.0
N B:GLY176 4.0 11.8 1.0
CB B:ASP198 4.0 11.2 1.0
OD2 B:ASP175 4.1 12.5 1.0
OE1 B:GLU201 4.1 18.8 1.0
C B:LYS177 4.2 20.9 1.0
C B:ASP175 4.2 13.7 1.0
CA B:ILE180 4.2 13.4 1.0
N B:ASP175 4.2 13.8 1.0
C B:GLY179 4.3 17.1 1.0
CA B:GLY178 4.3 14.7 1.0
OD1 B:ASP198 4.4 14.5 1.0
CA B:GLY176 4.4 14.3 1.0
N B:LEU181 4.4 12.0 1.0
N B:LYS177 4.4 15.4 1.0
CA B:LYS177 4.4 18.5 1.0
CG B:GLU201 4.6 15.9 1.0
CA B:ASP175 4.6 12.9 1.0
N B:GLY179 4.6 13.2 1.0
CA B:LEU181 4.6 12.1 1.0
O B:ASP175 4.6 14.4 1.0
CB B:ASP175 4.6 13.7 1.0
CA B:GLY179 4.7 14.4 1.0
CB B:ILE180 4.8 13.4 1.0
O B:LYS177 4.9 19.4 1.0
O B:HOH453 4.9 13.4 1.0
O B:GLY179 4.9 15.8 1.0

Calcium binding site 5 out of 6 in 5l7f

Go back to Calcium Binding Sites List in 5l7f
Calcium binding site 5 out of 6 in the Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.


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 MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:15.5
occ:1.00
 O B:ASP158 2.3 13.9 1.0
O B:HOH449 2.3 16.1 1.0
O B:GLY190 2.3 17.7 1.0
O B:GLY192 2.3 16.3 1.0
OD1 B:ASP194 2.3 13.9 1.0
O B:HOH430 2.4 16.9 1.0
CG B:ASP194 3.4 14.2 1.0
C B:ASP158 3.4 11.9 1.0
C B:GLY192 3.5 12.1 1.0
C B:GLY190 3.5 18.7 1.0
OD2 B:ASP194 3.8 16.9 1.0
C B:ILE191 4.0 14.6 1.0
N B:GLY192 4.1 12.6 1.0
O B:ILE191 4.2 13.3 1.0
CA B:ASP158 4.2 14.5 1.0
N B:ASP194 4.3 12.4 1.0
CA B:GLY192 4.3 12.7 1.0
CA B:ILE191 4.3 17.2 1.0
N B:GLY190 4.4 20.8 1.0
O B:GLY188 4.4 19.8 1.0
O B:ALA157 4.4 11.8 1.0
N B:ILE191 4.4 17.4 1.0
N B:ILE159 4.4 12.1 1.0
N B:GLY193 4.4 11.4 1.0
CA B:GLY190 4.5 20.0 1.0
CA B:ILE159 4.5 13.1 1.0
CA B:GLY193 4.6 10.3 1.0
CB B:ASP194 4.6 12.9 1.0
O B:HOH485 4.6 21.1 1.0
C B:GLY193 4.7 10.1 1.0
N B:LEU160 4.7 12.3 0.6
N B:LEU160 4.7 12.5 0.4
C B:SER189 4.7 18.6 1.0
CG B:LEU160 4.8 13.9 0.6
CA B:ASP194 4.8 12.1 1.0
CH2 B:TRP109 4.9 16.8 1.0
O B:SER189 5.0 17.7 1.0

Calcium binding site 6 out of 6 in 5l7f

Go back to Calcium Binding Sites List in 5l7f
Calcium binding site 6 out of 6 in the Crystal Structure of MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21.


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 MMP12 Mutant K421A in Complex with RXP470.1 Conjugated with Fluorophore CY5,5 in Space Group P21. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:15.3
occ:1.00
 O B:HOH540 2.3 18.9 1.0
O B:GLU199 2.4 12.8 1.0
O B:HOH531 2.4 14.4 1.0
O B:GLU201 2.4 13.0 1.0
OD2 B:ASP124 2.4 17.3 1.0
OE2 B:GLU199 2.5 17.0 1.0
OD1 B:ASP124 2.7 16.4 1.0
CG B:ASP124 2.9 20.7 1.0
C B:GLU199 3.4 12.3 1.0
CD B:GLU199 3.6 14.3 1.0
C B:GLU201 3.6 15.5 1.0
CG B:GLU199 3.9 13.7 1.0
CA B:GLU199 4.1 13.1 1.0
O B:HOH578 4.2 30.1 1.0
CA B:PHE202 4.2 16.0 1.0
OG1 B:THR122 4.2 15.4 1.0
N B:PHE202 4.3 15.9 1.0
CD1 B:TRP203 4.4 15.7 1.0
CB B:ASP124 4.4 21.2 1.0
O B:HOH454 4.4 22.3 1.0
N B:ASP200 4.5 14.9 1.0
O B:HOH497 4.5 24.1 1.0
N B:GLU201 4.5 16.6 1.0
C B:ASP200 4.5 15.5 1.0
CB B:GLU199 4.6 14.3 1.0
OE1 B:GLU199 4.6 16.2 1.0
CA B:ASP200 4.6 15.8 1.0
CA B:GLU201 4.7 15.7 1.0
O B:HOH440 4.7 23.6 1.0
O B:HOH537 4.7 20.1 1.0
N B:TRP203 4.8 15.3 1.0
CD1 B:PHE202 4.8 19.6 1.0
NE1 B:TRP203 4.9 15.8 1.0
O B:ASP200 4.9 19.0 1.0

Reference:

T.Bordenave, M.Helle, F.Beau, D.Georgiadis, L.Tepshi, M.Bernes, Y.Ye, L.Levenez, E.Poquet, H.Nozach, M.Razavian, J.Toczek, E.A.Stura, V.Dive, M.M.Sadeghi, L.Devel. Synthesis and in Vitro and in Vivo Evaluation of Mmp-12 Selective Optical Probes. Bioconjug.Chem. V. 27 2407 2016.
ISSN: ISSN 1043-1802
PubMed: 27564088
DOI: 10.1021/ACS.BIOCONJCHEM.6B00377
Page generated: Mon Jul 15 07:21:16 2024

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