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Magnesium in PDB 4dlc: Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+:
3.6.1.23;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+, PDB code: 4dlc 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) 48.28 / 1.76
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.280, 68.280, 123.660, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.4

Other elements in 4dlc:

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+ also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+ (pdb code 4dlc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+, PDB code: 4dlc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4dlc

Go back to Magnesium Binding Sites List in 4dlc
Magnesium binding site 1 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+


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, MGF3- Transition State Analogue, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:31.2
occ:1.00
 MG A:MGF302 0.0 31.2 1.0
F1 A:MGF302 1.7 28.8 1.0
F3 A:MGF302 1.8 28.5 1.0
F2 A:MGF302 1.8 36.9 1.0
O A:HOH405 1.9 24.7 1.0
OP1 A:UMP301 2.0 38.7 1.0
MG A:MG304 3.0 18.2 1.0
P A:UMP301 3.2 0.9 1.0
O A:HOH406 3.4 37.3 1.0
O A:HOH404 3.4 32.5 1.0
MG A:MG303 3.5 32.2 1.0
OP2 A:UMP301 3.6 41.7 1.0
OD2 A:ASP79 3.6 19.2 1.0
NZ A:LYS227 3.7 29.5 1.0
OE1 A:GLU51 3.7 29.1 1.0
MG A:MG305 3.7 27.1 1.0
NH1 A:ARG215 4.0 19.5 1.0
NZ A:LYS208 4.0 18.3 1.0
OD1 A:ASN235 4.1 21.7 1.0
NH2 A:ARG215 4.1 19.1 1.0
O5' A:UMP301 4.2 26.9 1.0
OP3 A:UMP301 4.3 30.5 1.0
C5' A:UMP301 4.4 20.8 1.0
CZ A:ARG215 4.5 17.1 1.0
OE1 A:GLU48 4.6 21.6 1.0
CG A:ASP79 4.7 19.2 1.0
CD A:GLU51 4.7 49.5 1.0
O A:HOH402 4.7 24.3 1.0
OE1 A:GLU76 4.7 21.2 1.0
OE2 A:GLU51 4.7 47.7 1.0
CE A:LYS227 4.8 34.9 1.0
OH A:TYR220 4.8 25.1 1.0
OE2 A:GLU48 4.9 24.6 1.0
CE A:LYS208 4.9 18.8 1.0
CD A:LYS227 5.0 45.5 1.0

Magnesium binding site 2 out of 4 in 4dlc

Go back to Magnesium Binding Sites List in 4dlc
Magnesium binding site 2 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+


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, MGF3- Transition State Analogue, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:32.2
occ:1.00
 OP2 A:UMP301 1.9 41.7 1.0
OE2 A:GLU51 2.2 47.7 1.0
F3 A:MGF302 2.2 28.5 1.0
OE2 A:GLU48 2.3 24.6 1.0
O A:HOH406 2.3 37.3 1.0
O A:HOH403 2.5 30.3 1.0
CD A:GLU51 3.0 49.5 1.0
CD A:GLU48 3.0 22.2 1.0
OE1 A:GLU51 3.1 29.1 1.0
OE1 A:GLU48 3.1 21.6 1.0
P A:UMP301 3.2 0.9 1.0
MG A:MG304 3.2 18.2 1.0
OP1 A:UMP301 3.5 38.7 1.0
MG A:MGF302 3.5 31.2 1.0
F2 A:MGF302 3.9 36.9 1.0
O A:HOH438 3.9 23.6 1.0
OP3 A:UMP301 4.0 30.5 1.0
O A:HOH405 4.1 24.7 1.0
C5' A:UMP301 4.2 20.8 1.0
O5' A:UMP301 4.3 26.9 1.0
CG A:GLU48 4.4 22.0 1.0
CG A:GLU51 4.4 28.2 1.0
O A:HOH559 4.6 39.5 1.0
OD2 A:ASP79 4.7 19.2 1.0
OE1 A:GLU76 4.9 21.2 1.0

