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Sodium 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
Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, Planar [ALF3-OPO3] Transition State Analogue, MG2+, and Na+, PDB code: 4dl8:

Sodium binding site 1 out of 1 in 4dl8

Go back to Sodium Binding Sites List in 4dl8
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na306

b:20.6
occ:1.00
 O A:HOH402 2.2 37.0 1.0
OE2 A:GLU76 2.2 20.9 1.0
O A:HOH401 2.2 16.9 1.0
O A:HOH403 2.3 23.5 1.0
OE1 A:GLU51 2.4 22.4 1.0
O A:HOH485 2.9 41.8 1.0
O1 A:PO4303 3.0 27.6 1.0
CD A:GLU76 3.1 20.3 1.0
MG A:MG305 3.3 18.3 1.0
OE1 A:GLU76 3.3 22.1 1.0
CD A:GLU51 3.5 23.0 1.0
AL A:AF3302 3.6 24.3 1.0
O3 A:PO4303 3.7 30.3 1.0
F3 A:AF3302 3.9 19.4 1.0
P A:PO4303 4.0 31.1 1.0
F2 A:AF3302 4.0 24.8 1.0
CG A:GLU51 4.1 19.8 1.0
CB A:GLU51 4.2 17.7 1.0
OE2 A:GLU51 4.4 22.7 1.0
OD1 A:ASN72 4.4 19.2 1.0
OE1 A:GLU233 4.4 27.5 1.0
ND2 A:ASN72 4.5 16.6 1.0
CG A:GLU76 4.5 18.0 1.0
ND2 A:ASN235 4.6 16.3 1.0
O A:HOH418 4.7 22.0 1.0
OD2 A:ASP79 4.8 17.0 1.0
F1 A:AF3302 4.8 22.6 1.0
O2 A:PO4303 4.9 24.7 1.0
OE1 A:GLU48 4.9 17.3 1.0
CG A:ASN72 4.9 16.4 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 Oct 7 14:57:31 2024

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