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Magnesium in PDB 6mxd: Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp, PDB code: 6mxd was solved by D.Teran, L.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.27 / 2.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.285, 64.984, 79.075, 85.74, 74.58, 62.87
R / Rfree (%) 25.2 / 30.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp (pdb code 6mxd). 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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp, PDB code: 6mxd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6mxd

Go back to Magnesium Binding Sites List in 6mxd
Magnesium binding site 1 out of 3 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:26.8
occ:1.00
O A:HOH402 2.1 26.3 1.0
O A:HOH401 2.1 28.8 1.0
N A:LYS87 3.5 27.2 1.0
N A:GLY88 3.6 47.8 1.0
NH1 A:ARG214 3.6 33.0 1.0
O2' A:IMP301 4.0 47.7 1.0
CA A:GLY88 4.1 47.2 1.0
NH2 A:ARG214 4.1 35.1 1.0
C A:LYS87 4.2 50.6 1.0
CA A:LYS87 4.2 55.9 1.0
CZ A:ARG214 4.3 33.4 1.0
CB A:LYS87 4.3 27.7 1.0
C A:LEU86 4.4 26.8 1.0
O A:LEU86 4.4 27.3 1.0
OD2 A:ASP148 4.6 46.7 1.0
CG A:GLU208 4.8 45.4 1.0

Magnesium binding site 2 out of 3 in 6mxd

Go back to Magnesium Binding Sites List in 6mxd
Magnesium binding site 2 out of 3 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3302

b:33.8
occ:1.00
O B:HOH3405 2.4 13.2 1.0
NH2 B:ARG214 3.6 52.6 1.0
N B:LYS87 3.7 28.9 1.0
N B:GLY88 4.1 29.8 1.0
CB B:LYS87 4.3 27.8 1.0
CA B:LYS87 4.4 27.6 1.0
O B:LEU86 4.5 30.0 1.0
O2' B:IMP3301 4.5 50.3 1.0
C B:LEU86 4.5 30.1 1.0
C B:LYS87 4.8 27.7 1.0
CZ B:ARG214 4.8 51.5 1.0
CA B:GLY88 5.0 30.2 1.0
OD1 B:ASP148 5.0 72.0 1.0

Magnesium binding site 3 out of 3 in 6mxd

Go back to Magnesium Binding Sites List in 6mxd
Magnesium binding site 3 out of 3 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Imp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:48.1
occ:1.00
NH2 C:ARG214 3.2 37.6 1.0
N C:LYS87 3.5 47.0 1.0
CB C:LYS87 3.7 47.7 1.0
CG C:LYS87 4.0 42.7 1.0
CA C:LYS87 4.1 49.8 1.0
CZ C:ARG214 4.1 35.9 1.0
OE2 C:GLU208 4.2 50.9 1.0
NH1 C:ARG214 4.2 33.5 1.0
N C:GLY88 4.3 57.4 1.0
C C:LYS87 4.6 57.1 1.0
C C:LEU86 4.6 43.5 1.0
O C:LEU86 4.7 42.0 1.0
CD C:GLU208 4.8 49.1 1.0

Reference:

D.Teran, E.Dolezelova, D.T.Keough, D.Hockova, A.Zikova, L.W.Guddat. Crystal Structures of Trypanosoma Brucei Hypoxanthine - Guanine - Xanthine Phosphoribosyltransferase in Complex with Imp, Gmp and Xmp. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31287615
DOI: 10.1111/FEBS.14987
Page generated: Tue Oct 1 12:22:14 2024

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