Atomistry » Fluorine » PDB 6ugz-6v34 » 6un5
Atomistry »
  Fluorine »
    PDB 6ugz-6v34 »
      6un5 »

Fluorine in PDB 6un5: Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51)

Protein crystallography data

The structure of Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51), PDB code: 6un5 was solved by C.-Y.Lin, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.93 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.394, 68.464, 60.596, 90.00, 102.07, 90.00
R / Rfree (%) 17.4 / 20.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51) (pdb code 6un5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51), PDB code: 6un5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6un5

Go back to Fluorine Binding Sites List in 6un5
Fluorine binding site 1 out of 6 in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F15

b:21.0
occ:1.00
F1 A:QC415 0.0 21.0 1.0
CE2 A:QC415 1.3 19.9 1.0
CD2 A:QC415 2.3 19.5 1.0
CZ A:QC415 2.4 22.9 1.0
F2 A:QC415 2.7 18.8 1.0
OH A:QC415 2.8 24.0 1.0
CB A:HIS98 3.4 19.5 1.0
CE2 A:PHE115 3.4 18.4 1.0
CG2 A:VAL100 3.4 20.0 1.0
CD2 A:PHE115 3.6 18.3 1.0
ND1 A:HIS98 3.7 20.8 1.0
CG2 A:QC415 3.7 18.7 1.0
CE1 A:QC415 3.7 28.2 1.0
CG A:HIS98 3.8 19.3 1.0
OG1 A:THR153 4.1 23.1 1.0
CD1 A:QC415 4.2 24.7 1.0
CG2 A:THR153 4.2 21.6 1.0
CZ A:PHE115 4.2 18.6 1.0
CG2 A:VAL117 4.3 21.8 1.0
CG2 A:THR12 4.4 15.7 1.0
CG A:PHE115 4.6 18.9 1.0
CA A:HIS98 4.6 20.9 1.0
CB A:THR153 4.7 21.1 1.0
CE1 A:HIS98 4.7 22.1 1.0
CB2 A:QC415 4.8 18.0 1.0
C A:HIS98 4.9 20.9 1.0
F3 A:QC415 4.9 33.9 1.0
O A:HOH541 4.9 25.8 1.0
CB A:VAL100 4.9 16.2 1.0
CD2 A:HIS98 4.9 19.0 1.0

Fluorine binding site 2 out of 6 in 6un5

Go back to Fluorine Binding Sites List in 6un5
Fluorine binding site 2 out of 6 in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F15

b:18.8
occ:1.00
F2 A:QC415 0.0 18.8 1.0
CD2 A:QC415 1.3 19.5 1.0
CG2 A:QC415 2.4 18.7 1.0
CE2 A:QC415 2.4 19.9 1.0
F1 A:QC415 2.7 21.0 1.0
CB2 A:QC415 2.7 18.0 1.0
CZ A:PHE115 3.0 18.6 1.0
CE2 A:PHE115 3.2 18.4 1.0
CG2 A:VAL100 3.3 20.0 1.0
O A:HOH541 3.6 25.8 1.0
CD1 A:QC415 3.7 24.7 1.0
NE2 A:GLN19 3.7 18.7 1.0
CZ A:QC415 3.8 22.9 1.0
CE1 A:PHE115 3.9 18.2 1.0
NH2 A:ARG46 4.0 15.8 1.0
CG2 A:THR12 4.0 15.7 1.0
CA2 A:QC415 4.1 15.5 1.0
CD2 A:PHE115 4.1 18.3 1.0
CE1 A:QC415 4.2 28.2 1.0
CB A:THR12 4.4 14.4 1.0
CB A:VAL100 4.5 16.2 1.0
CG1 A:VAL100 4.6 16.4 1.0
CD1 A:PHE115 4.7 19.6 1.0
OH A:QC415 4.8 24.0 1.0
CZ A:ARG46 4.8 14.8 1.0
CG A:PHE115 4.8 18.9 1.0
C2 A:QC415 4.9 13.9 1.0
CD A:GLN19 4.9 15.5 1.0
O2 A:QC415 4.9 14.8 1.0

