Atomistry » Sodium » PDB 2yfa-2zgb » 2yig
Atomistry »
  Sodium »
    PDB 2yfa-2zgb »
      2yig »

Sodium in PDB 2yig: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor

Protein crystallography data

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig 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) 67.12 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.417, 36.074, 95.206, 90.00, 131.49, 90.00
R / Rfree (%) 18.4 / 22.1

Other elements in 2yig:

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor (pdb code 2yig). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2yig

Go back to Sodium Binding Sites List in 2yig
Sodium binding site 1 out of 3 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


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 Novel Selective Non Zinc Binding Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:18.3
occ:1.00
O A:GLU205 2.4 13.6 1.0
OD2 A:ASP128 2.5 16.6 1.0
O A:ASP203 2.9 11.9 1.0
OD1 A:ASP203 2.9 12.7 1.0
CG A:ASP128 3.2 14.7 1.0
OD1 A:ASP128 3.3 16.1 1.0
O A:HOH485 3.4 24.7 1.0
C A:ASP203 3.6 10.8 1.0
C A:GLU205 3.7 11.9 1.0
OG1 A:THR126 3.9 9.4 1.0
CG A:ASP203 4.0 11.8 1.0
CA A:ASP203 4.1 9.7 1.0
CD1 A:TRP207 4.2 9.6 1.0
CA A:THR206 4.4 12.2 1.0
N A:GLU205 4.4 10.1 1.0
N A:THR206 4.5 11.6 1.0
CD A:PRO127 4.5 10.3 1.0
CB A:ASP203 4.5 11.5 1.0
CB A:ASP128 4.5 12.6 1.0
C A:ASP204 4.6 11.1 1.0
N A:ASP204 4.6 9.7 1.0
CA A:GLU205 4.7 10.2 1.0
N A:TRP207 4.7 11.1 1.0
CA A:ASP204 4.8 10.6 1.0
NE1 A:TRP207 4.8 8.8 1.0
OD2 A:ASP203 5.0 13.6 1.0

Sodium binding site 2 out of 3 in 2yig

Go back to Sodium Binding Sites List in 2yig
Sodium binding site 2 out of 3 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


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 Novel Selective Non Zinc Binding Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:26.4
occ:1.00
O A:HOH551 1.9 16.3 1.0
O A:HOH543 2.1 18.7 1.0
O A:HOH504 2.4 16.8 1.0
O A:HOH481 2.4 25.2 1.0
O A:HOH474 3.4 15.3 1.0
O A:ALA188 3.5 8.9 1.0
O A:HOH523 3.7 16.9 1.0
CE1 B:PHE107 4.4 19.5 1.0
CZ B:PHE107 4.4 21.4 1.0
ND1 A:HIS226 4.5 8.4 1.0
CG A:HIS226 4.5 7.9 1.0
CE1 A:HIS226 4.6 8.6 1.0
CD2 A:HIS226 4.7 7.8 1.0
C A:ALA188 4.7 8.7 1.0
NE2 A:HIS226 4.8 7.9 1.0
CD A:PRO190 4.9 11.4 1.0
CB A:HIS226 5.0 8.0 1.0

Sodium binding site 3 out of 3 in 2yig

Go back to Sodium Binding Sites List in 2yig
Sodium binding site 3 out of 3 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:17.3
occ:1.00
OD2 B:ASP128 2.5 15.6 1.0
O B:GLU205 2.6 13.2 1.0
OD1 B:ASP203 2.7 12.1 1.0
O B:ASP203 3.0 12.0 1.0
CG B:ASP128 3.3 15.1 1.0
OG1 B:THR126 3.6 11.3 1.0
OD1 B:ASP128 3.6 16.6 1.0
C B:ASP203 3.7 11.5 1.0
C B:GLU205 3.8 13.0 1.0
CG B:ASP203 3.8 11.4 1.0
CD1 B:TRP207 4.1 9.9 1.0
CA B:ASP203 4.1 10.7 1.0
CD B:PRO127 4.3 10.0 1.0
CA B:THR206 4.3 12.0 1.0
CB B:ASP203 4.5 11.2 1.0
N B:THR206 4.5 12.2 1.0
N B:GLU205 4.5 12.5 1.0
CB B:ASP128 4.5 13.9 1.0
NE1 B:TRP207 4.7 9.7 1.0
N B:TRP207 4.7 11.1 1.0
N B:ASP204 4.7 11.2 1.0
OD2 B:ASP203 4.8 11.4 1.0
CA B:GLU205 4.8 12.8 1.0
C B:ASP204 4.8 12.3 1.0
CB B:THR126 4.9 9.2 1.0
CG B:PRO127 4.9 10.9 1.0
CA B:ASP204 5.0 12.3 1.0

Reference:

C.D.Savi, A.D.Morley, A.Ting, I.Nash, K.Karabelas, C.M.Wood, M.James, S.J.Norris, G.Karoutchi, N.Rankine, G.Hamlin, P.A.Macfaul, D.Ryan, S.V.Baker, D.Hargreaves, S.Gerhardt. Selective Non Zinc Binding Inhibitors of MMP13. Bioorg.Med.Chem.Lett. V. 21 4215 2011.
ISSN: ISSN 0960-894X
PubMed: 21669521
DOI: 10.1016/J.BMCL.2011.05.075
Page generated: Mon Oct 7 05:26:08 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