Manganese in PDB 4ifz: Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Mn(II)-Amp Product Bound Form

The structure of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Mn(II)-Amp Product Bound Form, PDB code: 4ifz 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)	29.53 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.632, 46.907, 57.625, 90.00, 102.17, 90.00
R / Rfree (%)	15.9 / 20.3

The structure of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Mn(II)-Amp Product Bound Form also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Mn(II)-Amp Product Bound Form (pdb code 4ifz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Mn(II)-Amp Product Bound Form, PDB code: 4ifz:

Manganese binding site 1 out of 1 in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Mn(II)-Amp Product Bound Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Mn(II)-Amp Product Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:18.8 occ:1.00 OD1 A:ASP284 2.1 14.8 1.0 O A:HOH604 2.2 16.1 1.0 O1P A:AMP501 2.2 14.2 1.0 O A:HOH601 2.2 19.0 1.0 O A:HOH602 2.2 15.3 1.0 O A:HOH603 2.3 21.1 1.0 CG A:ASP284 3.1 17.8 1.0 MG A:MG502 3.2 14.5 1.0 P A:AMP501 3.3 17.1 1.0 OD2 A:ASP284 3.4 14.7 1.0 HE2 A:LYS165 3.5 25.0 1.0 HZ1 A:LYS165 3.5 28.3 1.0 O3P A:AMP501 3.6 17.4 1.0 HG11 A:VAL238 3.8 22.8 1.0 HA A:ALA162 3.9 15.1 1.0 HZ3 A:LYS165 4.0 28.3 1.0 HG12 A:VAL238 4.0 22.8 1.0 HG13 A:VAL238 4.0 22.8 1.0 NZ A:LYS165 4.0 23.6 1.0 O A:HOH728 4.2 29.8 1.0 CG1 A:VAL238 4.2 19.0 1.0 O A:HOH605 4.2 46.1 1.0 HB2 A:LYS165 4.2 21.6 1.0 CE A:LYS165 4.2 20.8 1.0 O5' A:AMP501 4.3 22.6 1.0 HA A:ASP284 4.4 14.4 1.0 O A:ALA162 4.4 16.6 1.0 O2P A:AMP501 4.4 17.1 1.0 OD1 A:ASN191 4.4 17.7 1.0 O A:GLY161 4.4 14.2 1.0 CB A:ASP284 4.5 11.5 1.0 HE3 A:LYS165 4.6 25.0 1.0 OG A:SER240 4.6 21.7 1.0 C A:ALA162 4.6 13.1 1.0 O A:HOH719 4.6 38.3 1.0 CA A:ALA162 4.7 12.6 1.0 HG A:SER240 4.8 26.0 1.0 O A:THR239 4.8 18.8 1.0 HB2 A:ASP284 4.8 13.8 1.0 HZ2 A:LYS165 4.9 28.3 1.0 CA A:ASP284 4.9 12.0 1.0 HB2 A:ASN191 4.9 21.4 1.0 O A:ASP284 4.9 12.0 1.0 OG1 A:THR288 5.0 18.1 1.0

R.K.Deka, C.A.Brautigam, W.Z.Liu, D.R.Tomchick, M.V.Norgard. The TP0796 Lipoprotein of Treponema Pallidum Is A Bimetal-Dependent Fad Pyrophosphatase with A Potential Role in Flavin Homeostasis. J.Biol.Chem. V. 288 11106 2013.
ISSN: ISSN 0021-9258
PubMed: 23447540
DOI: 10.1074/JBC.M113.449975