Atomistry » Magnesium » PDB 4rri-4s1k » 4rxd
Atomistry »
  Magnesium »
    PDB 4rri-4s1k »
      4rxd »

Magnesium in PDB 4rxd: T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate, PDB code: 4rxd was solved by R.Cao, Y.-L.Liu, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.340, 90.305, 88.709, 90.00, 89.91, 90.00
R / Rfree (%) 21.1 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate (pdb code 4rxd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate, PDB code: 4rxd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 1 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:17.7
occ:1.00
OD2 A:ASP103 2.0 19.4 1.0
O12 A:RIS1404 2.1 16.8 1.0
O15 A:RIS1404 2.1 18.1 1.0
O A:HOH1642 2.1 18.2 1.0
OD2 A:ASP107 2.1 16.8 1.0
O A:HOH1653 2.2 20.8 1.0
CG A:ASP103 3.0 18.4 1.0
MG A:MG1403 3.0 16.4 1.0
CG A:ASP107 3.2 18.6 1.0
OD1 A:ASP103 3.3 18.3 1.0
P14 A:RIS1404 3.3 18.4 1.0
P9 A:RIS1404 3.4 18.1 1.0
CB A:ASP107 3.7 19.4 1.0
C8 A:RIS1404 3.7 17.9 1.0
O16 A:RIS1404 3.9 18.9 1.0
O A:HOH1534 3.9 20.1 1.0
C7 A:RIS1404 3.9 18.2 1.0
O11 A:RIS1404 4.1 18.3 1.0
O A:HOH1654 4.3 17.4 1.0
CB A:ASP103 4.3 16.5 1.0
OD1 A:ASP107 4.3 16.6 1.0
O A:ASP103 4.3 15.4 1.0
O A:HOH1644 4.4 21.9 1.0
NH2 A:ARG112 4.4 21.9 1.0
OG A:SER109 4.4 24.6 1.0
O A:HOH1524 4.4 22.7 1.0
O17 A:RIS1404 4.5 19.2 1.0
O10 A:RIS1404 4.6 17.8 1.0
C A:ASP103 4.6 16.8 1.0
OD1 A:ASP104 4.6 21.2 1.0
O A:HOH1641 4.7 15.4 1.0
O A:HOH1501 4.8 19.9 1.0
C2 A:RIS1404 4.9 17.3 1.0
O A:HOH1545 4.9 20.7 1.0
MG A:MG1402 4.9 22.8 1.0
O A:HOH1518 5.0 24.6 1.0

Magnesium binding site 2 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 2 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1402

b:22.8
occ:1.00
O A:HOH1644 2.0 21.9 1.0
O16 A:RIS1404 2.0 18.9 1.0
O11 A:RIS1404 2.1 18.3 1.0
OD2 A:ASP255 2.1 23.0 1.0
O A:HOH1643 2.1 16.0 1.0
O A:HOH1652 2.2 23.2 1.0
CG A:ASP255 3.2 22.4 1.0
P9 A:RIS1404 3.3 18.1 1.0
P14 A:RIS1404 3.4 18.4 1.0
C8 A:RIS1404 3.6 17.9 1.0
OD1 A:ASP255 3.7 22.1 1.0
O13 A:RIS1404 3.7 19.7 1.0
O A:HOH1545 3.8 20.7 1.0
OD1 A:ASP259 3.8 26.6 1.0
O12 A:RIS1404 4.1 16.8 1.0
O A:HOH1653 4.1 20.8 1.0
OD1 A:ASP273 4.1 23.7 1.0
OD2 A:ASP273 4.2 24.0 1.0
O A:ASP255 4.2 20.4 1.0
O15 A:RIS1404 4.3 18.1 1.0
NZ A:LYS269 4.3 31.6 1.0
NE2 A:GLN252 4.3 19.1 1.0
CB A:ASP255 4.4 21.2 1.0
CG A:ASP259 4.4 28.7 1.0
O17 A:RIS1404 4.4 19.2 1.0
OD1 A:ASP256 4.5 22.6 1.0
O10 A:RIS1404 4.5 17.8 1.0
C A:ASP255 4.5 21.1 1.0
CG A:ASP273 4.6 24.2 1.0
O A:HOH1647 4.6 47.6 1.0
CB A:ASP259 4.7 28.6 1.0
CE A:LYS269 4.8 31.0 1.0
O A:HOH1534 4.8 20.1 1.0
MG A:MG1401 4.9 17.7 1.0
N A:ASP256 5.0 21.4 1.0

Magnesium binding site 3 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 3 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1403

b:16.4
occ:1.00
OD1 A:ASP103 2.0 18.3 1.0
O15 A:RIS1404 2.1 18.1 1.0
O A:HOH1641 2.1 15.4 1.0
O A:HOH1501 2.1 19.9 1.0
OD2 A:ASP107 2.1 16.8 1.0
O A:HOH1654 2.1 17.4 1.0
CG A:ASP103 3.0 18.4 1.0
CG A:ASP107 3.0 18.6 1.0
MG A:MG1401 3.0 17.7 1.0
OD2 A:ASP103 3.2 19.4 1.0
OD1 A:ASP107 3.2 16.6 1.0
P14 A:RIS1404 3.3 18.4 1.0
O17 A:RIS1404 3.5 19.2 1.0
OD1 A:ASP175 4.0 21.0 1.0
NZ A:LYS278 4.1 31.4 1.0
O A:HOH1653 4.2 20.8 1.0
OD2 A:ASP175 4.2 21.2 1.0
NE2 A:GLN172 4.2 16.4 1.0
O A:HOH1545 4.3 20.7 1.0
O16 A:RIS1404 4.3 18.9 1.0
CG A:ASP175 4.3 20.8 1.0
CB A:ASP103 4.3 16.5 1.0
OE1 A:GLN172 4.3 18.7 1.0
CB A:ASP107 4.4 19.4 1.0
C1 A:RIS1404 4.5 17.4 1.0
C8 A:RIS1404 4.6 17.9 1.0
C7 A:RIS1404 4.6 18.2 1.0
C2 A:RIS1404 4.6 17.3 1.0
NZ A:LYS212 4.6 19.0 1.0
O12 A:RIS1404 4.6 16.8 1.0
CD A:GLN172 4.7 17.2 1.0
O A:HOH1642 4.8 18.2 1.0
O A:ASP103 4.8 15.4 1.0
CA A:ASP103 5.0 16.5 1.0

Magnesium binding site 4 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 4 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1501

b:17.7
occ:1.00
OD2 B:ASP103 2.0 19.7 1.0
O12 B:RIS1504 2.0 16.8 1.0
O B:HOH1747 2.1 20.9 1.0
O B:HOH1752 2.1 19.5 1.0
O15 B:RIS1504 2.1 16.4 1.0
OD2 B:ASP107 2.1 15.8 1.0
CG B:ASP103 3.0 19.4 1.0
MG B:MG1503 3.0 17.5 1.0
CG B:ASP107 3.2 18.0 1.0
P14 B:RIS1504 3.3 17.7 1.0
P9 B:RIS1504 3.3 17.5 1.0
OD1 B:ASP103 3.4 19.1 1.0
C8 B:RIS1504 3.6 16.8 1.0
CB B:ASP107 3.7 18.8 1.0
O16 B:RIS1504 3.9 18.5 1.0
C7 B:RIS1504 3.9 17.2 1.0
O B:HOH1749 4.0 20.9 1.0
O11 B:RIS1504 4.1 18.7 1.0
O B:HOH1624 4.2 17.8 1.0
OD1 B:ASP107 4.3 15.4 1.0
CB B:ASP103 4.3 17.4 1.0
O B:HOH1753 4.4 23.3 1.0
O B:ASP103 4.4 16.8 1.0
OG B:SER109 4.4 24.9 1.0
NH2 B:ARG112 4.4 21.0 1.0
O B:HOH1631 4.4 21.5 1.0
O17 B:RIS1504 4.5 15.6 1.0
O10 B:RIS1504 4.5 18.5 1.0
C B:ASP103 4.6 17.7 1.0
OD1 B:ASP104 4.7 21.4 1.0
O B:HOH1746 4.7 16.6 1.0
O B:HOH1751 4.8 19.5 1.0
C2 B:RIS1504 4.9 16.9 1.0
O B:HOH1748 4.9 20.6 1.0
MG B:MG1502 4.9 22.8 1.0

Magnesium binding site 5 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 5 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1502

b:22.8
occ:1.00
O B:HOH1753 2.0 23.3 1.0
O16 B:RIS1504 2.1 18.5 1.0
OD2 B:ASP255 2.1 20.7 1.0
O B:HOH1745 2.1 19.8 1.0
O11 B:RIS1504 2.1 18.7 1.0
O B:HOH1604 2.1 15.6 1.0
CG B:ASP255 3.1 21.7 1.0
P9 B:RIS1504 3.3 17.5 1.0
P14 B:RIS1504 3.4 17.7 1.0
O13 B:RIS1504 3.6 19.4 1.0
C8 B:RIS1504 3.6 16.8 1.0
OD1 B:ASP255 3.6 22.2 1.0
OD1 B:ASP259 3.7 27.2 1.0
O B:HOH1748 3.8 20.6 1.0
O12 B:RIS1504 4.1 16.8 1.0
OD2 B:ASP273 4.1 25.5 1.0
O B:ASP255 4.2 20.2 1.0
O B:HOH1747 4.2 20.9 1.0
OD1 B:ASP273 4.2 23.8 1.0
O15 B:RIS1504 4.3 16.4 1.0
CG B:ASP259 4.3 29.1 1.0
NZ B:LYS269 4.3 29.1 1.0
CB B:ASP255 4.3 20.6 1.0
NE2 B:GLN252 4.3 18.5 1.0
O17 B:RIS1504 4.4 15.6 1.0
O10 B:RIS1504 4.5 18.5 1.0
C B:ASP255 4.5 20.9 1.0
OD1 B:ASP256 4.5 23.2 1.0
CG B:ASP273 4.6 25.0 1.0
CE B:LYS269 4.6 28.7 1.0
CB B:ASP259 4.7 28.6 1.0
O B:HOH1749 4.7 20.9 1.0
MG B:MG1501 4.9 17.7 1.0
N B:ASP256 5.0 21.2 1.0
CA B:ASP255 5.0 21.1 1.0

Magnesium binding site 6 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 6 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1503

b:17.5
occ:1.00
O15 B:RIS1504 2.0 16.4 1.0
OD1 B:ASP103 2.0 19.1 1.0
O B:HOH1746 2.1 16.6 1.0
OD2 B:ASP107 2.1 15.8 1.0
O B:HOH1624 2.2 17.8 1.0
O B:HOH1751 2.2 19.5 1.0
CG B:ASP103 2.9 19.4 1.0
CG B:ASP107 3.0 18.0 1.0
MG B:MG1501 3.0 17.7 1.0
OD2 B:ASP103 3.1 19.7 1.0
OD1 B:ASP107 3.2 15.4 1.0
P14 B:RIS1504 3.3 17.7 1.0
O17 B:RIS1504 3.5 15.6 1.0
OD1 B:ASP175 4.0 19.6 1.0
O B:HOH1747 4.1 20.9 1.0
OD2 B:ASP175 4.2 19.9 1.0
NZ B:LYS278 4.2 30.4 1.0
NE2 B:GLN172 4.2 14.4 1.0
O16 B:RIS1504 4.3 18.5 1.0
OE1 B:GLN172 4.3 18.6 1.0
CG B:ASP175 4.3 20.6 1.0
CB B:ASP103 4.3 17.4 1.0
O B:HOH1748 4.4 20.6 1.0
C1 B:RIS1504 4.4 17.2 1.0
CB B:ASP107 4.4 18.8 1.0
C8 B:RIS1504 4.5 16.8 1.0
C7 B:RIS1504 4.5 17.2 1.0
C2 B:RIS1504 4.6 16.9 1.0
O12 B:RIS1504 4.6 16.8 1.0
NZ B:LYS212 4.7 19.1 1.0
CD B:GLN172 4.7 16.8 1.0
O B:HOH1752 4.8 19.5 1.0
O B:ASP103 4.8 16.8 1.0
CA B:ASP103 4.9 17.1 1.0

Magnesium binding site 7 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 7 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1601

b:18.7
occ:1.00
OD2 C:ASP103 2.0 20.9 1.0
O C:HOH1849 2.0 19.6 1.0
O12 C:RIS1600 2.1 18.4 1.0
O C:HOH1842 2.1 22.4 1.0
OD2 C:ASP107 2.1 17.2 1.0
O15 C:RIS1600 2.1 17.3 1.0
CG C:ASP103 3.0 19.7 1.0
MG C:MG1603 3.1 16.6 1.0
CG C:ASP107 3.2 19.9 1.0
P14 C:RIS1600 3.3 18.1 1.0
P9 C:RIS1600 3.3 18.5 1.0
OD1 C:ASP103 3.4 19.8 1.0
C8 C:RIS1600 3.6 17.8 1.0
CB C:ASP107 3.7 19.7 1.0
O16 C:RIS1600 3.9 17.7 1.0
C7 C:RIS1600 3.9 19.1 1.0
O C:HOH1845 3.9 22.3 1.0
O11 C:RIS1600 4.0 19.2 1.0
O C:HOH1732 4.2 18.0 1.0
OD1 C:ASP107 4.3 17.6 1.0
CB C:ASP103 4.3 17.9 1.0
OG C:SER109 4.3 25.1 1.0
NH2 C:ARG112 4.3 21.6 1.0
O C:HOH1715 4.4 20.9 1.0
O C:ASP103 4.4 16.4 1.0
O C:HOH1709 4.4 23.2 1.0
O10 C:RIS1600 4.5 19.3 1.0
O17 C:RIS1600 4.6 17.0 1.0
OD1 C:ASP104 4.6 21.3 1.0
C C:ASP103 4.6 17.8 1.0
O C:HOH1841 4.7 17.0 1.0
O C:HOH1850 4.8 20.1 1.0
C2 C:RIS1600 4.9 17.9 1.0
MG C:MG1602 4.9 22.0 1.0
O C:HOH1844 5.0 20.6 1.0
O C:HOH1744 5.0 24.7 1.0

Magnesium binding site 8 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 8 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1602

b:22.0
occ:1.00
O C:HOH1715 2.0 20.9 1.0
O16 C:RIS1600 2.0 17.7 1.0
O11 C:RIS1600 2.1 19.2 1.0
O C:HOH1843 2.1 18.6 1.0
OD2 C:ASP255 2.1 21.9 1.0
O C:HOH1851 2.2 22.6 1.0
CG C:ASP255 3.2 21.8 1.0
P9 C:RIS1600 3.3 18.5 1.0
P14 C:RIS1600 3.3 18.1 1.0
C8 C:RIS1600 3.6 17.8 1.0
O13 C:RIS1600 3.6 20.3 1.0
OD1 C:ASP255 3.7 21.9 1.0
O C:HOH1844 3.7 20.6 1.0
OD1 C:ASP259 3.8 27.6 1.0
OD2 C:ASP273 4.1 24.4 1.0
O12 C:RIS1600 4.1 18.4 1.0
O C:HOH1842 4.1 22.4 1.0
OD1 C:ASP273 4.1 22.9 1.0
O C:ASP255 4.2 20.8 1.0
O15 C:RIS1600 4.3 17.3 1.0
NE2 C:GLN252 4.3 18.9 1.0
NZ C:LYS269 4.4 28.7 1.0
CG C:ASP259 4.4 29.2 1.0
CB C:ASP255 4.4 20.7 1.0
O17 C:RIS1600 4.4 17.0 1.0
O10 C:RIS1600 4.5 19.3 1.0
OD1 C:ASP256 4.5 22.2 1.0
CG C:ASP273 4.5 24.0 1.0
C C:ASP255 4.5 20.9 1.0
CB C:ASP259 4.7 28.5 1.0
CE C:LYS269 4.7 28.6 1.0
O C:HOH1845 4.7 22.3 1.0
MG C:MG1601 4.9 18.7 1.0

Magnesium binding site 9 out of 9 in 4rxd

Go back to Magnesium Binding Sites List in 4rxd
Magnesium binding site 9 out of 9 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1603

b:16.6
occ:1.00
OD1 C:ASP103 2.0 19.8 1.0
O15 C:RIS1600 2.0 17.3 1.0
O C:HOH1841 2.0 17.0 1.0
O C:HOH1732 2.1 18.0 1.0
O C:HOH1850 2.1 20.1 1.0
OD2 C:ASP107 2.1 17.2 1.0
CG C:ASP103 2.9 19.7 1.0
CG C:ASP107 3.0 19.9 1.0
MG C:MG1601 3.1 18.7 1.0
OD2 C:ASP103 3.2 20.9 1.0
OD1 C:ASP107 3.2 17.6 1.0
P14 C:RIS1600 3.3 18.1 1.0
O17 C:RIS1600 3.5 17.0 1.0
OD1 C:ASP175 4.0 21.2 1.0
OD2 C:ASP175 4.2 20.7 1.0
O C:HOH1842 4.2 22.4 1.0
OE1 C:GLN172 4.2 19.9 1.0
O16 C:RIS1600 4.3 17.7 1.0
NE2 C:GLN172 4.3 15.5 1.0
CG C:ASP175 4.3 20.5 1.0
CB C:ASP103 4.3 17.9 1.0
O C:HOH1844 4.3 20.6 1.0
NZ C:LYS278 4.4 31.2 1.0
C1 C:RIS1600 4.4 18.6 1.0
CB C:ASP107 4.5 19.7 1.0
C8 C:RIS1600 4.5 17.8 1.0
C7 C:RIS1600 4.5 19.1 1.0
C2 C:RIS1600 4.6 17.9 1.0
NZ C:LYS212 4.6 18.2 1.0
O12 C:RIS1600 4.7 18.4 1.0
CD C:GLN172 4.7 17.2 1.0
O C:HOH1849 4.7 19.6 1.0
O C:ASP103 4.8 16.4 1.0
CA C:ASP103 5.0 17.4 1.0
CE C:LYS278 5.0 27.6 1.0
O C:HOH1709 5.0 23.2 1.0

Reference:

Y.L.Liu, R.Cao, Y.Wang, E.Oldfield. Farnesyl Diphosphate Synthase Inhibitors with Unique Ligand-Binding Geometries. Acs Med Chem Lett V. 6 349 2015.
PubMed: 25815158
DOI: 10.1021/ML500528X
Page generated: Tue Aug 20 03:33:24 2024

Last articles

Na in 5M6H
Na in 5M5K
Na in 5M65
Na in 5M6F
Na in 5M6E
Na in 5M60
Na in 5M5A
Na in 5M4L
Na in 5M5Z
Na in 5M5J
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy