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Sodium in PDB 4ytg: Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) Mutant C351A in Complex with Dipeptide Met-Arg.

Protein crystallography data

The structure of Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) Mutant C351A in Complex with Dipeptide Met-Arg., PDB code: 4ytg 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) 48.57 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.360, 59.320, 84.610, 90.00, 126.59, 90.00
R / Rfree (%) 15.6 / 18.2

Other elements in 4ytg:

The structure of Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) Mutant C351A in Complex with Dipeptide Met-Arg. 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) Mutant C351A in Complex with Dipeptide Met-Arg. (pdb code 4ytg). 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) Mutant C351A in Complex with Dipeptide Met-Arg., PDB code: 4ytg:

Sodium binding site 1 out of 1 in 4ytg

Go back to Sodium Binding Sites List in 4ytg
Sodium binding site 1 out of 1 in the Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) Mutant C351A in Complex with Dipeptide Met-Arg.


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) Mutant C351A in Complex with Dipeptide Met-Arg. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:19.6
occ:1.00
O A:HOH797 2.3 18.2 1.0
O A:PHE148 2.3 19.2 1.0
OD1 A:ASP158 2.4 19.5 1.0
O A:ASP158 2.4 20.0 1.0
OD1 A:ASP147 2.5 20.9 1.0
C A:ASP158 3.3 20.8 1.0
CG A:ASP158 3.4 25.2 1.0
CG A:ASP147 3.5 25.2 1.0
C A:PHE148 3.6 20.4 1.0
CA A:ASP158 3.6 17.9 1.0
OD2 A:ASP147 3.8 27.6 1.0
O A:HOH767 3.8 28.1 1.0
N A:PHE148 4.0 17.0 1.0
N A:TYR150 4.1 18.6 1.0
CB A:ASP158 4.1 20.7 1.0
CG A:PRO161 4.1 22.3 1.0
CD A:PRO161 4.1 18.2 1.0
OD2 A:ASP158 4.2 32.7 1.0
CA A:PHE148 4.4 16.5 1.0
N A:ILE149 4.5 17.3 1.0
CA A:ILE149 4.5 17.3 1.0
N A:GLU159 4.6 17.7 1.0
CB A:TYR150 4.6 17.2 1.0
O A:TYR131 4.7 20.1 1.0
CD1 A:PHE45 4.7 26.4 1.0
CB A:PHE45 4.7 26.5 1.0
C A:ILE149 4.7 19.8 1.0
CB A:ASP147 4.8 17.5 1.0
CD1 A:PHE148 4.8 19.2 1.0
O A:ASP157 4.9 15.3 1.0
CA A:TYR150 4.9 17.0 1.0
N A:ASP158 4.9 16.9 1.0
CG A:PHE148 5.0 17.7 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

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