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Calcium in PDB 3lka: Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide

Enzymatic activity of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide

All present enzymatic activity of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide:
3.4.24.65;

Protein crystallography data

The structure of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide, PDB code: 3lka was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.91 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.566, 60.194, 54.215, 90.00, 115.09, 90.00
R / Rfree (%) 16.9 / 21

Other elements in 3lka:

The structure of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide (pdb code 3lka). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide, PDB code: 3lka:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3lka

Go back to Calcium Binding Sites List in 3lka
Calcium binding site 1 out of 3 in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:17.5
occ:1.00
 O A:GLY190 2.2 11.3 1.0
O A:HOH289 2.3 15.7 1.0
O A:GLY192 2.5 6.7 1.0
O A:ASP158 2.6 8.3 1.0
OD2 A:ASP194 2.6 7.0 1.0
O A:HOH7 2.7 8.5 1.0
C A:GLY190 3.4 12.3 1.0
CG A:ASP194 3.5 7.2 1.0
C A:ASP158 3.6 8.0 1.0
C A:GLY192 3.6 7.2 1.0
OD1 A:ASP194 3.7 11.2 1.0
C A:ILE191 3.8 10.8 1.0
O A:ALA157 3.9 11.4 1.0
O A:ILE191 4.0 11.0 1.0
N A:GLY192 4.1 10.0 1.0
O A:HOH32 4.1 10.5 1.0
CA A:ILE191 4.1 11.7 1.0
N A:ILE191 4.2 11.3 1.0
N A:ASP194 4.4 5.8 1.0
CA A:ASP158 4.4 9.0 1.0
CA A:GLY192 4.4 8.5 1.0
N A:ILE159 4.5 7.5 1.0
CA A:GLY190 4.5 12.5 1.0
CA A:ILE159 4.6 7.0 1.0
O A:GLY188 4.6 12.4 1.0
N A:LEU160 4.6 6.0 1.0
N A:GLY190 4.6 11.7 1.0
N A:GLY193 4.6 7.3 1.0
CB A:ASP194 4.7 6.5 1.0
O A:HOH27 4.7 10.5 1.0
CA A:GLY193 4.7 6.5 1.0
C A:GLY193 4.8 6.5 1.0
C A:ALA157 4.9 11.6 1.0
CA A:ASP194 4.9 7.1 1.0
C A:SER189 4.9 12.1 1.0

Calcium binding site 2 out of 3 in 3lka

Go back to Calcium Binding Sites List in 3lka
Calcium binding site 2 out of 3 in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:8.1
occ:1.00
 OD2 A:ASP124 2.3 4.6 1.0
O A:GLU199 2.3 5.1 1.0
OE2 A:GLU199 2.4 5.2 1.0
O A:HOH16 2.5 5.6 1.0
O A:HOH21 2.6 6.5 1.0
O A:GLU201 2.6 5.5 1.0
OD1 A:ASP124 2.6 2.0 1.0
CG A:ASP124 2.8 5.2 1.0
CD A:GLU199 3.4 6.4 1.0
C A:GLU199 3.5 6.3 1.0
C A:GLU201 3.8 5.6 1.0
CG A:GLU199 3.8 4.7 1.0
OG1 A:THR122 4.0 4.8 1.0
CA A:GLU199 4.1 5.4 1.0
O A:HOH40 4.3 15.0 1.0
CB A:ASP124 4.3 5.5 1.0
CA A:PHE202 4.3 5.2 1.0
CD1 A:TRP203 4.4 3.2 1.0
N A:PHE202 4.5 5.0 1.0
OE1 A:GLU199 4.6 7.4 1.0
N A:ASP200 4.6 7.2 1.0
CB A:GLU199 4.6 5.0 1.0
N A:GLU201 4.6 7.0 1.0
C A:ASP200 4.7 7.7 1.0
N A:TRP203 4.8 4.9 1.0
CA A:ASP200 4.8 7.6 1.0
NH2 A:ARG165 4.8 13.2 1.0
CA A:GLU201 4.8 6.3 1.0
O A:HOH29 4.8 8.6 1.0
CD1 A:PHE202 4.8 5.9 1.0
NE1 A:TRP203 4.9 2.0 1.0

Calcium binding site 3 out of 3 in 3lka

Go back to Calcium Binding Sites List in 3lka
Calcium binding site 3 out of 3 in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:10.3
occ:1.00
 OE2 A:GLU201 2.3 14.0 1.0
OD1 A:ASP198 2.3 4.3 1.0
O A:GLY176 2.3 10.9 1.0
O A:ILE180 2.3 8.8 1.0
O A:GLY178 2.4 11.9 1.0
OD2 A:ASP175 2.4 12.1 1.0
CG A:ASP198 3.3 4.5 1.0
C A:ILE180 3.5 8.4 1.0
CD A:GLU201 3.5 10.3 1.0
C A:GLY176 3.5 10.1 1.0
C A:GLY178 3.6 10.2 1.0
CG A:ASP175 3.6 13.2 1.0
N A:GLY178 3.9 10.3 1.0
CB A:ASP198 4.0 4.0 1.0
N A:ILE180 4.0 8.8 1.0
OE1 A:GLU201 4.1 8.1 1.0
OD1 A:ASP175 4.2 12.3 1.0
C A:LYS177 4.2 10.9 1.0
N A:GLY176 4.2 9.0 1.0
OD2 A:ASP198 4.3 4.1 1.0
CA A:ILE180 4.3 8.9 1.0
N A:ASP175 4.3 9.8 1.0
CA A:GLY178 4.3 11.2 1.0
C A:GLY179 4.3 9.9 1.0
C A:ASP175 4.3 9.4 1.0
N A:LEU181 4.4 7.8 1.0
N A:LYS177 4.4 10.0 1.0
CA A:LYS177 4.4 10.8 1.0
CA A:GLY176 4.4 9.4 1.0
CA A:LEU181 4.5 7.3 1.0
CG A:GLU201 4.5 7.7 1.0
N A:GLY179 4.6 11.1 1.0
O A:ASP175 4.6 9.3 1.0
CA A:ASP175 4.7 10.2 1.0
CA A:GLY179 4.7 9.7 1.0
CB A:ILE180 4.7 9.3 1.0
CB A:ASP175 4.7 10.2 1.0
O A:LYS177 4.8 10.6 1.0
O A:GLY179 4.8 9.8 1.0

Reference:

V.Borsi, V.Calderone, M.Fragai, C.Luchinat, N.Sarti. Entropic Contribution to the Linking Coefficient in Fragment Based Drug Design: A Case Study. J.Med.Chem. V. 53 4285 2010.
ISSN: ISSN 0022-2623
PubMed: 20415416
DOI: 10.1021/JM901723Z
Page generated: Sat Jul 13 13:08:57 2024

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