Atomistry » Magnesium » PDB 4dhf-4do9 » 4dl8
Atomistry »
  Magnesium »
    PDB 4dhf-4do9 »
      4dl8 »

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: Thu Aug 15 17:13:42 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy