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Magnesium in PDB 3g6w: Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half

Enzymatic activity of Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half

All present enzymatic activity of Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half:
2.4.2.9;

Protein crystallography data

The structure of Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half, PDB code: 3g6w was solved by A.Kadziola, S.Christoffersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.038, 98.758, 73.528, 90.00, 92.80, 90.00
R / Rfree (%) 21.6 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half (pdb code 3g6w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half, PDB code: 3g6w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3g6w

Go back to Magnesium Binding Sites List in 3g6w
Magnesium binding site 1 out of 4 in the Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:92.1
occ:1.00
 O1B A:GTP301 1.9 30.5 1.0
O1A D:GTP217 2.0 24.1 1.0
O1A A:GTP301 2.0 28.1 1.0
O A:HOH229 2.1 56.6 1.0
O1B D:GTP217 2.1 26.8 1.0
O A:HOH219 2.6 29.5 1.0
PB A:GTP301 3.1 27.8 1.0
PA A:GTP301 3.2 28.8 1.0
PA D:GTP217 3.3 27.7 1.0
PB D:GTP217 3.4 25.7 1.0
O3A A:GTP301 3.4 29.4 1.0
O3A D:GTP217 3.6 25.4 1.0
O2G A:GTP301 3.7 35.6 1.0
O A:HOH221 3.8 21.8 1.0
O5' A:GTP301 3.9 29.5 1.0
O2G D:GTP217 4.0 29.5 1.0
O2B A:GTP301 4.1 31.4 1.0
O5' D:GTP217 4.1 29.9 1.0
O3B A:GTP301 4.2 33.0 1.0
O2B D:GTP217 4.2 28.5 1.0
CE A:LYS30 4.4 28.9 1.0
O2A A:GTP301 4.4 30.1 1.0
PG A:GTP301 4.4 36.1 1.0
O2A D:GTP217 4.4 24.9 1.0
NZ A:LYS30 4.5 25.7 1.0
O3B D:GTP217 4.5 29.4 1.0
N7 D:GTP217 4.6 23.6 1.0
O3G A:GTP301 4.6 35.5 1.0
C8 D:GTP217 4.6 22.9 1.0
CE D:LYS30 4.7 28.4 1.0
C8 A:GTP301 4.7 29.1 1.0
PG D:GTP217 4.8 31.0 1.0
NZ D:LYS30 4.9 27.5 1.0
N7 A:GTP301 4.9 28.3 1.0

Magnesium binding site 2 out of 4 in 3g6w

Go back to Magnesium Binding Sites List in 3g6w
Magnesium binding site 2 out of 4 in the Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:65.5
occ:1.00
 O A:HOH218 2.2 40.2 1.0
O2B A:PRP303 2.2 71.3 1.0
O A:HOH217 2.2 42.9 1.0
O3A A:PRP303 2.3 71.6 1.0
PB A:PRP303 2.3 72.2 1.0
O1B A:PRP303 2.3 70.0 1.0
O1 A:PRP303 2.8 69.0 1.0
PA A:PRP303 3.2 69.6 1.0
O A:LEU79 3.5 35.4 1.0
O2 A:PRP303 3.5 66.5 1.0
O3 A:PRP303 3.5 63.8 1.0
CB A:ARG80 3.6 33.1 1.0
O3B A:PRP303 3.8 71.5 1.0
N A:ALA81 4.0 31.2 1.0
O1A A:PRP303 4.0 68.8 1.0
C1 A:PRP303 4.1 67.2 1.0
C2 A:PRP303 4.2 66.5 1.0
CB A:ALA81 4.3 31.0 1.0
O2A A:PRP303 4.3 69.0 1.0
C3 A:PRP303 4.5 65.2 1.0
C A:LEU79 4.6 36.4 1.0
CG A:ARG80 4.6 33.2 1.0
CA A:ARG80 4.7 33.8 1.0
CA A:ALA81 4.8 30.9 1.0
C A:ARG80 4.8 32.6 1.0
NE A:ARG80 5.0 36.1 1.0

Magnesium binding site 3 out of 4 in 3g6w

Go back to Magnesium Binding Sites List in 3g6w
Magnesium binding site 3 out of 4 in the Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:35.0
occ:1.00
 O D:HOH218 1.9 28.2 1.0
O1A B:GTP301 2.0 35.5 1.0
O1B D:GTP301 2.0 40.9 1.0
O1A D:GTP301 2.1 32.9 1.0
O B:HOH218 2.1 22.6 1.0
O1B B:GTP301 2.1 38.7 1.0
PA D:GTP301 3.3 36.1 1.0
PB D:GTP301 3.3 37.1 1.0
PA B:GTP301 3.3 38.6 1.0
PB B:GTP301 3.4 35.5 1.0
O3A D:GTP301 3.5 36.7 1.0
O2G B:GTP301 3.6 41.2 1.0
O3A B:GTP301 3.6 37.2 1.0
O5' D:GTP301 3.9 35.2 1.0
O3G D:GTP301 3.9 39.5 1.0
O5' B:GTP301 4.0 38.8 1.0
O2B D:GTP301 4.2 38.6 1.0
C8 D:GTP301 4.3 41.1 1.0
O3B D:GTP301 4.3 38.8 1.0
N7 D:GTP301 4.3 41.6 1.0
O2B B:GTP301 4.3 41.4 1.0
O3B B:GTP301 4.4 39.4 1.0
C8 B:GTP301 4.5 39.0 1.0
O2A B:GTP301 4.5 39.5 1.0
CE B:LYS30 4.5 29.3 1.0
O2A D:GTP301 4.5 35.5 1.0
N7 B:GTP301 4.5 38.9 1.0
PG D:GTP301 4.5 39.5 1.0
O2G D:GTP301 4.6 39.2 1.0
NZ B:LYS30 4.6 27.7 1.0
PG B:GTP301 4.6 42.7 1.0
CE C:LYS30 4.8 30.1 1.0
NZ C:LYS30 5.0 28.9 1.0

Magnesium binding site 4 out of 4 in 3g6w

Go back to Magnesium Binding Sites List in 3g6w
Magnesium binding site 4 out of 4 in the Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Asymetric Gtp Bound Structure of Uprtase From Sulfolobus Solfataricus Containing Prpp-MG2+ in Half of the Active Sites and R5P and Ppi in the Other Half within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:80.6
occ:1.00
 O1B D:PRP303 1.9 66.0 1.0
O D:HOH220 2.0 42.1 1.0
O D:HOH219 2.1 38.5 1.0
O3B D:PRP303 2.2 63.2 1.0
PB D:PRP303 2.2 66.0 1.0
O3A D:PRP303 2.5 65.3 1.0
O1 D:PRP303 2.6 64.3 1.0
O2 D:PRP303 2.9 59.0 1.0
O D:LEU79 3.2 26.4 1.0
PA D:PRP303 3.3 65.7 1.0
N D:ALA81 3.6 27.5 1.0
CB D:ARG80 3.6 28.0 1.0
C1 D:PRP303 3.7 61.6 1.0
CB D:ALA81 3.7 29.5 1.0
O2B D:PRP303 3.7 66.4 1.0
C2 D:PRP303 3.9 59.4 1.0
C D:LEU79 4.2 27.4 1.0
O1A D:PRP303 4.2 67.7 1.0
O3 D:PRP303 4.2 57.8 1.0
CA D:ALA81 4.3 26.6 1.0
O2A D:PRP303 4.3 65.8 1.0
CA D:ARG80 4.5 28.5 1.0
C D:ARG80 4.5 28.3 1.0
CG D:ARG80 4.7 29.1 1.0
N D:ARG80 4.7 30.0 1.0
C3 D:PRP303 4.7 57.6 1.0
O D:ALA103 4.8 53.2 1.0
NH1 D:ARG80 4.8 28.6 1.0
O4 D:PRP303 4.9 60.0 1.0

Reference:

S.Christoffersen, A.Kadziola, E.Johansson, M.Rasmussen, M.Willemoes, K.F.Jensen. Structural and Kinetic Studies of the Allosteric Transition in Sulfolobus Solfataricus Uracil Phosphoribosyltransferase: Permanent Activation By Engineering of the C-Terminus J.Mol.Biol. V. 393 464 2009.
ISSN: ISSN 0022-2836
PubMed: 19683539
DOI: 10.1016/J.JMB.2009.08.019
Page generated: Wed Aug 14 14:08:31 2024

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