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Magnesium 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:

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, Fad Bound Form (pdb code 4xdt). 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, Fad Bound Form, PDB code: 4xdt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4xdt

Go back to Magnesium Binding Sites List in 4xdt
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, Fad 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, Fad Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:13.5
occ:1.00
 O1A A:FAD401 2.3 14.7 1.0
OG1 A:THR288 2.3 13.8 1.0
OD1 A:ASP284 2.3 12.4 1.0
O A:ASP284 2.3 11.7 1.0
O A:ALA162 2.4 12.1 1.0
O A:HOH670 2.8 30.8 1.0
HB1 A:ALA162 3.0 15.8 1.0
C A:ASP284 3.1 12.0 1.0
MG A:MG403 3.2 22.0 1.0
HA A:ALA162 3.2 14.4 1.0
CG A:ASP284 3.3 11.8 1.0
C A:ALA162 3.3 11.2 1.0
H A:THR288 3.4 13.7 1.0
PA A:FAD401 3.5 17.5 1.0
HA A:ASP284 3.5 15.2 1.0
CB A:THR288 3.5 12.2 1.0
CA A:ALA162 3.6 12.0 1.0
HB A:THR288 3.6 14.6 1.0
O2A A:FAD401 3.6 21.2 1.0
CA A:ASP284 3.7 12.6 1.0
CB A:ALA162 3.8 13.2 1.0
HA A:ALA285 3.9 13.3 1.0
HB3 A:ALA287 3.9 16.1 1.0
CB A:ASP284 4.0 10.7 1.0
N A:THR288 4.0 11.4 1.0
HG A:SER240 4.1 28.7 1.0
N A:ALA285 4.1 11.3 1.0
OD2 A:ASP284 4.1 12.4 1.0
OG A:SER240 4.2 23.9 1.0
HB2 A:ALA162 4.3 15.8 1.0
O5B A:FAD401 4.3 18.0 1.0
HG11 A:VAL238 4.3 18.5 1.0
HB3 A:ASP284 4.3 12.9 1.0
CA A:THR288 4.3 12.8 1.0
CA A:ALA285 4.4 11.1 1.0
HA A:ILE163 4.4 12.2 1.0
HB3 A:ALA162 4.5 15.8 1.0
N A:ILE163 4.5 10.8 1.0
O A:HOH688 4.5 31.7 1.0
HG21 A:THR288 4.5 17.5 1.0
HA A:THR288 4.6 15.4 1.0
CG2 A:THR288 4.6 14.6 1.0
O A:HOH607 4.7 17.9 1.0
HG12 A:VAL238 4.7 18.5 1.0
O3P A:FAD401 4.7 20.2 1.0
H A:ALA287 4.8 13.9 1.0
H A:ALA285 4.8 13.6 1.0
O A:HOH601 4.8 18.2 1.0
HB2 A:ASP284 4.8 12.9 1.0
CB A:ALA287 4.8 13.4 1.0
C A:ALA285 4.9 12.2 1.0
HG23 A:THR288 4.9 17.5 1.0
O A:HOH671 4.9 34.8 1.0
HE1 A:PHE97 4.9 17.8 1.0
O1P A:FAD401 4.9 25.8 1.0
O A:ALA285 4.9 12.6 1.0
CG1 A:VAL238 5.0 15.4 1.0
C A:ALA287 5.0 11.9 1.0

Magnesium binding site 2 out of 2 in 4xdt

Go back to Magnesium Binding Sites List in 4xdt
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, Fad 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, Fad Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:22.0
occ:1.00
 O A:HOH601 2.1 18.2 1.0
O1A A:FAD401 2.1 14.7 1.0
O1P A:FAD401 2.2 25.8 1.0
OD1 A:ASP284 2.3 12.4 1.0
O A:HOH670 2.8 30.8 1.0
O A:HOH607 2.9 17.9 1.0
HZ1 A:LYS165 2.9 34.2 1.0
O A:HOH671 3.2 34.8 1.0
MG A:MG402 3.2 13.5 1.0
CG A:ASP284 3.2 11.8 1.0
HZ3 A:LYS165 3.3 34.2 1.0
PA A:FAD401 3.4 17.5 1.0
P A:FAD401 3.4 23.4 1.0
NZ A:LYS165 3.5 28.5 1.0
OD2 A:ASP284 3.5 12.4 1.0
O3P A:FAD401 3.6 20.2 1.0
HA A:ALA162 3.8 14.4 1.0
HE2 A:LYS165 3.9 25.4 1.0
HG11 A:VAL238 3.9 18.5 1.0
H5'1 A:FAD401 3.9 64.1 1.0
O A:HOH662 4.0 37.2 1.0
HB2 A:LYS165 4.1 14.2 1.0
HG13 A:VAL238 4.1 18.5 1.0
HZ2 A:LYS165 4.2 34.2 1.0
CE A:LYS165 4.3 21.2 1.0
O A:HOH688 4.3 31.7 1.0
O A:GLY161 4.3 15.1 1.0
O5B A:FAD401 4.3 18.0 1.0
O2P A:FAD401 4.3 32.8 1.0
CG1 A:VAL238 4.3 15.4 1.0
O A:ALA162 4.3 12.1 1.0
HG12 A:VAL238 4.3 18.5 1.0
O2A A:FAD401 4.4 21.2 1.0
OD1 A:ASN191 4.4 15.6 1.0
HA A:ASP284 4.5 15.2 1.0
O5' A:FAD401 4.5 48.3 1.0
C A:ALA162 4.6 11.2 1.0
CA A:ALA162 4.6 12.0 1.0
CB A:ASP284 4.6 10.7 1.0
C5' A:FAD401 4.7 53.4 1.0
HB2 A:ASN191 4.7 18.1 1.0
HE3 A:LYS165 4.7 25.4 1.0
HG A:SER240 4.8 28.7 1.0
OG1 A:THR288 5.0 13.8 1.0
HB2 A:ASP284 5.0 12.9 1.0
CB A:LYS165 5.0 11.8 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 15:26:41 2024

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