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Sodium in PDB 5ak7: Structure of Wt Porphyromonas Gingivalis Peptidylarginine Deiminase

Protein crystallography data

The structure of Structure of Wt Porphyromonas Gingivalis Peptidylarginine Deiminase, PDB code: 5ak7 was solved by J.Kopec, A.Montgomery, L.Shrestha, W.Kiyani, R.Nowak, N.Burgess-Brown, P.J.Venables, W.W.Yue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.08 / 1.46
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.860, 84.660, 55.660, 90.00, 92.50, 90.00
R / Rfree (%) 12.8 / 15.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Wt Porphyromonas Gingivalis Peptidylarginine Deiminase (pdb code 5ak7). 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 Wt Porphyromonas Gingivalis Peptidylarginine Deiminase, PDB code: 5ak7:

Sodium binding site 1 out of 1 in 5ak7

Go back to Sodium Binding Sites List in 5ak7
Sodium binding site 1 out of 1 in the Structure of Wt Porphyromonas Gingivalis Peptidylarginine Deiminase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Wt Porphyromonas Gingivalis Peptidylarginine Deiminase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1483

b:15.1
occ:1.00
O A:PHE148 2.3 14.4 1.0
O A:HOH2123 2.4 15.1 1.0
OD1 A:ASP158 2.4 16.5 1.0
OD1 A:ASP147 2.4 14.9 1.0
O A:ASP158 2.4 16.1 1.0
O A:HOH2143 2.7 18.5 1.0
C A:ASP158 3.4 16.2 1.0
CG A:ASP147 3.4 15.1 1.0
CG A:ASP158 3.4 16.4 1.0
C A:PHE148 3.5 14.2 1.0
CA A:ASP158 3.7 16.0 1.0
OD2 A:ASP147 3.7 17.6 1.0
N A:PHE148 3.9 13.5 1.0
N A:TYR150 4.1 14.3 1.0
CB A:ASP158 4.1 16.2 1.0
O A:HOH2167 4.2 19.1 1.0
CG A:PRO161 4.2 14.1 1.0
CD A:PRO161 4.2 15.1 1.0
OD2 A:ASP158 4.3 18.0 1.0
CA A:PHE148 4.4 13.8 1.0
N A:ILE149 4.5 13.9 1.0
CA A:ILE149 4.5 14.9 1.0
N A:GLU159 4.6 17.0 1.0
CB A:TYR150 4.7 15.9 1.0
CB A:ASP147 4.7 14.6 1.0
C A:ILE149 4.8 14.7 1.0
O A:TYR131 4.8 13.1 1.0
CD2 A:PHE148 4.9 12.4 1.0
O A:HOH2145 4.9 26.6 1.0
C A:ASP147 4.9 14.4 1.0
O A:ASP157 4.9 15.0 1.0
CA A:ASP147 5.0 13.9 1.0

Reference:

A.B.Montgomery, J.Kopec, L.Shrestha, M.L.Thezenas, N.A.Burgess-Brown, R.Fischer, W.W.Yue, P.J.Venables. Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications For Autoimmunity in Rheumatoid Arthritis. Ann.Rheum.Dis. V. 75 1255 2016.
ISSN: ISSN 0003-4967
PubMed: 26209657
DOI: 10.1136/ANNRHEUMDIS-2015-207656
Page generated: Tue Dec 15 10:23:21 2020

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