Magnesium in PDB 4pfy: Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution

The structure of Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution, PDB code: 4pfy was solved by X.Lu, S.Ghimire-Rijal, M.J.Cuneo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.53 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	96.638, 53.600, 106.269, 90.00, 110.51, 90.00
R / Rfree (%)	16.3 / 18.7

The binding sites of Magnesium atom in the Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution (pdb code 4pfy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution, PDB code: 4pfy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution


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 Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:13.8 occ:0.38 O A:HOH876 2.1 29.5 1.0 O A:HOH774 2.1 19.3 1.0 O A:HOH823 2.2 33.1 1.0 O A:HOH1218 2.3 26.9 1.0 O A:HOH866 4.2 32.9 1.0 O A:LYS257 4.2 19.3 1.0 OE1 A:GLU267 4.3 30.5 1.0 O A:ILE262 4.5 15.8 1.0 O A:HOH726 4.6 25.2 1.0 OE2 A:GLU267 4.6 54.1 1.0 CE A:LYS257 4.8 17.3 1.0 CD A:GLU267 4.9 38.4 1.0 O A:HOH770 4.9 34.8 1.0 C A:LYS257 5.0 16.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution


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 Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:18.7 occ:1.00 OD1 A:ASP362 2.0 20.7 1.0 O A:PHE368 2.1 20.4 1.0 OD1 A:ASN364 2.1 21.9 1.0 OE2 A:GLU370 2.1 20.1 1.0 OD1 A:ASP366 2.1 21.7 1.0 OE1 A:GLU370 2.3 21.9 1.0 CD A:GLU370 2.5 20.0 1.0 CG A:ASP366 3.0 30.2 1.0 CG A:ASP362 3.1 25.0 1.0 CG A:ASN364 3.2 24.2 1.0 C A:PHE368 3.2 20.6 1.0 OD2 A:ASP366 3.3 27.0 1.0 ND2 A:ASN364 3.7 31.2 1.0 N A:PHE368 3.8 21.5 1.0 OD2 A:ASP362 3.9 24.8 1.0 CA A:ASP362 3.9 20.7 1.0 CA A:PHE368 3.9 20.8 1.0 CB A:ASP362 3.9 23.2 1.0 N A:ASN364 4.0 23.1 1.0 CG A:GLU370 4.0 20.4 1.0 N A:ASP366 4.1 24.2 1.0 N A:VAL363 4.1 22.0 1.0 CB A:PHE368 4.1 20.9 1.0 CB A:ASP366 4.3 25.6 1.0 N A:ARG369 4.3 20.1 1.0 O A:HOH1230 4.3 37.7 1.0 N A:GLU370 4.4 19.6 1.0 C A:ASP362 4.4 22.8 1.0 CB A:ASN364 4.4 24.4 1.0 C A:ARG369 4.5 18.9 1.0 CA A:ASN364 4.5 25.6 1.0 CA A:ARG369 4.6 19.5 1.0 CA A:ASP366 4.6 28.0 1.0 N A:LYS365 4.6 23.5 1.0 O A:HOH1022 4.6 20.0 1.0 N A:GLY367 4.6 21.9 1.0 C A:ASN364 4.6 28.7 1.0 C A:ASP366 4.8 26.9 1.0 O A:HOH773 4.8 36.7 1.0 CB A:GLU370 4.9 20.4 1.0 C A:GLY367 4.9 22.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mannohexaose Bound Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein (TM1223) From Thermotoga Maritima at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:16.1 occ:1.00 O B:PHE368 2.0 14.6 1.0 OE2 B:GLU370 2.0 18.1 1.0 O B:HOH990 2.0 19.9 1.0 OD1 B:ASN364 2.1 16.7 1.0 OD1 B:ASP362 2.1 17.1 1.0 OD1 B:ASP366 2.1 15.8 1.0 CG B:ASP366 3.0 21.4 1.0 CG B:ASN364 3.0 22.0 1.0 CD B:GLU370 3.1 23.0 1.0 C B:PHE368 3.2 16.4 1.0 CG B:ASP362 3.2 18.7 1.0 OD2 B:ASP366 3.4 22.1 1.0 ND2 B:ASN364 3.5 17.8 1.0 N B:PHE368 3.8 18.1 1.0 CG B:GLU370 3.8 17.8 1.0 CA B:PHE368 3.9 18.2 1.0 CA B:ASP362 3.9 17.6 1.0 CB B:ASP362 3.9 19.2 1.0 N B:ASP366 4.0 16.5 1.0 OD2 B:ASP362 4.1 19.2 1.0 CB B:PHE368 4.1 16.8 1.0 OE1 B:GLU370 4.1 27.5 1.0 N B:ARG369 4.2 15.9 1.0 CB B:ASP366 4.2 18.0 1.0 O B:HOH902 4.3 16.2 1.0 N B:ASN364 4.3 18.2 1.0 N B:LYS365 4.3 18.9 1.0 C B:ASP362 4.3 19.0 1.0 CB B:ASN364 4.4 18.8 1.0 C B:ARG369 4.4 18.1 1.0 N B:GLU370 4.4 18.0 1.0 CA B:ARG369 4.5 15.1 1.0 CA B:ASP366 4.5 17.0 1.0 N B:GLY367 4.5 16.3 1.0 C B:ASN364 4.6 22.7 1.0 CA B:ASN364 4.6 21.7 1.0 N B:VAL363 4.6 19.6 1.0 C B:ASP366 4.7 19.2 1.0 O B:ASP362 4.9 21.2 1.0 O B:ARG369 4.9 18.1 1.0 C B:GLY367 4.9 18.0 1.0

S.Ghimire-Rijal, X.Lu, D.A.Myles, M.J.Cuneo. Duplication of Genes in An Atp-Binding Cassette Transport System Increases Dynamic Range While Maintaining Ligand Specificity. J.Biol.Chem. V. 289 30090 2014.
ISSN: ESSN 1083-351X
PubMed: 25210043
DOI: 10.1074/JBC.M114.590992