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Magnesium 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:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4xdu

Go back to Magnesium Binding Sites List in 4xdu
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg501

b:10.7
occ:1.00
 O A:ASP284 2.3 9.3 1.0
OG1 A:THR288 2.3 10.8 1.0
O1A A:ADP505 2.3 9.2 1.0
OD1 A:ASP284 2.3 10.4 1.0
O A:ALA162 2.3 10.6 1.0
HG1 A:THR288 2.7 12.9 1.0
HB1 A:ALA162 2.9 13.8 1.0
C A:ASP284 3.0 9.4 1.0
HA A:ALA162 3.1 11.2 1.0
CG A:ASP284 3.2 8.5 1.0
C A:ALA162 3.2 9.6 1.0
MG A:MG502 3.2 10.0 1.0
H A:THR288 3.3 11.8 1.0
PA A:ADP505 3.4 9.8 1.0
HA A:ASP284 3.4 10.9 1.0
CA A:ALA162 3.5 9.3 1.0
CB A:THR288 3.5 10.5 1.0
O A:HOH718 3.6 11.3 1.0
HB A:THR288 3.6 12.7 1.0
CA A:ASP284 3.6 9.1 1.0
CB A:ALA162 3.6 11.5 1.0
O2A A:ADP505 3.7 12.2 1.0
HA A:ALA285 3.7 11.9 1.0
HB3 A:ALA287 3.8 12.3 1.0
CB A:ASP284 3.9 8.2 1.0
OG A:SER240 3.9 12.1 1.0
N A:THR288 3.9 9.8 1.0
HG A:SER240 4.0 14.5 1.0
N A:ALA285 4.0 9.2 1.0
OD2 A:ASP284 4.0 10.1 1.0
O A:HOH717 4.0 13.5 1.0
HB2 A:ALA162 4.2 13.8 1.0
HB3 A:ASP284 4.2 9.9 1.0
O5' A:ADP505 4.3 11.3 1.0
CA A:ALA285 4.3 9.9 1.0
CA A:THR288 4.3 10.0 1.0
HB3 A:ALA162 4.3 13.8 1.0
HA A:ILE163 4.4 10.9 1.0
N A:ILE163 4.4 9.6 1.0
HG11 A:VAL238 4.5 12.9 1.0
HA A:THR288 4.5 12.0 1.0
HG21 A:THR288 4.6 13.4 1.0
CG2 A:THR288 4.6 11.2 1.0
H A:ALA285 4.7 11.0 1.0
O3A A:ADP505 4.7 12.2 1.0
C A:ALA285 4.7 9.9 1.0
HE1 A:PHE97 4.7 16.7 1.0
HB2 A:ASP284 4.7 9.9 1.0
CB A:ALA287 4.7 10.3 1.0
H A:ALA287 4.8 11.1 1.0
O A:ALA285 4.8 10.7 1.0
HG12 A:VAL238 4.8 12.9 1.0
O1B A:ADP505 4.9 11.4 1.0
HG23 A:THR288 4.9 13.4 1.0
O A:HOH850 4.9 10.4 1.0
HD1 A:PHE97 4.9 17.1 1.0
C A:ALA287 4.9 9.5 1.0
N A:ALA162 4.9 8.9 1.0
CA A:ILE163 5.0 9.1 1.0

Magnesium binding site 2 out of 2 in 4xdu

Go back to Magnesium Binding Sites List in 4xdu
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502

b:10.0
occ:1.00
 O1B A:ADP505 2.0 11.4 1.0
O A:HOH850 2.1 10.4 1.0
O1A A:ADP505 2.1 9.2 1.0
O A:HOH717 2.1 13.5 1.0
O A:HOH718 2.1 11.3 1.0
OD1 A:ASP284 2.2 10.4 1.0
CG A:ASP284 3.1 8.5 1.0
MG A:MG501 3.2 10.7 1.0
PA A:ADP505 3.2 9.8 1.0
PB A:ADP505 3.3 12.2 1.0
HZ1 A:LYS165 3.3 17.2 1.0
OD2 A:ASP284 3.4 10.1 1.0
O3A A:ADP505 3.5 12.2 1.0
HE2 A:LYS165 3.6 16.6 1.0
HA A:ALA162 3.8 11.2 1.0
HG11 A:VAL238 3.9 12.9 1.0
HZ3 A:LYS165 3.9 17.2 1.0
NZ A:LYS165 3.9 14.3 1.0
HG13 A:VAL238 4.1 12.9 1.0
HG A:SER240 4.1 14.5 1.0
O A:HOH789 4.1 22.1 1.0
O5' A:ADP505 4.1 11.3 1.0
O3B A:ADP505 4.2 16.5 1.0
HG12 A:VAL238 4.2 12.9 1.0
CE A:LYS165 4.2 13.8 1.0
CG1 A:VAL238 4.2 10.8 1.0
HB2 A:LYS165 4.2 11.3 1.0
O A:ALA162 4.3 10.6 1.0
O2B A:ADP505 4.4 16.4 1.0
HA A:ASP284 4.4 10.9 1.0
O A:GLY161 4.4 11.2 1.0
O2A A:ADP505 4.4 12.2 1.0
OD1 A:ASN191 4.4 10.0 1.0
CB A:ASP284 4.5 8.2 1.0
OG A:SER240 4.5 12.1 1.0
HE3 A:LYS165 4.5 16.6 1.0
C A:ALA162 4.6 9.6 1.0
CA A:ALA162 4.7 9.3 1.0
HZ2 A:LYS165 4.7 17.2 1.0
NA A:NA504 4.8 22.6 1.0
HG1 A:THR288 4.8 12.9 1.0
HB2 A:ASN191 4.8 11.0 1.0
HB2 A:ASP284 4.9 9.9 1.0
O A:THR239 4.9 11.7 1.0
CA A:ASP284 4.9 9.1 1.0
OG1 A:THR288 4.9 10.8 1.0
O A:HOH733 4.9 17.1 1.0
O A:ASP284 5.0 9.3 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 Aug 20 15:27:14 2024

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