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

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

All present enzymatic activity of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Fad 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, Fad Bound Form, PDB code: 4xdt 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) 28.53 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.777, 46.992, 57.566, 90.00, 102.21, 90.00
R / Rfree (%) 16.7 / 19.7

Other elements in 4xdt:

The structure of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, A Bifunctional Fmn Transferase/Fad Pyrophosphatase, N55Y Mutant, Fad 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, Fad Bound Form (pdb code 4xdt). 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, Fad Bound Form, PDB code: 4xdt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4xdt

Go back to Sodium Binding Sites List in 4xdt
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, Fad 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, Fad Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:36.1
occ:1.00
 OE2 A:GLU125 2.4 41.1 1.0
HG2 A:GLU125 2.7 35.4 1.0
OG1 A:THR128 3.1 25.2 1.0
HG1 A:THR128 3.1 30.3 1.0
CD A:GLU125 3.2 33.5 1.0
O A:HOH564 3.3 25.9 1.0
CG A:GLU125 3.4 29.5 1.0
HG3 A:ARG129 3.4 32.9 1.0
HD3 A:ARG129 3.5 36.2 1.0
HE A:ARG129 3.5 34.1 1.0
HG3 A:GLU125 3.8 35.4 1.0
O A:GLU125 3.8 26.4 1.0
O A:HOH503 3.9 33.2 1.0
CD A:ARG129 4.0 30.1 1.0
CG A:ARG129 4.1 27.4 1.0
NE A:ARG129 4.1 28.4 1.0
HG2 A:ARG129 4.2 32.9 1.0
OE1 A:GLU125 4.4 34.3 1.0
CB A:THR128 4.4 27.7 1.0
HA A:GLU125 4.4 36.7 1.0
C A:GLU125 4.6 26.5 1.0
HG21 A:THR128 4.6 34.9 1.0
CB A:GLU125 4.7 30.0 1.0
HB A:THR128 4.7 33.2 1.0
CA A:GLU125 4.8 30.6 1.0
O A:HOH582 4.8 35.1 1.0
HD2 A:ARG129 4.9 36.2 1.0
CG2 A:THR128 5.0 29.1 1.0

Sodium binding site 2 out of 2 in 4xdt

Go back to Sodium Binding Sites List in 4xdt
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, Fad 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, Fad Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:34.6
occ:1.00
 O A:HOH708 2.1 33.1 1.0
O A:HIS267 2.2 25.7 1.0
O A:HOH619 2.3 25.5 1.0
O A:HOH668 2.5 42.7 1.0
O A:HOH700 2.6 23.3 1.0
HA A:THR268 3.3 19.8 1.0
C A:HIS267 3.4 22.5 1.0
O A:HOH611 3.8 19.5 1.0
O A:VAL292 4.0 15.7 1.0
H A:HIS267 4.0 22.9 1.0
HB2 A:HIS267 4.0 33.4 1.0
O A:HOH635 4.1 27.3 1.0
HB A:THR268 4.1 24.0 1.0
CA A:THR268 4.1 16.5 1.0
N A:THR268 4.2 19.6 1.0
N A:HIS267 4.4 19.1 1.0
CA A:HIS267 4.4 24.7 1.0
O A:HOH687 4.4 36.0 1.0
OD2 A:ASP259 4.5 24.4 1.0
CB A:THR268 4.6 20.0 1.0
HB1 A:ALA266 4.6 23.9 1.0
CB A:HIS267 4.6 27.9 1.0
HB3 A:HIS267 4.8 33.4 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: Tue Dec 15 09:44:43 2020

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