Atomistry » Magnesium » PDB 3m1v-3mfh » 3mbi
Atomistry »
  Magnesium »
    PDB 3m1v-3mfh »
      3mbi »

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

Go back to Magnesium Binding Sites List in 3mbi
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

Go back to Magnesium Binding Sites List in 3mbi
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

Go back to Magnesium Binding Sites List in 3mbi
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: Wed Aug 14 19:12:46 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy