Atomistry » Fluorine » PDB 1bwf-1dvy » 1d1b
Atomistry »
  Fluorine »
    PDB 1bwf-1dvy »
      1d1b »

Fluorine in PDB 1d1b: Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride.

Protein crystallography data

The structure of Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride., PDB code: 1d1b was solved by A.M.Gulick, C.B.Bauer, J.B.Thoden, E.Pate, R.G.Yount, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.880, 180.460, 54.070, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1d1b:

The structure of Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride. (pdb code 1d1b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride., PDB code: 1d1b:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1d1b

Go back to Fluorine Binding Sites List in 1d1b
Fluorine binding site 1 out of 3 in the Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:23.4
occ:1.00
F1 A:DAQ999 0.0 23.4 1.0
BE A:DAQ999 1.5 9.0 1.0
F2 A:DAQ999 2.5 27.5 1.0
F3 A:DAQ999 2.5 21.5 1.0
OB3 A:DAQ999 2.6 17.9 1.0
O A:HOH1531 2.8 56.9 1.0
NZ A:LYS185 2.8 15.2 1.0
CA A:SER181 3.2 11.8 1.0
O A:HOH1526 3.2 79.9 1.0
CE A:LYS185 3.4 19.8 1.0
CB A:SER181 3.5 17.2 1.0
OG A:SER181 3.7 22.6 1.0
OG A:SER456 3.7 63.8 1.0
PB A:DAQ999 3.7 15.6 1.0
N A:SER181 3.8 13.6 1.0
OB1 A:DAQ999 3.9 10.0 1.0
O A:HOH1541 4.0 13.8 1.0
OB2 A:DAQ999 4.1 11.8 1.0
MG A:MG998 4.2 18.7 1.0
N A:GLY182 4.3 23.1 1.0
O A:GLU180 4.3 20.0 1.0
C A:SER181 4.3 28.3 1.0
C A:GLU180 4.3 13.5 1.0
O A:HOH1245 4.5 51.3 1.0
OG A:SER236 4.6 21.7 1.0
O A:HOH1123 4.6 33.7 1.0
O A:SER237 4.7 14.2 1.0
N A:SER237 4.8 15.8 1.0
O A:GLY179 4.8 13.5 1.0
CD A:LYS185 4.9 11.0 1.0

Fluorine binding site 2 out of 3 in 1d1b

Go back to Fluorine Binding Sites List in 1d1b
Fluorine binding site 2 out of 3 in the Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:27.5
occ:1.00
F2 A:DAQ999 0.0 27.5 1.0
BE A:DAQ999 1.5 9.0 1.0
OG A:SER181 2.4 22.6 1.0
F3 A:DAQ999 2.4 21.5 1.0
OB3 A:DAQ999 2.4 17.9 1.0
F1 A:DAQ999 2.5 23.4 1.0
OG A:SER236 2.7 21.7 1.0
ND2 A:ASN233 3.2 27.9 1.0
CB A:SER181 3.2 17.2 1.0
CA A:SER181 3.5 11.8 1.0
CB A:SER236 3.5 18.1 1.0
CA A:SER236 3.5 15.8 1.0
O A:HOH1531 3.5 56.9 1.0
N A:SER237 3.7 15.8 1.0
N A:GLY182 3.7 23.1 1.0
CB A:ASN233 4.0 17.3 1.0
C A:SER181 4.0 28.3 1.0
PB A:DAQ999 4.0 15.6 1.0
CG A:ASN233 4.1 28.8 1.0
C A:SER236 4.1 13.6 1.0
O A:HOH1526 4.2 79.9 1.0
MG A:MG998 4.4 18.7 1.0
O A:HOH1061 4.4 23.1 1.0
OB2 A:DAQ999 4.5 11.8 1.0
O A:SER237 4.6 14.2 1.0
O A:HOH1540 4.6 16.0 1.0
N A:SER236 4.7 15.0 1.0
N A:SER181 4.7 13.6 1.0
CA A:GLY182 4.8 11.2 1.0
OA3 A:DAQ999 4.8 22.6 1.0
OB1 A:DAQ999 4.8 10.0 1.0
CA A:SER237 4.9 14.2 1.0
NZ A:LYS185 5.0 15.2 1.0
NH2 A:ARG238 5.0 21.0 1.0

Fluorine binding site 3 out of 3 in 1d1b

Go back to Fluorine Binding Sites List in 1d1b
Fluorine binding site 3 out of 3 in the Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dictyostelium Myosin S1DC (Motor Domain Fragment) Complexed with O,P- Dinitrophenyl Aminopropyldiphosphate Beryllium Trifluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:21.5
occ:1.00
F3 A:DAQ999 0.0 21.5 1.0
BE A:DAQ999 1.5 9.0 1.0
MG A:MG998 2.1 18.7 1.0
F2 A:DAQ999 2.4 27.5 1.0
OB3 A:DAQ999 2.5 17.9 1.0
F1 A:DAQ999 2.5 23.4 1.0
OG A:SER237 2.8 21.7 1.0
N A:SER237 2.8 15.8 1.0
OB2 A:DAQ999 2.9 11.8 1.0
O A:HOH1541 2.9 13.8 1.0
O A:HOH1540 3.1 16.0 1.0
CB A:SER237 3.2 16.1 1.0
PB A:DAQ999 3.3 15.6 1.0
O A:HOH1526 3.5 79.9 1.0
CA A:SER237 3.6 14.2 1.0
O A:SER237 3.8 14.2 1.0
C A:SER236 3.9 13.6 1.0
OG A:SER236 4.0 21.7 1.0
ND2 A:ASN233 4.0 27.9 1.0
CA A:SER236 4.1 15.8 1.0
OG1 A:THR186 4.1 25.4 1.0
O A:HOH1531 4.2 56.9 1.0
OB1 A:DAQ999 4.3 10.0 1.0
C A:SER237 4.3 11.4 1.0
NZ A:LYS185 4.5 15.2 1.0
OA3 A:DAQ999 4.5 22.6 1.0
CE A:LYS185 4.6 19.8 1.0
O A:HOH1245 4.7 51.3 1.0
O A:ASN235 4.7 24.0 1.0
CB A:SER236 4.7 18.1 1.0
OG A:SER181 4.8 22.6 1.0
OA2 A:DAQ999 4.8 16.0 1.0
O A:SER236 5.0 27.9 1.0

Reference:

A.M.Gulick, C.B.Bauer, J.B.Thoden, E.Pate, R.G.Yount, I.Rayment. X-Ray Structures of the Dictyostelium Discoideum Myosin Motor Domain with Six Non-Nucleotide Analogs. J.Biol.Chem. V. 275 398 2000.
ISSN: ISSN 0021-9258
PubMed: 10617631
DOI: 10.1074/JBC.275.1.398
Page generated: Wed Jul 31 11:02:44 2024

Last articles

Na in 4IGB
Na in 4IIB
Na in 4IEF
Na in 4IGU
Na in 4IHS
Na in 4II8
Na in 4IA6
Na in 4IB0
Na in 4I2R
Na in 4I9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy