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Magnesium in PDB 5i1f: Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose

Enzymatic activity of Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose

All present enzymatic activity of Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose:
2.7.7.9;

Protein crystallography data

The structure of Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose, PDB code: 5i1f was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 84.900, 84.900, 252.700, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20.3

Other elements in 5i1f:

The structure of Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose (pdb code 5i1f). 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 Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose, PDB code: 5i1f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5i1f

Go back to Magnesium Binding Sites List in 5i1f
Magnesium binding site 1 out of 2 in the Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose


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 Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:45.2
occ:1.00
 O A:HOH419 1.9 42.3 1.0
O2A A:UPG301 2.0 27.2 1.0
O A:HOH488 2.2 40.2 1.0
O A:HOH427 2.2 41.4 1.0
O A:HOH455 2.3 38.2 1.0
O A:HOH510 2.3 48.8 1.0
PA A:UPG301 3.4 29.3 1.0
OE2 A:GLU228 3.9 62.2 1.0
O3A A:UPG301 3.9 33.2 1.0
O5C A:UPG301 4.0 30.9 1.0
O A:HOH535 4.1 36.7 1.0
OE1 A:GLU228 4.2 56.1 1.0
O A:HOH536 4.3 28.2 1.0
O A:HOH576 4.4 65.3 1.0
O1B A:UPG301 4.4 30.8 1.0
O1A A:UPG301 4.5 22.1 1.0
CD A:GLU228 4.5 61.2 1.0
O A:HOH554 4.5 38.5 1.0
O A:HOH503 4.5 44.5 1.0
O A:HOH570 4.6 49.9 1.0
C6 A:UPG301 4.7 27.8 1.0
CL A:CL308 4.7 34.8 0.8
O A:HOH476 4.7 50.5 1.0
C5 A:UPG301 4.7 30.8 1.0
PB A:UPG301 4.9 32.3 1.0

Magnesium binding site 2 out of 2 in 5i1f

Go back to Magnesium Binding Sites List in 5i1f
Magnesium binding site 2 out of 2 in the Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose


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 Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:29.6
occ:1.00
 O A:HOH465 2.0 28.2 1.0
OD1 A:ASP133 2.1 28.9 1.0
O1A A:UPG301 2.1 22.1 1.0
O2B A:UPG301 2.2 24.8 1.0
O A:HOH418 2.2 26.3 1.0
O A:HOH506 2.2 26.8 1.0
CG A:ASP133 3.1 41.0 1.0
PA A:UPG301 3.3 29.3 1.0
PB A:UPG301 3.4 32.3 1.0
OD2 A:ASP133 3.5 33.0 1.0
O3A A:UPG301 3.5 33.2 1.0
O6' A:UPG301 3.8 35.5 1.0
NZ A:LYS27 3.9 26.3 1.0
O A:HOH473 4.1 40.7 1.0
O A:HOH413 4.2 33.1 1.0
O5' A:UPG301 4.2 28.0 1.0
O A:HOH535 4.2 36.7 1.0
O1B A:UPG301 4.3 30.8 1.0
O5C A:UPG301 4.4 30.9 1.0
O2A A:UPG301 4.4 27.2 1.0
O3B A:UPG301 4.4 30.8 1.0
OD1 A:ASP255 4.4 59.8 1.0
CB A:ASP133 4.4 28.2 1.0
C5C A:UPG301 4.5 27.9 1.0
CA A:GLY257 4.6 37.3 1.0
C1' A:UPG301 4.7 22.6 1.0
CE A:LYS27 4.8 33.3 1.0
C5' A:UPG301 4.8 36.2 1.0
O A:HOH424 4.9 36.7 1.0
C6' A:UPG301 4.9 29.6 1.0

Reference:

J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of Utp-Glucose-1-Phosphate Uridylyltransferase From Burkholderia Vietnamiensis in Complex with Uridine-5'-Diphosphate-Glucose To Be Published.
Page generated: Tue Aug 12 11:22:01 2025

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