Magnesium in PDB 4ifw: Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Adp Inhibited Form

The structure of Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Adp Inhibited Form, PDB code: 4ifw 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)	29.65 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.829, 47.252, 57.643, 90.00, 102.03, 90.00
R / Rfree (%)	17.7 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Adp Inhibited Form (pdb code 4ifw). 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, Adp Inhibited Form, PDB code: 4ifw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Adp Inhibited 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, Adp Inhibited Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:3.3 occ:1.00 O A:HOH601 2.1 24.0 1.0 OD1 A:ASP284 2.1 18.8 1.0 O A:ASP284 2.1 1.8 1.0 OG1 A:THR288 2.2 9.4 1.0 O1A A:ADP501 2.3 9.7 1.0 O A:ALA162 2.4 3.4 1.0 HG1 A:THR288 2.6 11.3 1.0 CG A:ASP284 3.1 12.2 1.0 C A:ASP284 3.1 5.4 1.0 HB1 A:ALA162 3.1 10.1 1.0 MG A:MG503 3.2 26.0 1.0 HA A:ALA162 3.3 8.3 1.0 C A:ALA162 3.4 4.2 1.0 H A:THR288 3.4 8.6 1.0 PA A:ADP501 3.4 27.3 1.0 CB A:THR288 3.5 7.1 1.0 HA A:ASP284 3.5 3.3 1.0 HB A:THR288 3.6 8.5 1.0 O2A A:ADP501 3.7 31.8 1.0 CA A:ALA162 3.7 6.9 1.0 CA A:ASP284 3.7 2.8 1.0 HB3 A:ALA287 3.8 2.3 1.0 CB A:ALA162 3.8 8.4 1.0 OD2 A:ASP284 3.8 10.4 1.0 HA A:ALA285 3.8 7.9 1.0 CB A:ASP284 3.9 4.0 1.0 N A:THR288 4.0 7.1 1.0 N A:ALA285 4.1 3.0 1.0 HG A:SER240 4.1 37.9 1.0 HB3 A:ASP284 4.2 4.8 1.0 CA A:THR288 4.2 7.5 1.0 HG11 A:VAL238 4.3 12.8 1.0 OG A:SER240 4.3 31.5 1.0 O5' A:ADP501 4.3 37.4 1.0 HB2 A:ALA162 4.3 10.1 1.0 O3B A:ADP501 4.4 33.8 1.0 CA A:ALA285 4.4 6.6 1.0 HA A:THR288 4.4 9.0 1.0 O A:HOH602 4.4 12.3 1.0 HB3 A:ALA162 4.5 10.1 1.0 HA A:ILE163 4.5 3.1 1.0 HG21 A:THR288 4.6 9.3 1.0 N A:ILE163 4.6 2.5 1.0 O A:HOH603 4.6 16.8 1.0 CG2 A:THR288 4.6 7.8 1.0 HE1 A:PHE97 4.7 24.4 1.0 O3A A:ADP501 4.7 15.4 1.0 CB A:ALA287 4.7 1.9 1.0 HG12 A:VAL238 4.7 12.8 1.0 HB2 A:ASP284 4.8 4.8 1.0 HG23 A:THR288 4.8 9.3 1.0 H A:ALA285 4.8 3.6 1.0 O A:HOH604 4.9 47.8 1.0 C A:ALA285 4.9 14.4 1.0 H A:ALA287 4.9 16.0 1.0 C A:ALA287 4.9 6.4 1.0 O A:ALA285 4.9 2.1 1.0 CG1 A:VAL238 4.9 10.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Treponema Pallidum TP0796 Flavin Trafficking Protein, Adp Inhibited 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, Adp Inhibited Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:26.0 occ:1.00 O A:HOH604 2.1 47.8 1.0 OD1 A:ASP284 2.1 18.8 1.0 O A:HOH602 2.1 12.3 1.0 O3B A:ADP501 2.1 33.8 1.0 O1A A:ADP501 2.4 9.7 1.0 OD2 A:ASP284 2.4 10.4 1.0 CG A:ASP284 2.5 12.2 1.0 MG A:MG502 3.2 3.3 1.0 O A:HOH601 3.3 24.0 1.0 O A:HOH603 3.3 16.8 1.0 HD21 A:ASN191 3.5 28.7 1.0 HB2 A:LYS165 3.6 13.1 1.0 PB A:ADP501 3.6 42.4 1.0 HD2 A:LYS165 3.6 27.7 1.0 HA A:ALA162 3.7 8.3 1.0 PA A:ADP501 3.8 27.3 1.0 HG11 A:VAL238 3.8 12.8 1.0 O A:ALA162 3.8 3.4 1.0 CB A:ASP284 4.0 4.0 1.0 O3A A:ADP501 4.1 15.4 1.0 HG13 A:VAL238 4.1 12.8 1.0 C A:ALA162 4.1 4.2 1.0 O A:GLY161 4.2 12.4 1.0 HZ3 A:LYS165 4.2 35.4 1.0 ND2 A:ASN191 4.3 23.9 1.0 HA A:ASP284 4.3 3.3 1.0 CG1 A:VAL238 4.3 10.7 1.0 HB2 A:ASP284 4.3 4.8 1.0 CA A:ALA162 4.4 6.9 1.0 HD22 A:ASN191 4.4 28.7 1.0 O2B A:ADP501 4.5 40.5 1.0 HZ2 A:LYS165 4.5 35.4 1.0 HG12 A:VAL238 4.5 12.8 1.0 CB A:LYS165 4.5 10.9 1.0 CD A:LYS165 4.5 23.1 1.0 O1B A:ADP501 4.6 43.9 1.0 HB3 A:ASP284 4.6 4.8 1.0 H A:LYS165 4.6 3.8 1.0 O A:ASP284 4.6 1.8 1.0 CA A:ASP284 4.7 2.8 1.0 O5' A:ADP501 4.7 37.4 1.0 HB2 A:ASN191 4.8 22.0 1.0 NZ A:LYS165 4.8 29.5 1.0 H A:GLY166 4.8 3.2 1.0 HG3 A:LYS165 4.8 15.2 1.0 HA A:ILE163 4.8 3.1 1.0 N A:ILE163 4.8 2.5 1.0 O2A A:ADP501 4.9 31.8 1.0 HB3 A:LYS165 4.9 13.1 1.0 CG A:LYS165 4.9 12.7 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