Magnesium binding site 3 out of 4 in 4dlc

Go back to Magnesium Binding Sites List in 4dlc
Magnesium binding site 3 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+


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 Dutpase with Dump, MGF3- Transition State Analogue, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:18.2
occ:1.00
 F3 A:MGF302 1.9 28.5 1.0
OE1 A:GLU76 2.0 21.2 1.0
OE1 A:GLU48 2.0 21.6 1.0
O A:HOH405 2.1 24.7 1.0
OD2 A:ASP79 2.1 19.2 1.0
OE1 A:GLU51 2.2 29.1 1.0
MG A:MGF302 3.0 31.2 1.0
CD A:GLU76 3.1 21.2 1.0
CD A:GLU48 3.1 22.2 1.0
CD A:GLU51 3.2 49.5 1.0
CG A:ASP79 3.2 19.2 1.0
MG A:MG303 3.2 32.2 1.0
MG A:MG305 3.3 27.1 1.0
OE2 A:GLU76 3.5 21.6 1.0
OE2 A:GLU48 3.5 24.6 1.0
OE2 A:GLU51 3.6 47.7 1.0
CB A:ASP79 3.8 15.7 1.0
F1 A:MGF302 4.0 28.8 1.0
F2 A:MGF302 4.2 36.9 1.0
OD1 A:ASP79 4.2 16.8 1.0
O A:HOH406 4.3 37.3 1.0
OP2 A:UMP301 4.4 41.7 1.0
CG A:GLU76 4.4 16.2 1.0
CG A:GLU48 4.4 22.0 1.0
OP1 A:UMP301 4.4 38.7 1.0
CG A:GLU51 4.5 28.2 1.0
CB A:GLU51 4.6 22.1 1.0
CA A:GLU76 4.6 16.1 1.0
NZ A:LYS208 4.8 18.3 1.0
O A:HOH402 4.8 24.3 1.0
O A:HOH404 4.8 32.5 1.0
CB A:GLU76 4.8 15.8 1.0
CB A:GLU48 4.9 23.1 1.0
P A:UMP301 4.9 0.9 1.0
C5' A:UMP301 4.9 20.8 1.0

Magnesium binding site 4 out of 4 in 4dlc

Go back to Magnesium Binding Sites List in 4dlc
Magnesium binding site 4 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Trypanosoma Brucei Dutpase with Dump, MGF3- Transition State Analogue, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:27.1
occ:1.00
 OE2 A:GLU76 2.0 21.6 1.0
O A:HOH402 2.1 24.3 1.0
O A:HOH405 2.2 24.7 1.0
O A:HOH401 2.2 33.4 1.0
O A:HOH404 2.4 32.5 1.0
OE1 A:GLU51 2.6 29.1 1.0
CD A:GLU76 3.0 21.2 1.0
OE1 A:GLU76 3.3 21.2 1.0
MG A:MG304 3.3 18.2 1.0
CD A:GLU51 3.6 49.5 1.0
F2 A:MGF302 3.7 36.9 1.0
MG A:MGF302 3.7 31.2 1.0
F3 A:MGF302 4.1 28.5 1.0
OD1 A:ASN72 4.2 21.1 1.0
CG A:GLU51 4.2 28.2 1.0
OE2 A:GLU233 4.3 31.2 1.0
CB A:GLU51 4.3 22.1 1.0
ND2 A:ASN72 4.3 18.2 1.0
CG A:GLU76 4.3 16.2 1.0
O A:HOH406 4.5 37.3 1.0
F1 A:MGF302 4.6 28.8 1.0
O A:HOH421 4.6 21.8 1.0
OE2 A:GLU51 4.6 47.7 1.0
CG A:ASN72 4.7 19.7 1.0
OD1 A:ASN235 4.7 21.7 1.0
OD2 A:ASP79 4.8 19.2 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 17:14:03 2024

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