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Magnesium in PDB 3mbi: Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate

Enzymatic activity of Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate

All present enzymatic activity of Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate:
2.7.6.1;

Protein crystallography data

The structure of Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate, PDB code: 3mbi was solved by L.T.Cherney, M.M.Cherney, C.R.Garen, M.N.G.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.47 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.599, 61.841, 127.938, 90.00, 103.94, 90.00
R / Rfree (%) 17.6 / 21.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate (pdb code 3mbi). 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 the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate, PDB code: 3mbi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3mbi

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate


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 the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg287

b:20.7
occ:0.41
 O A:HOH294 2.1 31.5 1.0
O A:HOH293 2.1 33.6 1.0
O A:HOH292 2.2 22.6 1.0
O A:HOH303 2.2 14.8 1.0
O2A A:ADP288 2.2 24.6 1.0
O2B A:ADP288 2.4 19.1 0.5
NE2 A:HIS93 3.0 15.8 1.0
NE2 A:HIS124 3.5 14.9 1.0
PA A:ADP288 3.5 16.4 1.0
O A:HOH295 3.6 34.8 1.0
PB A:ADP288 3.8 20.9 1.0
OH A:TYR96 3.8 15.7 1.0
CE1 A:HIS93 3.9 13.7 1.0
CD2 A:HIS124 3.9 12.3 1.0
O3A A:ADP288 4.0 13.2 0.9
CD2 A:HIS93 4.1 10.4 1.0
O5' A:ADP288 4.1 17.3 0.9
C5' A:ADP288 4.5 15.5 1.0
O3B A:ADP288 4.5 23.6 0.9
CE1 A:HIS124 4.7 15.8 1.0
OD1 A:ASP125 4.7 15.1 1.0
O1A A:ADP288 4.8 20.4 1.0
O1B A:ADP288 4.8 20.6 1.0
O A:ARG91 4.9 8.4 1.0
CZ A:TYR96 4.9 14.7 1.0
O A:HOH304 5.0 11.8 1.0

Magnesium binding site 2 out of 4 in 3mbi

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate


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 the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg287

b:38.9
occ:1.00
 O2A B:ADP288 2.0 24.6 1.0
O2B B:ADP288 2.1 21.7 0.5
O B:HOH293 2.1 18.8 1.0
O B:HOH291 3.0 25.7 1.0
NE2 B:HIS124 3.1 15.0 1.0
PA B:ADP288 3.2 20.5 1.0
PB B:ADP288 3.3 26.7 0.9
O B:HOH294 3.3 31.3 1.0
O3A B:ADP288 3.6 15.9 0.8
CD2 B:HIS124 3.7 15.2 1.0
NE2 B:HIS93 3.7 18.3 1.0
O5' B:ADP288 3.7 20.3 0.8
O3B B:ADP288 3.9 24.0 1.0
OH B:TYR96 4.1 18.3 1.0
CE1 B:HIS124 4.2 17.7 1.0
C5' B:ADP288 4.2 18.5 1.0
O B:HOH295 4.4 14.8 1.0
O B:HOH1245 4.5 42.7 1.0
O1A B:ADP288 4.5 22.0 1.0
O1B B:ADP288 4.5 25.4 0.9
O B:HOH595 4.6 34.7 1.0
CD2 B:HIS93 4.6 13.5 1.0
CE1 B:HIS93 4.6 14.5 1.0
O B:ARG91 4.9 9.0 1.0
CG B:HIS124 5.0 11.2 1.0

Magnesium binding site 3 out of 4 in 3mbi

Go back to Magnesium Binding Sites List in 3mbi
Magnesium binding site 3 out of 4 in the Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate


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 the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg289

b:31.5
occ:1.00
 O2B C:ADP286 1.9 35.7 1.0
O2A C:ADP286 1.9 38.2 1.0
O C:HOH1253 2.0 37.5 1.0
O C:HOH343 2.1 32.6 1.0
O C:HOH1252 2.1 26.5 1.0
NE2 C:HIS124 2.8 22.6 1.0
PA C:ADP286 3.1 32.4 1.0
PB C:ADP286 3.1 37.4 1.0
O5' C:ADP286 3.5 29.1 1.0
O3A C:ADP286 3.5 31.5 1.0
O C:HOH291 3.5 23.2 1.0
O C:HOH290 3.6 32.8 1.0
CE1 C:HIS124 3.7 23.2 1.0
O3B C:ADP286 3.7 41.1 1.0
CD2 C:HIS124 3.8 17.7 1.0
C5' C:ADP286 3.9 26.0 1.0
OH C:TYR96 4.0 25.7 1.0
NE2 C:HIS93 4.4 19.4 1.0
O1B C:ADP286 4.4 31.7 1.0
O1A C:ADP286 4.4 35.3 1.0
O C:HOH722 4.5 37.7 1.0
ND1 C:HIS124 4.8 16.9 1.0
O C:ARG91 4.8 15.6 1.0
CG C:HIS124 4.9 18.2 1.0

Magnesium binding site 4 out of 4 in 3mbi

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate


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 the Phosphoribosylpyrophosphate (Prpp) Synthetase From Thermoplasma Volcanium in Complex with Adp-MG2+ and Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg287

b:26.2
occ:1.00
 O D:HOH295 2.0 33.2 1.0
O D:HOH290 2.1 27.9 1.0
O D:HOH289 2.1 20.0 1.0
O2A D:ADP288 2.1 28.9 1.0
O3B D:ADP288 2.2 27.7 1.0
NE2 D:HIS124 2.7 21.2 1.0
PB D:ADP288 3.4 34.6 1.0
PA D:ADP288 3.4 26.8 1.0
CD2 D:HIS124 3.5 18.8 1.0
O D:HOH292 3.6 22.4 1.0
CE1 D:HIS124 3.7 21.5 1.0
O1B D:ADP288 3.8 31.8 1.0
O5' D:ADP288 3.8 21.9 1.0
O3A D:ADP288 3.9 25.6 1.0
OH D:TYR96 4.0 22.1 1.0
O1 D:HSX286 4.3 30.6 0.6
NE2 D:HIS93 4.3 15.1 1.0
O D:HOH296 4.3 18.4 1.0
C5' D:ADP288 4.3 19.8 1.0
O D:HOH1254 4.4 34.8 1.0
O2B D:ADP288 4.7 26.2 1.0
O1A D:ADP288 4.7 27.9 1.0
CG D:HIS124 4.8 19.4 1.0
ND1 D:HIS124 4.8 20.3 1.0
O D:ARG91 4.8 15.2 1.0
CD2 D:HIS93 5.0 16.1 1.0

Reference:

M.M.Cherney, L.T.Cherney, C.R.Garen, M.N.James. The Structures of Thermoplasma Volcanium Phosphoribosyl Pyrophosphate Synthetase Bound to Ribose-5-Phosphate and Atp Analogs. J.Mol.Biol. V. 413 844 2011.
ISSN: ISSN 0022-2836
PubMed: 21963988
DOI: 10.1016/J.JMB.2011.09.007
Page generated: Mon Dec 14 08:25:45 2020

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