Fluorine binding site 3 out of 6 in 6un5

Go back to Fluorine Binding Sites List in 6un5
Fluorine binding site 3 out of 6 in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F15

b:33.9
occ:1.00
F3 A:QC415 0.0 33.9 1.0
CE1 A:QC415 1.4 28.2 1.0
CD1 A:QC415 2.4 24.7 1.0
CZ A:QC415 2.4 22.9 1.0
OG1 A:THR155 2.7 23.5 0.8
OH A:QC415 2.8 24.0 1.0
OE1 A:GLU172 2.9 40.3 1.0
O A:HOH471 3.1 21.6 1.0
CD A:GLU172 3.3 32.0 1.0
CG2 A:THR155 3.6 27.3 0.2
CE2 A:QC415 3.7 19.9 1.0
CG2 A:QC415 3.8 18.7 1.0
CE2 A:PHE95 3.8 24.1 1.0
OE2 A:GLU172 3.8 30.7 1.0
CB A:THR155 3.9 23.2 0.8
CB A:THR155 4.0 28.2 0.2
CD2 A:PHE95 4.0 24.8 1.0
CG1 A:VAL11 4.0 17.8 1.0
CG A:GLU172 4.0 27.1 1.0
CB A:THR153 4.2 21.1 1.0
CD2 A:QC415 4.2 19.5 1.0
OG1 A:THR153 4.3 23.1 1.0
CG2 A:THR155 4.4 24.3 0.8
CG2 A:THR153 4.7 21.6 1.0
OG1 A:THR155 4.7 29.3 0.2
OG1 A:QC415 4.7 22.0 1.0
CZ A:PHE95 4.8 24.9 1.0
F1 A:QC415 4.9 21.0 1.0
CB2 A:QC415 5.0 18.0 1.0

Fluorine binding site 4 out of 6 in 6un5

Go back to Fluorine Binding Sites List in 6un5
Fluorine binding site 4 out of 6 in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F15

b:28.6
occ:1.00
F1 B:QC415 0.0 28.6 1.0
CE2 B:QC415 1.4 24.9 1.0
CD2 B:QC415 2.4 24.0 1.0
CZ B:QC415 2.4 26.1 1.0
F2 B:QC415 2.7 30.4 1.0
OH B:QC415 2.8 27.9 1.0
CE2 B:PHE115 3.4 28.8 1.0
CG2 B:VAL100 3.5 30.0 1.0
CB B:HIS98 3.5 25.2 1.0
ND1 B:HIS98 3.6 24.6 1.0
CD2 B:PHE115 3.7 28.3 1.0
CG2 B:QC415 3.7 23.5 1.0
CE1 B:QC415 3.8 29.5 1.0
CG B:HIS98 3.8 24.7 1.0
CG2 B:VAL117 4.0 24.8 1.0
CG2 B:THR12 4.2 22.2 1.0
OG1 B:THR153 4.2 28.8 1.0
CD1 B:QC415 4.2 28.1 1.0
CZ B:PHE115 4.3 27.2 1.0
CG2 B:THR153 4.5 28.6 1.0
CE1 B:HIS98 4.7 25.7 1.0
CG B:PHE115 4.7 28.1 1.0
CA B:HIS98 4.8 26.2 1.0
CB2 B:QC415 4.9 24.4 1.0
F3 B:QC415 4.9 34.4 1.0
CD2 B:HIS98 4.9 26.2 1.0
CB B:THR153 4.9 30.1 1.0
CB B:VAL100 5.0 31.7 1.0

Fluorine binding site 5 out of 6 in 6un5

Go back to Fluorine Binding Sites List in 6un5
Fluorine binding site 5 out of 6 in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F15

b:30.4
occ:1.00
F2 B:QC415 0.0 30.4 1.0
CD2 B:QC415 1.4 24.0 1.0
CE2 B:QC415 2.4 24.9 1.0
CG2 B:QC415 2.4 23.5 1.0
F1 B:QC415 2.7 28.6 1.0
CB2 B:QC415 2.8 24.4 1.0
CZ B:PHE115 3.1 27.2 1.0
CE2 B:PHE115 3.1 28.8 1.0
CG2 B:VAL100 3.3 30.0 1.0
CD1 B:QC415 3.7 28.1 1.0
CZ B:QC415 3.8 26.1 1.0
O B:HOH470 3.9 34.5 1.0
NH2 B:ARG46 3.9 22.2 1.0
CG2 B:THR12 3.9 22.2 1.0
CE1 B:PHE115 4.0 27.0 1.0
NE2 B:GLN19 4.1 34.4 1.0
CA2 B:QC415 4.1 23.7 1.0
CD2 B:PHE115 4.1 28.3 1.0
CE1 B:QC415 4.2 29.5 1.0
CB B:THR12 4.2 20.1 1.0
CB B:VAL100 4.5 31.7 1.0
CG1 B:VAL100 4.6 32.0 1.0
CZ B:ARG46 4.6 23.7 1.0
OH B:QC415 4.8 27.9 1.0
CD1 B:PHE115 4.8 29.7 1.0
CG B:PHE115 4.9 28.1 1.0
C2 B:QC415 4.9 23.0 1.0
O2 B:QC415 4.9 23.6 1.0
CA B:THR12 4.9 18.4 1.0

Fluorine binding site 6 out of 6 in 6un5

Go back to Fluorine Binding Sites List in 6un5
Fluorine binding site 6 out of 6 in the Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Green Fluorescent Protein (Gfp); S65T, Y66(2,3,5- F3Y); Ih Circular Permutant (50-51) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F15

b:34.4
occ:1.00
F3 B:QC415 0.0 34.4 1.0
CE1 B:QC415 1.4 29.5 1.0
CD1 B:QC415 2.4 28.1 1.0
CZ B:QC415 2.5 26.1 1.0
OG1 B:THR155 2.7 29.3 0.9
CG2 B:THR155 2.8 31.5 0.1
OH B:QC415 2.8 27.9 1.0
O B:HOH456 3.0 24.6 1.0
CD B:GLU172 3.4 35.0 1.0
OE1 B:GLU172 3.5 35.5 1.0
OE2 B:GLU172 3.5 34.3 1.0
CE2 B:QC415 3.8 24.9 1.0
CG2 B:QC415 3.8 23.5 1.0
CB B:THR153 3.8 30.1 1.0
CE2 B:PHE95 4.0 26.3 1.0
CB B:THR155 4.0 29.7 0.9
CG B:GLU172 4.0 31.2 1.0
CB B:THR155 4.1 31.2 0.1
OG1 B:THR153 4.1 28.8 1.0
OG1 B:THR155 4.2 34.0 0.1
CG2 B:THR153 4.2 28.6 1.0
CD2 B:PHE95 4.2 23.7 1.0
CD2 B:QC415 4.2 24.0 1.0
CG1 B:VAL11 4.4 18.1 1.0
CG2 B:THR155 4.6 28.4 0.9
F1 B:QC415 4.9 28.6 1.0
OG1 B:QC415 4.9 22.8 1.0
CB2 B:QC415 5.0 24.4 1.0

Reference:

C.Y.Lin, S.G.Boxer. Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: Gfp and Pyp As Model Systems. J.Phys.Chem.B V. 124 9513 2020.
ISSN: ISSN 1089-5647
PubMed: 33073990
DOI: 10.1021/ACS.JPCB.0C07730
Page generated: Tue Jul 15 16:19:47 2025

Last articles

Na in 5ZPR
Na in 5ZS3
Na in 5ZPQ
Na in 5ZPO
Na in 5ZPP
Na in 5ZPN
Na in 5ZPM
Na in 5ZPL
Na in 5ZPK
Na in 5ZPJ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy