Atomistry » Calcium » PDB 4je0-4jyv » 4jpa
Atomistry »
  Calcium »
    PDB 4je0-4jyv »
      4jpa »

Calcium in PDB 4jpa: MMP13 in Complex with A Piperazine Hydantoin Ligand

Protein crystallography data

The structure of MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.90 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.771, 35.986, 101.492, 90.00, 134.99, 90.00
R / Rfree (%) 17.7 / 23

Other elements in 4jpa:

The structure of MMP13 in Complex with A Piperazine Hydantoin Ligand also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the MMP13 in Complex with A Piperazine Hydantoin Ligand (pdb code 4jpa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4jpa

Go back to Calcium Binding Sites List in 4jpa
Calcium binding site 1 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:13.1
occ:1.00
O A:ASN194 2.3 17.7 1.0
O A:GLY196 2.3 13.0 1.0
O A:HOH402 2.3 12.2 1.0
O A:HOH584 2.4 9.8 1.0
O A:ASP162 2.4 13.0 1.0
OD1 A:ASP198 2.5 11.0 1.0
CG A:ASP198 3.4 11.1 1.0
C A:ASN194 3.5 17.2 1.0
C A:GLY196 3.5 12.9 1.0
C A:ASP162 3.5 13.2 1.0
OD2 A:ASP198 3.8 11.8 1.0
C A:TYR195 4.0 15.7 1.0
N A:GLY196 4.1 14.4 1.0
O A:ALA161 4.2 14.3 1.0
N A:ASP198 4.2 11.0 1.0
CA A:ASP162 4.3 13.5 1.0
O A:TYR195 4.3 15.4 1.0
CA A:GLY196 4.3 13.7 1.0
N A:TYR195 4.3 17.0 1.0
CA A:TYR195 4.4 16.8 1.0
CA A:ASN194 4.4 17.6 1.0
O A:GLY192 4.4 15.0 1.0
N A:ASN194 4.4 17.2 1.0
N A:GLY197 4.5 12.1 1.0
O A:HOH530 4.5 18.2 1.0
O A:HOH553 4.5 11.1 1.0
N A:ILE163 4.5 12.9 1.0
CA A:GLY197 4.6 11.7 1.0
CB A:ASP198 4.6 10.6 1.0
C A:GLY197 4.6 11.3 1.0
CG A:MET164 4.6 11.8 1.0
N A:MET164 4.7 12.1 1.0
CA A:ILE163 4.7 12.5 1.0
CA A:ASP198 4.8 10.7 1.0
CH2 A:TRP113 4.8 19.5 1.0
C A:PRO193 4.8 16.7 1.0

Calcium binding site 2 out of 4 in 4jpa

Go back to Calcium Binding Sites List in 4jpa
Calcium binding site 2 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:11.0
occ:1.00
OE2 A:GLU205 2.2 13.5 1.0
O A:GLY180 2.2 15.8 1.0
OD2 A:ASP202 2.2 10.5 1.0
O A:LEU184 2.3 13.6 1.0
O A:SER182 2.4 15.7 1.0
OD1 A:ASP179 2.5 12.8 1.0
CG A:ASP202 3.3 11.4 1.0
CD A:GLU205 3.4 12.0 1.0
C A:GLY180 3.4 15.6 1.0
C A:LEU184 3.5 13.6 1.0
C A:SER182 3.5 15.9 1.0
CG A:ASP179 3.6 14.0 1.0
N A:SER182 3.9 16.2 1.0
C A:PRO181 3.9 16.2 1.0
N A:LEU184 4.0 14.1 1.0
CB A:ASP202 4.0 11.4 1.0
N A:GLY180 4.1 14.7 1.0
OD2 A:ASP179 4.1 11.9 1.0
OE1 A:GLU205 4.1 11.6 1.0
CA A:LEU184 4.2 14.0 1.0
CA A:SER182 4.2 16.4 1.0
C A:ASP179 4.2 14.4 1.0
OD1 A:ASP202 4.2 10.2 1.0
N A:ASP179 4.3 14.3 1.0
C A:GLY183 4.3 14.7 1.0
CA A:PRO181 4.3 16.1 1.0
O A:PRO181 4.3 16.3 1.0
N A:PRO181 4.3 15.9 1.0
CG A:GLU205 4.4 12.0 1.0
CA A:GLY180 4.4 15.2 1.0
N A:LEU185 4.5 13.1 1.0
N A:GLY183 4.5 15.6 1.0
O A:ASP179 4.6 14.3 1.0
CB A:LEU184 4.6 14.0 1.0
CA A:ASP179 4.6 14.3 1.0
CA A:LEU185 4.7 12.8 1.0
CA A:GLY183 4.7 15.1 1.0
CB A:ASP179 4.7 14.2 1.0
O A:GLY183 4.8 15.2 1.0

Calcium binding site 3 out of 4 in 4jpa

Go back to Calcium Binding Sites List in 4jpa
Calcium binding site 3 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:9.0
occ:1.00
O B:HOH428 2.2 11.1 1.0
O B:ASP162 2.3 8.7 1.0
O B:ASN194 2.3 15.7 1.0
O B:HOH427 2.4 5.6 1.0
O B:GLY196 2.4 13.4 1.0
OD1 B:ASP198 2.5 9.1 1.0
C B:ASP162 3.4 9.7 1.0
CG B:ASP198 3.5 10.3 1.0
C B:ASN194 3.5 16.3 1.0
C B:GLY196 3.5 13.6 1.0
OD2 B:ASP198 3.9 11.3 1.0
C B:TYR195 4.0 15.9 1.0
O B:ALA161 4.0 11.2 1.0
N B:GLY196 4.0 14.9 1.0
O B:TYR195 4.2 15.8 1.0
CA B:ASP162 4.2 10.2 1.0
O B:HOH512 4.2 18.0 1.0
N B:ASP198 4.3 11.6 1.0
CA B:GLY196 4.3 14.1 1.0
O B:GLY192 4.4 15.3 1.0
N B:TYR195 4.4 16.3 1.0
CA B:ASN194 4.4 16.5 1.0
N B:ASN194 4.4 16.4 1.0
CA B:TYR195 4.4 16.7 1.0
N B:ILE163 4.5 9.6 1.0
N B:GLY197 4.5 12.9 1.0
O B:HOH577 4.5 17.2 1.0
CA B:GLY197 4.6 12.7 1.0
CA B:ILE163 4.7 9.7 1.0
N B:MET164 4.7 9.6 1.0
CB B:ASP198 4.7 10.9 1.0
C B:GLY197 4.8 12.1 1.0
C B:PRO193 4.8 16.1 1.0
CG B:MET164 4.8 9.9 1.0
CA B:ASP198 4.9 10.9 1.0
C B:ALA161 4.9 10.7 1.0
CH2 B:TRP113 5.0 18.4 1.0

Calcium binding site 4 out of 4 in 4jpa

Go back to Calcium Binding Sites List in 4jpa
Calcium binding site 4 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:13.8
occ:1.00
OE2 B:GLU205 2.2 13.3 1.0
O B:LEU184 2.3 15.4 1.0
OD2 B:ASP202 2.3 10.7 1.0
OD1 B:ASP179 2.3 14.6 1.0
O B:GLY180 2.4 17.9 1.0
O B:SER182 2.4 17.4 1.0
C B:LEU184 3.4 15.2 1.0
CG B:ASP202 3.4 11.3 1.0
CD B:GLU205 3.4 13.6 1.0
C B:SER182 3.5 17.9 1.0
CG B:ASP179 3.5 15.8 1.0
C B:GLY180 3.6 17.6 1.0
N B:SER182 3.9 18.4 1.0
N B:LEU184 3.9 16.3 1.0
C B:PRO181 4.0 18.5 1.0
CB B:ASP202 4.1 11.1 1.0
OD2 B:ASP179 4.1 15.9 1.0
N B:GLY180 4.2 16.9 1.0
CA B:LEU184 4.2 16.1 1.0
OE1 B:GLU205 4.2 14.2 1.0
CA B:SER182 4.3 18.6 1.0
N B:ASP179 4.3 15.4 1.0
C B:ASP179 4.3 16.4 1.0
C B:GLY183 4.3 16.7 1.0
CG B:GLU205 4.3 13.3 1.0
O B:PRO181 4.4 18.8 1.0
OD1 B:ASP202 4.4 9.2 1.0
N B:LEU185 4.4 14.3 1.0
CA B:PRO181 4.5 18.4 1.0
N B:PRO181 4.5 18.1 1.0
CA B:GLY180 4.5 17.4 1.0
CB B:LEU184 4.5 16.4 1.0
N B:GLY183 4.5 17.5 1.0
CA B:ASP179 4.6 16.0 1.0
CA B:LEU185 4.6 13.6 1.0
O B:ASP179 4.7 16.7 1.0
CB B:ASP179 4.7 16.1 1.0
CA B:GLY183 4.7 17.2 1.0
O B:GLY183 4.8 16.5 1.0
CD2 B:LEU185 5.0 13.4 1.0

Reference:

C.De Savi, D.Waterson, A.Pape, S.Lamont, E.Hadley, M.Mills, K.M.Page, J.Bowyer, R.A.Maciewicz. Hydantoin Based Inhibitors of MMP13--Discovery of AZD6605. Bioorg.Med.Chem.Lett. V. 23 4705 2013.
ISSN: ISSN 0960-894X
PubMed: 23810497
DOI: 10.1016/J.BMCL.2013.05.089
Page generated: Sat Dec 12 04:53:22 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy