Atomistry » Magnesium » PDB 2ouq-2p88 » 2p1c
Atomistry »
  Magnesium »
    PDB 2ouq-2p88 »
      2p1c »

Magnesium in PDB 2p1c: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210, PDB code: 2p1c was solved by R.Cao, Y.Gao, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 2.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.124, 92.124, 177.747, 90.00, 90.00, 120.00
R / Rfree (%) 26.6 / 29.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 (pdb code 2p1c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210, PDB code: 2p1c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:52.4
occ:1.00
 OD2 A:ASP107 2.5 50.7 1.0
O17 A:GG33001 2.5 41.6 1.0
O A:HOH8124 2.5 47.4 1.0
O A:HOH8135 2.5 57.3 1.0
OD2 A:ASP103 2.6 45.5 1.0
O10 A:GG33001 2.6 39.3 1.0
CG A:ASP107 3.3 44.5 1.0
CG A:ASP103 3.5 52.7 1.0
CB A:ASP107 3.5 45.4 1.0
O A:HOH8110 3.5 37.2 1.0
OD1 A:ASP103 3.7 55.0 1.0
P14 A:GG33001 3.8 48.7 1.0
OG A:SER109 3.8 50.0 1.0
P9 A:GG33001 3.9 49.8 1.0
O13 A:GG33001 4.1 47.9 1.0
MG A:MG3004 4.1 38.5 1.0
C8 A:GG33001 4.2 46.6 1.0
NH2 A:ARG112 4.3 45.6 1.0
O A:ASP103 4.4 48.8 1.0
OD1 A:ASP107 4.4 46.6 1.0
O A:HOH8134 4.5 44.0 1.0
OG1 A:THR272 4.5 49.0 1.0
O16 A:GG33001 4.6 58.3 1.0
O11 A:GG33001 4.6 50.9 1.0
C A:ASP103 4.7 48.1 1.0
CB A:ASP103 4.8 49.4 1.0
OD1 A:ASP104 4.8 49.9 1.0
O15 A:GG33001 4.9 61.7 1.0
MG A:MG3003 4.9 45.9 1.0
O A:HOH8108 4.9 42.0 1.0

Magnesium binding site 2 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:45.9
occ:1.00
 O11 A:GG33001 2.4 50.9 1.0
OD2 A:ASP255 2.7 46.2 1.0
O16 A:GG33001 2.7 58.3 1.0
O A:HOH8112 2.7 74.9 1.0
OD1 A:ASP259 3.2 52.1 1.0
OD1 A:ASP273 3.6 44.9 1.0
P9 A:GG33001 3.6 49.8 1.0
CG A:ASP259 3.7 42.7 1.0
CG A:ASP255 3.7 45.6 1.0
OD2 A:ASP273 3.7 42.4 1.0
P14 A:GG33001 3.8 48.7 1.0
O10 A:GG33001 3.8 39.3 1.0
O A:HOH8124 3.8 47.4 1.0
CB A:ASP259 4.0 41.6 1.0
CG A:ASP273 4.1 45.0 1.0
O17 A:GG33001 4.1 41.6 1.0
OD1 A:ASP255 4.2 42.3 1.0
C8 A:GG33001 4.3 46.6 1.0
O A:ASP255 4.4 45.2 1.0
OD2 A:ASP259 4.4 40.4 1.0
OD1 A:ASP256 4.6 50.2 1.0
O A:HOH8110 4.7 37.2 1.0
C A:ASP255 4.8 43.0 1.0
NZ A:LYS269 4.8 44.7 1.0
CB A:ASP255 4.9 45.1 1.0
NE2 A:GLN252 4.9 43.8 1.0
O12 A:GG33001 4.9 45.8 1.0
MG A:MG3002 4.9 52.4 1.0
C7 A:GG33001 4.9 43.2 1.0

Magnesium binding site 3 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:38.5
occ:1.00
 O A:HOH8115 2.5 35.9 1.0
OD2 A:ASP107 2.5 50.7 1.0
OD1 A:ASP103 2.7 55.0 1.0
OD1 A:ASP107 2.9 46.6 1.0
O10 A:GG33001 3.1 39.3 1.0
CG A:ASP107 3.1 44.5 1.0
OD1 A:ASP175 3.4 42.1 1.0
NE2 A:GLN172 3.5 55.5 1.0
NZ A:LYS278 3.5 50.6 1.0
O12 A:GG33001 3.7 45.8 1.0
CG A:ASP103 3.8 52.7 1.0
OD2 A:ASP175 3.9 36.5 1.0
CG A:ASP175 3.9 34.7 1.0
P9 A:GG33001 3.9 49.8 1.0
MG A:MG3002 4.1 52.4 1.0
OD2 A:ASP103 4.3 45.5 1.0
CD A:GLN172 4.3 53.9 1.0
CE A:LYS278 4.4 51.9 1.0
CB A:ASP107 4.6 45.4 1.0
OE1 A:GLN172 4.6 50.9 1.0
NZ A:LYS212 4.9 29.3 1.0
O13 A:GG33001 4.9 47.9 1.0
O A:HOH8124 5.0 47.4 1.0

