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Magnesium in PDB 4dl8: Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+:
3.6.1.23;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+, PDB code: 4dl8 was solved by G.R.Hemsworth, D.Gonzalez-Pacanowska, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.20 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.590, 68.590, 123.759, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.4

Other elements in 4dl8:

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+ also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Aluminium (Al) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+ (pdb code 4dl8). 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 Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+, PDB code: 4dl8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4dl8

Go back to Magnesium Binding Sites List in 4dl8
Magnesium binding site 1 out of 2 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+


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 Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:18.9
occ:1.00
 OP2 A:UMP301 1.9 17.4 1.0
O2 A:PO4303 1.9 24.7 1.0
F3 A:AF3302 2.0 19.4 1.0
OE2 A:GLU51 2.0 22.7 1.0
OE2 A:GLU48 2.1 19.6 1.0
O A:HOH437 2.2 20.9 1.0
CD A:GLU48 3.0 18.8 1.0
CD A:GLU51 3.0 23.0 1.0
P A:PO4303 3.1 31.1 1.0
P A:UMP301 3.2 17.5 1.0
OE1 A:GLU48 3.2 17.3 1.0
OE1 A:GLU51 3.3 22.4 1.0
O1 A:PO4303 3.3 27.6 1.0
OP1 A:UMP301 3.4 16.1 1.0
AL A:AF3302 3.4 24.3 1.0
MG A:MG305 3.5 18.3 1.0
O A:HOH416 3.8 20.7 1.0
O3 A:PO4303 3.9 30.3 1.0
C5' A:UMP301 4.1 15.7 1.0
O5' A:UMP301 4.2 16.4 1.0
O A:HOH464 4.2 37.9 1.0
OP3 A:UMP301 4.2 17.8 1.0
O A:HOH401 4.3 16.9 1.0
CG A:GLU48 4.3 17.8 1.0
O4 A:PO4303 4.3 30.5 1.0
CG A:GLU51 4.4 19.8 1.0
F1 A:AF3302 4.5 22.6 1.0
OD2 A:ASP79 4.9 17.0 1.0

Magnesium binding site 2 out of 2 in 4dl8

Go back to Magnesium Binding Sites List in 4dl8
Magnesium binding site 2 out of 2 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+


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 Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:18.3
occ:1.00
 OE1 A:GLU76 1.9 22.1 1.0
F3 A:AF3302 2.0 19.4 1.0
OE1 A:GLU48 2.0 17.3 1.0
OD2 A:ASP79 2.0 17.0 1.0
O A:HOH401 2.1 16.9 1.0
OE1 A:GLU51 2.1 22.4 1.0
CD A:GLU76 3.0 20.3 1.0
AL A:AF3302 3.0 24.3 1.0
CD A:GLU48 3.1 18.8 1.0
CD A:GLU51 3.1 23.0 1.0
CG A:ASP79 3.2 22.5 1.0
NA A:NA306 3.3 20.6 1.0
OE2 A:GLU76 3.4 20.9 1.0
OE2 A:GLU51 3.5 22.7 1.0
F1 A:AF3302 3.5 22.6 1.0
MG A:MG304 3.5 18.9 1.0
OE2 A:GLU48 3.5 19.6 1.0
O1 A:PO4303 3.7 27.6 1.0
CB A:ASP79 3.8 15.9 1.0
OD1 A:ASP79 4.2 16.5 1.0
CG A:GLU76 4.3 18.0 1.0
CG A:GLU51 4.4 19.8 1.0
CG A:GLU48 4.4 17.8 1.0
CA A:GLU76 4.4 14.4 1.0
OP1 A:UMP301 4.5 16.1 1.0
CB A:GLU51 4.5 17.7 1.0
F2 A:AF3302 4.5 24.8 1.0
OP2 A:UMP301 4.6 17.4 1.0
O2 A:PO4303 4.6 24.7 1.0
CB A:GLU76 4.7 15.9 1.0
NZ A:LYS208 4.7 15.4 1.0
P A:PO4303 4.7 31.1 1.0
C5' A:UMP301 4.8 15.7 1.0
CB A:GLU48 4.9 18.4 1.0
CG2 A:ILE75 4.9 17.7 1.0
O A:HOH403 5.0 23.5 1.0

Reference:

G.R.Hemsworth, D.Gonzalez-Pacanowska, K.S.Wilson. On the Catalytic Mechanism of Dimeric Dutpases. Biochem.J. V. 456 81 2013.
ISSN: ISSN 0264-6021
PubMed: 24001052
DOI: 10.1042/BJ20130796
Page generated: Mon Aug 11 07:33:59 2025

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