Atomistry » Calcium » PDB 3ljz-3lzk » 3lka
Atomistry »
  Calcium »
    PDB 3ljz-3lzk »
      3lka »

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: Tue Jul 8 14:16:38 2025

Last articles

Mg in 3G73
Mg in 3G37
Mg in 3G6Y
Mg in 3G6X
Mg in 3G6W
Mg in 3G6V
Mg in 3G6K
Mg in 3G5A
Mg in 3G5S
Mg in 3G58
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy