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Sodium 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:

Calcium (Ca) 4 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4jpa

Go back to Sodium Binding Sites List in 4jpa
Sodium binding site 1 out of 2 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na305

b:15.4
occ:1.00
O A:GLU205 2.4 13.6 1.0
OD2 A:ASP128 2.5 18.7 1.0
O A:ASP203 2.6 13.6 1.0
OD2 A:ASP203 2.6 13.8 1.0
O A:HOH526 2.7 31.4 1.0
CG A:ASP128 3.4 15.3 1.0
C A:ASP203 3.4 12.7 1.0
O A:HOH473 3.4 28.1 1.0
OD1 A:ASP128 3.5 18.1 1.0
C A:GLU205 3.6 13.4 1.0
CG A:ASP203 3.7 13.1 1.0
CA A:ASP203 3.9 12.5 1.0
OG1 A:THR126 4.0 10.2 1.0
O A:HOH447 4.0 11.3 1.0
N A:GLU205 4.3 12.7 1.0
CB A:ASP203 4.3 12.7 1.0
CD1 A:TRP207 4.4 13.1 1.0
N A:ASP204 4.4 12.4 1.0
CA A:THR206 4.4 13.9 1.0
N A:THR206 4.4 13.7 1.0
C A:ASP204 4.5 12.7 1.0
CD A:PRO127 4.5 11.7 1.0
O A:HOH477 4.5 43.3 1.0
CA A:ASP204 4.6 12.5 1.0
CA A:GLU205 4.6 12.9 1.0
OD1 A:ASP203 4.7 12.8 1.0
CB A:ASP128 4.7 13.7 1.0
NE1 A:TRP207 4.8 13.7 1.0
N A:TRP207 4.9 14.5 1.0
CG A:PRO127 4.9 12.4 1.0

Sodium binding site 2 out of 2 in 4jpa

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:10.6
occ:1.00
OD2 B:ASP128 2.3 15.2 1.0
O B:GLU205 2.4 13.1 1.0
OD2 B:ASP203 2.6 13.1 1.0
O B:ASP203 2.7 13.5 1.0
CG B:ASP128 3.1 14.2 1.0
OD1 B:ASP128 3.2 16.6 1.0
C B:ASP203 3.5 12.9 1.0
C B:GLU205 3.6 12.8 1.0
CG B:ASP203 3.7 12.5 1.0
OG1 B:THR126 3.8 10.0 1.0
CA B:ASP203 4.0 12.4 1.0
CD1 B:TRP207 4.2 12.1 1.0
CA B:THR206 4.3 12.2 1.0
CB B:ASP203 4.3 12.5 1.0
N B:GLU205 4.3 13.1 1.0
N B:THR206 4.3 12.5 1.0
N B:ASP204 4.5 13.0 1.0
CB B:ASP128 4.5 12.6 1.0
C B:ASP204 4.6 13.3 1.0
CD B:PRO127 4.6 12.1 1.0
CA B:GLU205 4.6 13.1 1.0
N B:TRP207 4.6 12.5 1.0
OD1 B:ASP203 4.7 12.4 1.0
NE1 B:TRP207 4.8 11.9 1.0
CA B:ASP204 4.8 13.2 1.0
C B:THR206 5.0 12.5 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: Tue Dec 15 06:46:56 2020

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