Atomistry » Calcium » PDB 3rke-3rxa » 3rts
Atomistry »
  Calcium »
    PDB 3rke-3rxa »
      3rts »

Calcium in PDB 3rts: Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide

Enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide

All present enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide:
3.4.24.65;

Protein crystallography data

The structure of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide, PDB code: 3rts was solved by I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Mori, C.Nativi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.99 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.643, 60.475, 54.162, 90.00, 115.15, 90.00
R / Rfree (%) 17 / 23.6

Other elements in 3rts:

The structure of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide (pdb code 3rts). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide, PDB code: 3rts:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3rts

Go back to Calcium Binding Sites List in 3rts
Calcium binding site 1 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:13.8
occ:1.00
 O A:GLY190 2.4 8.1 1.0
O A:GLY192 2.4 5.1 1.0
O A:ASP158 2.5 5.6 1.0
OD2 A:ASP194 2.6 5.2 1.0
O A:HOH8 2.7 2.3 1.0
CG A:ASP194 3.5 5.7 1.0
C A:ASP158 3.5 4.8 1.0
C A:GLY190 3.6 8.5 1.0
C A:GLY192 3.6 4.4 1.0
OD1 A:ASP194 3.8 8.6 1.0
C A:ILE191 3.8 6.7 1.0
O A:ALA157 4.0 6.4 1.0
N A:GLY192 4.0 6.1 1.0
O A:ILE191 4.0 7.1 1.0
CA A:ILE191 4.1 8.0 1.0
O A:HOH58 4.2 13.0 1.0
N A:ILE191 4.3 7.2 1.0
CA A:ASP158 4.3 5.5 1.0
N A:ASP194 4.4 2.0 1.0
CA A:GLY192 4.4 5.2 1.0
N A:ILE159 4.4 4.3 1.0
N A:GLY193 4.5 4.8 1.0
O A:GLY188 4.5 8.2 1.0
O A:HOH270 4.5 26.6 1.0
CA A:ILE159 4.6 3.3 1.0
N A:LEU160 4.6 2.3 1.0
CA A:GLY193 4.6 2.9 1.0
CA A:GLY190 4.6 8.9 1.0
CB A:ASP194 4.7 3.0 1.0
C A:GLY193 4.7 2.8 1.0
N A:GLY190 4.7 8.2 1.0
O A:HOH53 4.7 4.5 1.0
CA A:ASP194 4.9 3.3 1.0
C A:ALA157 4.9 7.8 1.0

Calcium binding site 2 out of 3 in 3rts

Go back to Calcium Binding Sites List in 3rts
Calcium binding site 2 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:4.9
occ:1.00
 O A:GLU199 2.3 2.0 1.0
OD2 A:ASP124 2.3 3.2 1.0
OE2 A:GLU199 2.4 2.0 1.0
O A:GLU201 2.5 2.0 1.0
O A:HOH10 2.5 3.4 1.0
OD1 A:ASP124 2.5 2.0 1.0
O A:HOH32 2.6 5.7 1.0
CG A:ASP124 2.8 2.2 1.0
C A:GLU199 3.5 2.8 1.0
CD A:GLU199 3.5 2.6 1.0
C A:GLU201 3.7 2.2 1.0
CG A:GLU199 3.9 2.0 1.0
OG1 A:THR122 4.1 2.0 1.0
CA A:GLU199 4.1 2.3 1.0
CA A:PHE202 4.3 3.3 1.0
CB A:ASP124 4.3 2.5 1.0
CD1 A:TRP203 4.4 2.5 1.0
N A:PHE202 4.4 2.2 1.0
N A:GLU201 4.5 3.0 1.0
N A:ASP200 4.5 3.2 1.0
OE1 A:GLU199 4.6 4.5 1.0
C A:ASP200 4.6 3.9 1.0
CB A:GLU199 4.6 2.3 1.0
CD1 A:PHE202 4.7 2.0 1.0
CA A:GLU201 4.7 2.9 1.0
CA A:ASP200 4.7 3.6 1.0
O A:HOH13 4.8 6.3 1.0
N A:TRP203 4.8 3.9 1.0
NH2 A:ARG165 4.8 12.9 1.0
NE1 A:TRP203 4.9 2.0 1.0

Calcium binding site 3 out of 3 in 3rts

Go back to Calcium Binding Sites List in 3rts
Calcium binding site 3 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:8.4
occ:1.00
 OE2 A:GLU201 2.2 14.2 1.0
OD1 A:ASP198 2.3 5.8 1.0
O A:ILE180 2.3 9.2 1.0
O A:GLY176 2.3 8.7 1.0
O A:GLY178 2.4 8.7 1.0
OD2 A:ASP175 2.4 7.8 1.0
CD A:GLU201 3.4 8.4 1.0
CG A:ASP198 3.4 2.7 1.0
C A:ILE180 3.5 8.4 1.0
C A:GLY176 3.5 8.5 1.0
C A:GLY178 3.6 8.8 1.0
CG A:ASP175 3.6 9.7 1.0
N A:GLY178 3.7 9.1 1.0
N A:ILE180 4.0 8.9 1.0
CB A:ASP198 4.0 2.3 1.0
C A:LYS177 4.1 9.5 1.0
OD1 A:ASP175 4.2 10.7 1.0
OE1 A:GLU201 4.2 12.2 1.0
N A:GLY176 4.2 8.4 1.0
CA A:GLY178 4.3 8.9 1.0
CG A:GLU201 4.3 4.2 1.0
CA A:ILE180 4.3 9.0 1.0
N A:ASP175 4.3 7.3 1.0
CA A:LYS177 4.3 9.8 1.0
C A:GLY179 4.3 9.4 1.0
OD2 A:ASP198 4.4 4.1 1.0
N A:LYS177 4.4 8.1 1.0
C A:ASP175 4.4 8.3 1.0
N A:LEU181 4.4 7.5 1.0
CA A:GLY176 4.5 8.1 1.0
N A:GLY179 4.6 8.6 1.0
CA A:LEU181 4.6 6.4 1.0
O A:LYS177 4.7 9.5 1.0
CA A:ASP175 4.7 8.1 1.0
CB A:ILE180 4.7 9.4 1.0
CB A:ASP175 4.7 8.3 1.0
CA A:GLY179 4.8 9.4 1.0
O A:GLY179 4.8 9.8 1.0
O A:ASP175 4.9 9.6 1.0
CD2 A:LEU181 5.0 5.1 1.0

Reference:

A.Mordini, M.Mori, A.Massaro, V.Calderone, M.Fragai, C.Luchinat. Contribution of Ligand Free Energy of Solvation to Design New Potent Mmps Inhibitors. J.Med.Chem. 2012.
ISSN: ISSN 0022-2623
Page generated: Sat Jul 13 18:12:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy