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Sodium in PDB 4in9: Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp

Protein crystallography data

The structure of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp, PDB code: 4in9 was solved by T.Guevara, M.Ksiazek, P.D.Skottrup, N.Cerda-Costa, S.Trillo-Muyo, I.Dediego, E.Riise, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.87 / 1.55
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 86.050, 86.050, 49.440, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.1

Other elements in 4in9:

The structure of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp (pdb code 4in9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp, PDB code: 4in9:

Sodium binding site 1 out of 1 in 4in9

Go back to Sodium Binding Sites List in 4in9
Sodium binding site 1 out of 1 in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:18.2
occ:1.00
O3 A:GOL307 2.5 28.9 1.0
O A:PHE108 2.5 16.8 1.0
O A:HOH548 2.6 39.4 1.0
O A:HOH478 2.6 33.2 1.0
O A:HOH595 2.7 46.9 1.0
O A:HOH427 2.7 15.1 1.0
O A:HOH596 3.4 48.8 1.0
C A:PHE108 3.6 16.6 1.0
C3 A:GOL307 3.7 34.0 1.0
OD2 A:ASP137 4.1 21.2 1.0
CB A:PHE108 4.1 11.1 1.0
O A:HOH590 4.2 50.3 1.0
CA A:GLY100 4.3 12.4 1.0
N A:GLY100 4.4 12.3 1.0
OD2 A:ASP135 4.4 13.5 1.0
O2 A:GOL307 4.4 44.1 1.0
CA A:PHE108 4.5 10.8 1.0
N A:ASP109 4.5 14.7 1.0
C2 A:GOL307 4.7 40.7 1.0
CA A:ASP109 4.7 14.6 1.0
OD1 A:ASP135 4.7 12.9 1.0
CB A:ASP137 4.8 15.9 1.0
CG A:ASP137 4.9 20.4 1.0
CG A:ASP135 5.0 12.4 1.0
O A:HOH469 5.0 24.9 1.0

Reference:

T.Guevara, M.Ksiazek, P.D.Skottrup, N.Cerda-Costa, S.Trillo-Muyo, I.De Diego, E.Riise, J.Potempa, F.X.Gomis-Ruth. Structure of the Catalytic Domain of the Tannerella Forsythia Matrix Metallopeptidase Karilysin in Complex with A Tetrapeptidic Inhibitor. Acta Crystallogr.,Sect.F V. 69 472 2013.
ISSN: ESSN 1744-3091
PubMed: 23695557
DOI: 10.1107/S1744309113007392
Page generated: Tue Dec 15 06:45:02 2020

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