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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: Tue Dec 15 06:00:40 2020

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