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Sodium in PDB 4xdu: Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form

Enzymatic activity of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form

All present enzymatic activity of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form:
2.7.1.180;

Protein crystallography data

The structure of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form, PDB code: 4xdu was solved by D.R.Tomchick, C.A.Brautigam, R.K.Deka, M.V.Norgard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.54 / 1.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.830, 46.814, 57.501, 90.00, 102.22, 90.00
R / Rfree (%) 16.7 / 18.8

Other elements in 4xdu:

The structure of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form (pdb code 4xdu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form, PDB code: 4xdu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4xdu

Go back to Sodium Binding Sites List in 4xdu
Sodium binding site 1 out of 2 in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form


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 Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:29.8
occ:1.00
 O A:HIS267 2.2 21.3 1.0
O A:HOH816 2.3 31.4 1.0
O A:HOH735 2.3 21.4 1.0
O A:HOH823 2.4 38.4 1.0
O A:HOH851 2.5 22.0 1.0
O1 A:EDO508 2.6 49.8 1.0
HO1 A:EDO508 2.9 59.7 1.0
C A:HIS267 3.4 16.1 1.0
HA A:THR268 3.4 15.8 1.0
O A:HOH726 3.8 18.2 1.0
HB2 A:HIS267 3.9 25.8 1.0
O2 A:EDO508 3.9 33.5 1.0
C1 A:EDO508 3.9 41.5 1.0
H A:HIS267 3.9 18.7 1.0
O A:VAL292 4.0 14.0 1.0
HB A:THR268 4.1 16.4 1.0
CA A:THR268 4.2 13.2 1.0
O A:HOH670 4.2 23.4 1.0
N A:THR268 4.2 15.0 1.0
H22 A:EDO508 4.2 34.8 1.0
C2 A:EDO508 4.3 29.0 1.0
CA A:HIS267 4.3 17.0 1.0
N A:HIS267 4.3 15.6 1.0
H11 A:EDO508 4.4 49.8 1.0
OD2 A:ASP259 4.4 21.1 1.0
O A:HOH768 4.4 32.0 1.0
CB A:HIS267 4.5 21.5 1.0
HO2 A:EDO508 4.5 40.2 1.0
HB1 A:ALA266 4.6 19.4 1.0
CB A:THR268 4.7 13.7 1.0
H12 A:EDO508 4.7 49.8 1.0
HB3 A:HIS267 4.7 25.8 1.0

Sodium binding site 2 out of 2 in 4xdu

Go back to Sodium Binding Sites List in 4xdu
Sodium binding site 2 out of 2 in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein,A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Adp Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:22.6
occ:1.00
 O A:HOH787 2.4 35.5 1.0
OE1 A:GLU244 2.5 44.1 1.0
O3B A:ADP505 2.5 16.5 1.0
O A:THR239 2.5 11.7 1.0
O A:HOH789 2.6 22.1 1.0
CD A:GLU244 3.5 38.5 1.0
O A:HOH811 3.6 22.2 1.0
O A:HOH727 3.6 15.3 1.0
PB A:ADP505 3.7 12.2 1.0
O A:HOH826 3.7 41.0 1.0
C A:THR239 3.7 11.0 1.0
HA A:SER240 3.7 12.5 1.0
O A:HOH718 3.7 11.3 1.0
OE2 A:GLU244 3.8 33.1 1.0
O1B A:ADP505 3.9 11.4 1.0
HB A:THR239 4.1 12.8 1.0
H A:THR239 4.3 11.2 1.0
O A:HOH850 4.5 10.4 1.0
O3A A:ADP505 4.5 12.2 1.0
CA A:SER240 4.5 10.4 1.0
N A:SER240 4.6 9.0 1.0
O A:HOH793 4.6 30.6 1.0
CA A:THR239 4.7 9.7 1.0
HB3 A:GLU244 4.7 27.1 1.0
HG A:SER240 4.7 14.5 1.0
HG22 A:THR239 4.7 14.9 1.0
MG A:MG502 4.8 10.0 1.0
O A:GLY189 4.8 17.2 1.0
CB A:THR239 4.8 10.7 1.0
CG A:GLU244 4.8 35.0 1.0
N A:THR239 4.8 9.3 1.0
O2B A:ADP505 4.9 16.4 1.0
H A:GLY241 4.9 16.6 1.0
HE3 A:LYS165 5.0 16.6 1.0

Reference:

R.K.Deka, C.A.Brautigam, W.Z.Liu, D.R.Tomchick, M.V.Norgard. Evidence For Posttranslational Protein Flavinylation in the Syphilis Spirochete Treponema Pallidum: Structural and Biochemical Insights From the Catalytic Core of A Periplasmic Flavin-Trafficking Protein. Mbio V. 6 00519 2015.
ISSN: ESSN 2150-7511
PubMed: 25944861
DOI: 10.1128/MBIO.00519-15
Page generated: Mon Oct 7 19:04:22 2024

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