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Magnesium in PDB 3gf0: Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium

Enzymatic activity of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium

All present enzymatic activity of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium:
3.5.4.30;

Protein crystallography data

The structure of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium, PDB code: 3gf0 was solved by J.H.B.Siggaard, E.Johansson, T.Vognsen, S.S.Helt, P.Harris, M.Willemoes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.26 / 2.62
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 171.569, 171.569, 171.569, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium (pdb code 3gf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium, PDB code: 3gf0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3gf0

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Magnesium binding site 1 out of 4 in the Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:57.5
occ:1.00
 O5 A:POP277 2.3 21.3 0.5
O2 A:POP277 2.4 22.2 0.5
P2 A:POP277 3.0 23.0 0.5
O A:POP277 3.0 21.8 0.5
P1 A:POP277 3.1 22.2 0.5
O4 A:POP277 3.4 21.0 0.5
O1 A:POP277 4.1 21.1 0.5
O3 A:POP277 4.1 21.5 0.5
O6 A:POP277 4.3 22.2 0.5
OD1 A:ASP135 4.5 41.9 1.0
OD2 A:ASP135 4.6 32.8 1.0
CE1 A:TYR177 4.6 18.8 0.5
O A:HOH340 4.6 43.7 1.0
O A:HOH307 4.7 35.2 1.0
CG A:ASP135 5.0 36.0 1.0

Magnesium binding site 2 out of 4 in 3gf0

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Magnesium binding site 2 out of 4 in the Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:15.7
occ:1.00
 O A:GLY95 2.5 17.2 1.0
O A:GLU93 2.6 19.8 1.0
O A:HOH299 3.1 29.3 1.0
C A:GLY95 3.6 16.6 1.0
N A:GLY95 3.6 14.9 1.0
CG2 A:ILE42 3.8 19.6 1.0
C A:GLU93 3.8 19.5 1.0
C A:GLY94 3.9 15.9 1.0
O A:HOH314 4.0 30.7 1.0
CA A:GLY95 4.0 15.5 1.0
CA A:GLY94 4.2 16.1 1.0
O A:HOH337 4.4 44.2 1.0
N A:GLY94 4.5 17.7 1.0
O A:GLY94 4.6 15.6 1.0
N A:VAL96 4.7 15.7 1.0
N A:GLU93 4.8 19.8 1.0
CD1 A:ILE42 4.8 28.5 1.0
CA A:GLU93 4.9 20.9 1.0

Magnesium binding site 3 out of 4 in 3gf0

Go back to Magnesium Binding Sites List in 3gf0
Magnesium binding site 3 out of 4 in the Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:36.2
occ:0.45
 O A:HOH348 3.9 37.6 0.5
CE1 A:HIS128 4.4 22.0 0.5
NE2 A:HIS128 4.6 24.4 0.5

Magnesium binding site 4 out of 4 in 3gf0

Go back to Magnesium Binding Sites List in 3gf0
Magnesium binding site 4 out of 4 in the Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex with Pyrophosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg276

b:36.6
occ:0.45
 CD2 A:HIS128 2.6 22.6 0.5
NE2 A:HIS128 2.7 24.4 0.5
O A:HOH348 3.0 37.6 0.5
N A:GLY116 3.2 23.9 1.0
CA A:GLN115 3.3 24.2 1.0
CB A:GLN115 3.5 25.4 1.0
C A:GLN115 3.7 23.9 1.0
CG A:HIS128 3.8 24.2 0.5
CE1 A:HIS128 3.8 22.0 0.5
O A:HOH349 3.9 15.6 0.6
O A:TYR114 4.2 20.9 1.0
CA A:GLY116 4.3 23.8 1.0
ND1 A:HIS128 4.3 22.8 0.5
N A:GLN115 4.6 22.9 1.0
CB A:HIS128 4.7 23.3 0.6
CG A:GLN115 4.7 33.0 1.0
C A:TYR114 4.8 21.1 1.0
CB A:HIS128 4.8 23.3 0.5
OE1 A:GLN115 4.8 48.2 1.0
O A:GLY116 4.9 24.3 1.0
O A:GLN115 4.9 25.2 1.0

Reference:

J.H.B.Siggaard, E.Johansson, T.Vognsen, S.S.Helt, P.Harris, S.Larsen, M.Willemoes. Pre-Steady State Kinetic and Structural Evidence For A Concerted Biofunctionality in Dctp Deaminase-Dutpase From Methanocaldococcus Jannaschii To Be Published.
Page generated: Sun Aug 10 21:39:51 2025

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