Fluorine in PDB 4ukd: Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride

All present enzymatic activity of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride:
2.7.4.14;

The structure of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride, PDB code: 4ukd 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)	39.00 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.100, 78.100, 101.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.2

The structure of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride (pdb code 4ukd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride, PDB code: 4ukd:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:15.2 occ:1.00 F1 A:BF2501 0.0 15.2 1.0 BE A:BF2501 1.5 19.4 1.0 F2 A:BF2501 2.4 19.7 1.0 O3B A:ADP195 2.5 17.1 1.0 O3B A:UDP196 2.5 19.5 1.0 NH2 A:ARG131 2.7 23.1 1.0 NH2 A:ARG148 2.8 19.2 1.0 NH1 A:ARG131 3.1 22.9 1.0 NH2 A:ARG137 3.1 26.6 1.0 PB A:UDP196 3.3 20.8 1.0 CZ A:ARG131 3.3 23.7 1.0 O2B A:UDP196 3.4 21.6 1.0 O3A A:UDP196 3.5 20.3 1.0 NH1 A:ARG137 3.7 27.1 1.0 N A:GLY16 3.8 17.8 1.0 CZ A:ARG137 3.8 27.2 1.0 CD2 A:LEU128 3.9 19.9 1.0 PB A:ADP195 4.0 18.0 1.0 CZ A:ARG148 4.1 19.7 1.0 MG A:MG500 4.3 18.4 1.0 CA A:GLY16 4.3 17.7 1.0 C A:PRO15 4.5 18.7 1.0 CA A:PRO15 4.5 18.6 1.0 O1B A:UDP196 4.6 22.1 1.0 O2B A:ADP195 4.6 18.8 1.0 NE A:ARG131 4.6 23.9 1.0 O A:HOH900 4.7 17.8 1.0 O3A A:ADP195 4.7 19.2 1.0 NH1 A:ARG148 4.7 17.9 1.0 O1A A:UDP196 4.7 21.8 1.0 PA A:UDP196 4.7 21.1 1.0 O1B A:ADP195 4.7 19.2 1.0 NE A:ARG137 4.9 25.7 1.0 CB A:PRO15 4.9 15.8 1.0 OD1 A:ASP140 4.9 23.6 1.0

Fluorine binding site 2 out of 2 in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Udp, Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:19.7 occ:1.00 F2 A:BF2501 0.0 19.7 1.0 BE A:BF2501 1.5 19.4 1.0 MG A:MG500 2.0 18.4 1.0 O3B A:ADP195 2.4 17.1 1.0 F1 A:BF2501 2.4 15.2 1.0 O3B A:UDP196 2.6 19.5 1.0 O3A A:UDP196 3.0 20.3 1.0 O A:HOH215 3.1 17.2 1.0 O A:HOH900 3.1 17.8 1.0 O2B A:ADP195 3.1 18.8 1.0 O A:HOH198 3.2 21.8 1.0 NH1 A:ARG137 3.3 27.1 1.0 O1A A:UDP196 3.3 21.8 1.0 PB A:ADP195 3.3 18.0 1.0 PB A:UDP196 3.4 20.8 1.0 PA A:UDP196 3.5 21.1 1.0 NH1 A:ARG131 3.8 22.9 1.0 NH2 A:ARG137 3.9 26.6 1.0 O2A A:UDP196 3.9 18.9 1.0 CZ A:ARG137 4.1 27.2 1.0 O A:HOH220 4.1 18.4 1.0 O1B A:UDP196 4.3 22.1 1.0 O1B A:ADP195 4.3 19.2 1.0 NH2 A:ARG131 4.3 23.1 1.0 O2B A:UDP196 4.4 21.6 1.0 O3A A:ADP195 4.4 19.2 1.0 O A:HOH553 4.4 29.4 1.0 CZ A:ARG131 4.5 23.7 1.0 O2A A:ADP195 4.6 17.3 1.0 NZ A:LYS19 4.7 12.8 1.0 NH2 A:ARG148 4.8 19.2 1.0

I.Schlichting, J.Reinstein. Structures of Active Conformations of Ump Kinase From Dictyostelium Discoideum Suggest Phosphoryl Transfer Is Associative. Biochemistry V. 36 9290 1997.
ISSN: ISSN 0006-2960
PubMed: 9280438
DOI: 10.1021/BI970974C