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Fluorine in PDB 1qf9: pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase

Enzymatic activity of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase

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

Protein crystallography data

The structure of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase, PDB code: 1qf9 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) 20.00 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.000, 78.000, 100.600, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 24.4

Other elements in 1qf9:

The structure of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase 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 in Ump/Cmp Kinase (pdb code 1qf9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase, PDB code: 1qf9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1qf9

Go back to Fluorine Binding Sites List in 1qf9
Fluorine binding site 1 out of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase


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 in Ump/Cmp Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F499

b:27.8
occ:1.00
 F1 A:ALF499 0.0 27.8 1.0
AL A:ALF499 1.7 23.9 1.0
F3 A:ALF499 2.3 29.5 1.0
F4 A:ALF499 2.4 24.7 1.0
O3B A:ADP195 2.7 12.7 1.0
O3P A:C5P196 2.7 16.1 1.0
NH2 A:ARG148 2.9 19.3 1.0
CA A:PRO15 3.0 15.4 1.0
NH1 A:ARG148 3.1 22.1 1.0
N A:GLY16 3.2 13.7 1.0
NH2 A:ARG93 3.3 15.7 1.0
F2 A:ALF499 3.3 24.9 1.0
CZ A:ARG148 3.4 26.1 1.0
NZ A:LYS19 3.5 9.5 1.0
C A:PRO15 3.6 14.2 1.0
CB A:PRO15 3.7 15.8 1.0
N A:PRO15 4.0 15.7 1.0
PB A:ADP195 4.1 14.1 1.0
P A:C5P196 4.1 15.9 1.0
O A:GLY14 4.1 16.4 1.0
O1B A:ADP195 4.3 13.8 1.0
O2P A:C5P196 4.3 14.4 1.0
O A:HOH712 4.4 22.4 0.9
C A:GLY14 4.4 16.7 1.0
CA A:GLY16 4.5 13.1 1.0
CE A:LYS19 4.5 14.0 1.0
CZ A:ARG93 4.6 17.2 1.0
CG A:PRO15 4.6 15.7 1.0
NE A:ARG148 4.7 25.0 1.0
O2B A:ADP195 4.7 13.4 1.0
NH2 A:ARG137 4.8 14.3 1.0
O A:PRO15 4.8 13.5 1.0
O A:HOH198 4.8 29.7 1.0
MG A:MG500 4.9 19.2 1.0
O5' A:C5P196 4.9 13.8 1.0

Fluorine binding site 2 out of 4 in 1qf9

Go back to Fluorine Binding Sites List in 1qf9
Fluorine binding site 2 out of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase


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 in Ump/Cmp Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F499

b:24.9
occ:1.00
 F2 A:ALF499 0.0 24.9 1.0
AL A:ALF499 1.6 23.9 1.0
MG A:MG500 2.3 19.2 1.0
F4 A:ALF499 2.3 24.7 1.0
F3 A:ALF499 2.4 29.5 1.0
O3P A:C5P196 2.5 16.1 1.0
O3B A:ADP195 2.5 12.7 1.0
NH1 A:ARG137 2.8 16.0 1.0
O A:HOH215 3.2 14.5 1.0
P A:C5P196 3.2 15.9 1.0
O1P A:C5P196 3.3 16.3 1.0
O2B A:ADP195 3.3 13.4 1.0
O A:HOH220 3.3 12.5 1.0
F1 A:ALF499 3.3 27.8 1.0
NH1 A:ARG131 3.3 12.7 1.0
PB A:ADP195 3.5 14.1 1.0
NH2 A:ARG137 3.6 14.3 1.0
CZ A:ARG137 3.6 16.9 1.0
O A:HOH198 3.7 29.7 1.0
O2P A:C5P196 3.8 14.4 1.0
NH2 A:ARG131 4.0 15.1 1.0
CZ A:ARG131 4.0 16.4 1.0
O3A A:ADP195 4.3 13.8 1.0
O A:HOH553 4.4 15.5 0.8
O A:HOH227 4.6 23.4 1.0
O2A A:ADP195 4.6 11.3 1.0
O1B A:ADP195 4.6 13.8 1.0
O5' A:C5P196 4.7 13.8 1.0
NH1 A:ARG148 4.7 22.1 1.0
NE A:ARG137 4.9 18.6 1.0
NH2 A:ARG148 4.9 19.3 1.0

Fluorine binding site 3 out of 4 in 1qf9

Go back to Fluorine Binding Sites List in 1qf9
Fluorine binding site 3 out of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase


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 in Ump/Cmp Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F499

b:29.5
occ:1.00
 F3 A:ALF499 0.0 29.5 1.0
AL A:ALF499 1.6 23.9 1.0
F1 A:ALF499 2.3 27.8 1.0
F2 A:ALF499 2.4 24.9 1.0
O3P A:C5P196 2.5 16.1 1.0
O3B A:ADP195 2.5 12.7 1.0
O A:HOH198 2.6 29.7 1.0
O2P A:C5P196 2.9 14.4 1.0
NZ A:LYS19 3.0 9.5 1.0
MG A:MG500 3.0 19.2 1.0
P A:C5P196 3.2 15.9 1.0
CE A:LYS19 3.3 14.0 1.0
O2B A:ADP195 3.3 13.4 1.0
PB A:ADP195 3.3 14.1 1.0
NH2 A:ARG93 3.3 15.7 1.0
F4 A:ALF499 3.3 24.7 1.0
O1B A:ADP195 3.7 13.8 1.0
O1P A:C5P196 4.0 16.3 1.0
CZ A:ARG93 4.3 17.2 1.0
O A:HOH215 4.3 14.5 1.0
NH2 A:ARG148 4.4 19.3 1.0
NH1 A:ARG93 4.4 14.5 1.0
O5' A:C5P196 4.5 13.8 1.0
N A:GLY16 4.7 13.7 1.0
O3A A:ADP195 4.7 13.8 1.0
CD A:LYS19 4.7 15.6 1.0
O A:HOH208 4.7 21.8 1.0
O A:HOH227 4.8 23.4 1.0
OD1 A:ASP89 4.8 14.4 1.0
O A:HOH220 5.0 12.5 1.0
NH1 A:ARG148 5.0 22.1 1.0

Fluorine binding site 4 out of 4 in 1qf9

Go back to Fluorine Binding Sites List in 1qf9
Fluorine binding site 4 out of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F499

b:24.7
occ:1.00
 F4 A:ALF499 0.0 24.7 1.0
AL A:ALF499 1.7 23.9 1.0
F2 A:ALF499 2.3 24.9 1.0
F1 A:ALF499 2.4 27.8 1.0
O3B A:ADP195 2.7 12.7 1.0
NH1 A:ARG148 2.7 22.1 1.0
NH2 A:ARG131 2.7 15.1 1.0
O3P A:C5P196 2.8 16.1 1.0
NH1 A:ARG131 3.1 12.7 1.0
NH2 A:ARG137 3.2 14.3 1.0
F3 A:ALF499 3.3 29.5 1.0
CZ A:ARG131 3.3 16.4 1.0
NH1 A:ARG137 3.5 16.0 1.0
CZ A:ARG148 3.6 26.1 1.0
CZ A:ARG137 3.6 16.9 1.0
NH2 A:ARG148 3.7 19.3 1.0
N A:GLY16 3.9 13.7 1.0
CD2 A:LEU128 4.0 14.1 1.0
P A:C5P196 4.1 15.9 1.0
PB A:ADP195 4.2 14.1 1.0
O A:HOH810 4.4 27.4 1.0
MG A:MG500 4.5 19.2 1.0
CA A:PRO15 4.5 15.4 1.0
CA A:GLY16 4.5 13.1 1.0
C A:PRO15 4.6 14.2 1.0
O1P A:C5P196 4.6 16.3 1.0
NE A:ARG131 4.7 16.3 1.0
NE A:ARG137 4.7 18.6 1.0
O3A A:ADP195 4.7 13.8 1.0
O2B A:ADP195 4.7 13.4 1.0
NE A:ARG148 4.7 25.0 1.0
CB A:PRO15 4.8 15.8 1.0
OD1 A:ASP140 5.0 16.2 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: Sun Dec 13 11:32:12 2020

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