Atomistry » Sodium » PDB 4yhq-4z2i » 4ytb
Atomistry »
  Sodium »
    PDB 4yhq-4z2i »
      4ytb »

Sodium in PDB 4ytb: Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln.

Protein crystallography data

The structure of Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln., PDB code: 4ytb was solved by T.Goulas, D.Mizgalska, I.Garcia-Ferrer, T.Kantyka, T.Guevara, B.Szmigielski, A.Sroka, C.Millan, I.Uson, F.Veillard, B.Potempa, P.Mydel, M.Sola, 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) 46.15 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.534, 71.306, 105.664, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 14.9

Other elements in 4ytb:

The structure of Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln. (pdb code 4ytb). 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 Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln., PDB code: 4ytb:

Sodium binding site 1 out of 1 in 4ytb

Go back to Sodium Binding Sites List in 4ytb
Sodium binding site 1 out of 1 in the Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:11.6
occ:1.00
O A:PHE148 2.3 10.0 1.0
O A:HOH890 2.4 12.2 1.0
OD1 A:ASP158 2.4 11.7 1.0
O A:ASP158 2.4 11.1 1.0
OD1 A:ASP147 2.4 11.1 1.0
O A:HOH806 2.6 15.9 1.0
C A:ASP158 3.4 11.2 1.0
CG A:ASP147 3.5 11.8 1.0
CG A:ASP158 3.5 12.2 1.0
C A:PHE148 3.5 10.6 1.0
CA A:ASP158 3.7 11.1 1.0
OD2 A:ASP147 3.8 14.7 1.0
N A:PHE148 4.0 9.2 1.0
N A:TYR150 4.1 9.7 1.0
CB A:ASP158 4.1 12.1 1.0
CD A:PRO161 4.2 11.1 1.0
CG A:PRO161 4.3 12.2 1.0
OD2 A:ASP158 4.4 14.9 1.0
CA A:PHE148 4.4 8.9 1.0
CE1 A:PHE45 4.4 11.9 1.0
N A:ILE149 4.5 9.6 1.0
CA A:ILE149 4.5 9.6 1.0
N A:GLU159 4.6 11.0 1.0
O A:HOH773 4.6 33.5 1.0
CB A:TYR150 4.7 10.2 1.0
C A:ILE149 4.7 10.9 1.0
CD1 A:PHE45 4.8 13.0 1.0
CB A:ASP147 4.8 10.5 1.0
O A:TYR131 4.8 10.5 1.0
CD1 A:PHE148 4.9 9.1 1.0
CA A:TYR150 5.0 9.3 1.0
O A:ASP157 5.0 10.6 1.0

Reference:

T.Goulas, D.Mizgalska, I.Garcia-Ferrer, T.Kantyka, T.Guevara, B.Szmigielski, A.Sroka, C.Millan, I.Uson, F.Veillard, B.Potempa, P.Mydel, M.Sola, J.Potempa, F.X.Gomis-Ruth. Structure and Mechanism of A Bacterial Host-Protein Citrullinating Virulence Factor, Porphyromonas Gingivalis Peptidylarginine Deiminase. Sci Rep V. 5 11969 2015.
ISSN: ESSN 2045-2322
PubMed: 26132828
DOI: 10.1038/SREP11969
Page generated: Tue Dec 15 10:04:29 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