Magnesium binding site 4 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4001

b:49.6
occ:1.00
 O B:HOH9150 2.6 41.0 1.0
O17 B:GG38004 2.6 41.7 1.0
OD2 B:ASP103 2.6 53.5 1.0
OD2 B:ASP107 2.8 56.4 1.0
O10 B:GG38004 3.1 44.8 1.0
OG B:SER109 3.3 45.1 1.0
CB B:ASP107 3.3 52.0 1.0
CG B:ASP103 3.5 44.1 1.0
O B:HOH9123 3.5 34.9 1.0
CG B:ASP107 3.5 54.9 1.0
O B:ASP103 3.7 44.2 1.0
OD1 B:ASP104 3.7 31.3 1.0
OD1 B:ASP103 3.9 39.0 1.0
NH2 B:ARG112 4.0 52.7 1.0
P14 B:GG38004 4.0 43.8 1.0
C B:ASP103 4.1 43.1 1.0
O13 B:GG38004 4.3 53.9 1.0
P9 B:GG38004 4.4 46.4 1.0
CA B:ASP104 4.4 44.0 1.0
CB B:SER109 4.5 53.5 1.0
N B:ASP104 4.5 40.5 1.0
CB B:ASP103 4.5 44.5 1.0
C8 B:GG38004 4.5 47.2 1.0
O B:HOH9065 4.6 41.7 1.0
OG1 B:THR272 4.6 53.1 1.0
CA B:ASP107 4.7 51.4 1.0
OD1 B:ASP107 4.7 60.4 1.0
MG B:MG4003 4.8 49.0 1.0
CG B:ASP104 4.8 45.1 1.0
O16 B:GG38004 4.8 53.4 1.0
CA B:ASP103 5.0 34.0 1.0
O15 B:GG38004 5.0 53.0 1.0

Magnesium binding site 5 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4002

b:45.4
occ:1.00
 O16 B:GG38004 2.5 53.4 1.0
O11 B:GG38004 2.6 46.0 1.0
O B:HOH9103 2.7 43.5 1.0
O B:HOH9131 2.8 38.4 1.0
O B:HOH9150 3.2 41.0 1.0
OD1 B:ASP259 3.2 56.2 1.0
OD2 B:ASP255 3.4 38.0 1.0
OD2 B:ASP273 3.4 39.6 1.0
OD1 B:ASP273 3.5 44.4 1.0
P14 B:GG38004 3.6 43.8 1.0
P9 B:GG38004 3.7 46.4 1.0
CG B:ASP259 3.7 52.7 1.0
CG B:ASP273 3.8 44.0 1.0
O17 B:GG38004 3.8 41.7 1.0
O10 B:GG38004 3.8 44.8 1.0
O B:HOH9123 4.2 34.9 1.0
CB B:ASP259 4.2 48.0 1.0
C8 B:GG38004 4.3 47.2 1.0
CG B:ASP255 4.4 39.9 1.0
OD2 B:ASP259 4.4 52.6 1.0
O B:ASP255 4.7 49.8 1.0
OD1 B:ASP255 4.8 41.8 1.0
NZ B:LYS269 4.9 43.5 1.0
O15 B:GG38004 4.9 53.0 1.0
C7 B:GG38004 4.9 50.5 1.0

Magnesium binding site 6 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4003

b:49.0
occ:1.00
 OD2 B:ASP107 2.6 56.4 1.0
OD1 B:ASP103 2.8 39.0 1.0
O10 B:GG38004 2.8 44.8 1.0
OD2 B:ASP175 3.3 41.0 1.0
O12 B:GG38004 3.3 44.2 1.0
CG B:ASP107 3.4 54.9 1.0
OD1 B:ASP175 3.4 44.2 1.0
OD1 B:ASP107 3.5 60.4 1.0
CG B:ASP175 3.5 41.2 1.0
P9 B:GG38004 3.5 46.4 1.0
CG B:ASP103 3.7 44.1 1.0
NE2 B:GLN172 3.8 41.5 1.0
OE1 B:GLN172 3.9 47.6 1.0
OD2 B:ASP103 3.9 53.5 1.0
NZ B:LYS212 4.0 27.1 1.0
NZ B:LYS278 4.3 58.8 1.0
CD B:GLN172 4.3 38.2 1.0
O11 B:GG38004 4.5 46.0 1.0
CB B:ASP175 4.6 39.5 1.0
C22 B:GG38004 4.7 53.2 1.0
O B:HOH9150 4.7 41.0 1.0
CE B:LYS278 4.7 48.0 1.0
C26 B:GG38004 4.8 46.8 1.0
MG B:MG4001 4.8 49.6 1.0
CB B:ASP107 4.8 52.0 1.0
O13 B:GG38004 4.9 53.9 1.0
C8 B:GG38004 5.0 47.2 1.0

Reference:

R.Cao, C.K.Chen, R.T.Guo, A.H.Wang, E.Oldfield. Structures of A Potent Phenylalkyl Bisphosphonate Inhibitor Bound to Farnesyl and Geranylgeranyl Diphosphate Synthases. Proteins V. 73 431 2008.
ISSN: ISSN 0887-3585
PubMed: 18442135
DOI: 10.1002/PROT.22066
Page generated: Wed Aug 14 02:02:18 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy