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Fluorine in PDB 5ukd: pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog

Enzymatic activity of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog

All present enzymatic activity of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog:
2.7.4.14;

Protein crystallography data

The structure of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog, PDB code: 5ukd was solved by I.Schlichting, J.Reinstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.500, 77.500, 100.200, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.1

Other elements in 5ukd:

The structure of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog (pdb code 5ukd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog, PDB code: 5ukd:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5ukd

Go back to Fluorine Binding Sites List in 5ukd
Fluorine binding site 1 out of 3 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:27.4
occ:1.00
F1 A:AF3501 0.0 27.4 1.0
AL A:AF3501 1.7 26.9 1.0
NH1 A:ARG148 2.5 17.9 1.0
O3B A:ADP195 2.8 10.7 1.0
NH2 A:ARG131 2.9 21.1 1.0
F3 A:AF3501 2.9 21.9 1.0
F2 A:AF3501 3.0 24.8 1.0
O3P A:C5P196 3.2 12.6 1.0
CZ A:ARG148 3.3 20.0 1.0
NH2 A:ARG148 3.3 18.5 1.0
NH1 A:ARG131 3.4 21.9 1.0
N A:GLY16 3.6 10.5 1.0
CZ A:ARG131 3.6 23.5 1.0
CD2 A:LEU128 3.6 13.1 1.0
CA A:PRO15 3.7 11.5 1.0
CB A:PRO15 3.7 12.1 1.0
NH2 A:ARG137 3.8 18.5 1.0
C A:PRO15 3.9 11.1 1.0
O A:HOH810 4.1 18.7 1.0
NH1 A:ARG137 4.2 20.2 1.0
CZ A:ARG137 4.2 22.0 1.0
PB A:ADP195 4.4 10.8 1.0
CA A:GLY16 4.4 9.7 1.0
NE A:ARG148 4.6 18.8 1.0
P A:C5P196 4.6 13.2 1.0
CD1 A:LEU128 4.8 12.5 1.0
CG A:LEU128 4.8 11.9 1.0
OD1 A:ASP140 4.9 14.8 1.0
NE A:ARG131 4.9 21.9 1.0
MG A:MG500 4.9 12.6 1.0
O2B A:ADP195 5.0 9.5 1.0
O A:PRO15 5.0 11.5 1.0

Fluorine binding site 2 out of 3 in 5ukd

Go back to Fluorine Binding Sites List in 5ukd
Fluorine binding site 2 out of 3 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:24.8
occ:1.00
F2 A:AF3501 0.0 24.8 1.0
AL A:AF3501 1.8 26.9 1.0
O3P A:C5P196 2.7 12.6 1.0
NZ A:LYS19 2.8 5.2 1.0
O3B A:ADP195 2.9 10.7 1.0
NH2 A:ARG93 3.0 20.0 1.0
F1 A:AF3501 3.0 27.4 1.0
F3 A:AF3501 3.1 21.9 1.0
O2P A:C5P196 3.3 10.8 1.0
O A:HOH198 3.4 15.6 1.0
NH2 A:ARG148 3.4 18.5 1.0
CE A:LYS19 3.5 7.1 1.0
P A:C5P196 3.6 13.2 1.0
CA A:PRO15 3.7 11.5 1.0
PB A:ADP195 3.9 10.8 1.0
O1B A:ADP195 4.0 9.5 1.0
CZ A:ARG93 4.1 18.1 1.0
O2B A:ADP195 4.2 9.5 1.0
O A:HOH712 4.2 22.6 0.9
N A:GLY16 4.2 10.5 1.0
MG A:MG500 4.2 12.6 1.0
O A:HOH994 4.3 12.2 0.4
O A:GLY14 4.3 11.1 1.0
CB A:PRO15 4.3 12.1 1.0
CZ A:ARG148 4.3 20.0 1.0
N A:PRO15 4.4 11.3 1.0
NH1 A:ARG93 4.4 17.9 1.0
NH1 A:ARG148 4.5 17.9 1.0
C A:PRO15 4.5 11.1 1.0
O1P A:C5P196 4.6 12.1 1.0
C A:GLY14 4.6 11.4 1.0
O5' A:C5P196 4.7 11.3 1.0
CD A:LYS19 4.9 8.2 1.0

Fluorine binding site 3 out of 3 in 5ukd

Go back to Fluorine Binding Sites List in 5ukd
Fluorine binding site 3 out of 3 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:21.9
occ:1.00
F3 A:AF3501 0.0 21.9 1.0
AL A:AF3501 1.7 26.9 1.0
MG A:MG500 2.2 12.6 1.0
O3B A:ADP195 2.6 10.7 1.0
NH1 A:ARG137 2.8 20.2 1.0
O3P A:C5P196 2.8 12.6 1.0
F1 A:AF3501 2.9 27.4 1.0
O A:HOH215 3.1 12.5 1.0
F2 A:AF3501 3.1 24.8 1.0
O2B A:ADP195 3.1 9.5 1.0
O A:HOH220 3.3 14.7 1.0
O A:HOH198 3.3 15.6 1.0
NH1 A:ARG131 3.3 21.9 1.0
O1P A:C5P196 3.4 12.1 1.0
P A:C5P196 3.5 13.2 1.0
PB A:ADP195 3.5 10.8 1.0
CZ A:ARG137 3.7 22.0 1.0
NH2 A:ARG137 3.8 18.5 1.0
O2P A:C5P196 3.9 10.8 1.0
NH2 A:ARG131 3.9 21.1 1.0
CZ A:ARG131 4.0 23.5 1.0
O3A A:ADP195 4.4 10.7 1.0
O A:HOH227 4.4 14.2 1.0
O2A A:ADP195 4.4 8.9 1.0
O A:HOH553 4.5 14.6 0.8
O1B A:ADP195 4.6 9.5 1.0
NH2 A:ARG148 4.9 18.5 1.0
NH1 A:ARG148 4.9 17.9 1.0
NE A:ARG137 4.9 22.3 1.0
O5' A:C5P196 5.0 11.3 1.0

Reference:

I.Schlichting, J.Reinstein. pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog. Nat.Struct.Biol. V. 6 721 1999.
ISSN: ISSN 1072-8368
PubMed: 10426946
DOI: 10.1038/11485
Page generated: Tue Jul 15 08:15:16 2025

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