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Fluorine in PDB 3ukd: Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3

Enzymatic activity of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3

All present enzymatic activity of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3:
2.7.4.14;

Protein crystallography data

The structure of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3, PDB code: 3ukd 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) 9.90 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.800, 78.800, 100.700, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.2

Other elements in 3ukd:

The structure of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3 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 Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3 (pdb code 3ukd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3, PDB code: 3ukd:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3ukd

Go back to Fluorine Binding Sites List in 3ukd
Fluorine binding site 1 out of 3 in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3


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, Cmp, and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:25.1
occ:1.00
F1 A:AF3501 0.0 25.1 1.0
AL A:AF3501 1.7 27.3 1.0
NH1 A:ARG148 2.7 21.6 1.0
O3B A:ADP195 2.8 14.8 1.0
F3 A:AF3501 2.8 25.6 1.0
NH2 A:ARG131 2.8 19.3 1.0
O3P A:C5P196 2.9 17.6 1.0
F2 A:AF3501 3.1 28.9 1.0
NH2 A:ARG137 3.3 19.9 1.0
NH1 A:ARG131 3.3 19.1 1.0
NH1 A:ARG137 3.3 23.8 1.0
NH2 A:ARG148 3.4 21.1 1.0
CZ A:ARG148 3.5 22.6 1.0
CZ A:ARG131 3.5 21.9 1.0
CZ A:ARG137 3.6 23.0 1.0
CD2 A:LEU128 3.9 18.7 1.0
N A:GLY16 3.9 14.8 1.0
O A:HOH810 4.2 19.2 1.0
PB A:ADP195 4.3 17.0 1.0
P A:C5P196 4.3 18.8 1.0
CA A:PRO15 4.4 18.2 1.0
C A:PRO15 4.5 17.7 1.0
CB A:PRO15 4.6 18.9 1.0
CA A:GLY16 4.6 15.2 1.0
NE A:ARG137 4.7 24.1 1.0
O1P A:C5P196 4.7 18.6 1.0
MG A:MG500 4.7 19.8 1.0
NE A:ARG148 4.8 21.9 1.0
NE A:ARG131 4.8 20.5 1.0
O2B A:ADP195 4.8 17.1 1.0
OD1 A:ASP140 4.8 21.8 1.0
O3A A:ADP195 4.9 18.3 1.0

Fluorine binding site 2 out of 3 in 3ukd

Go back to Fluorine Binding Sites List in 3ukd
Fluorine binding site 2 out of 3 in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3


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, Cmp, and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.9
occ:1.00
F2 A:AF3501 0.0 28.9 1.0
AL A:AF3501 1.7 27.3 1.0
O3B A:ADP195 2.6 14.8 1.0
NZ A:LYS19 2.7 14.5 1.0
O3P A:C5P196 2.8 17.6 1.0
F3 A:AF3501 2.9 25.6 1.0
F1 A:AF3501 3.1 25.1 1.0
NH2 A:ARG93 3.1 19.5 1.0
NH2 A:ARG148 3.2 21.1 1.0
O A:HOH198 3.4 24.1 1.0
CE A:LYS19 3.5 15.6 1.0
CA A:PRO15 3.6 18.2 1.0
PB A:ADP195 3.6 17.0 1.0
O2P A:C5P196 3.6 18.1 1.0
O1B A:ADP195 3.7 18.0 1.0
N A:GLY16 3.7 14.8 1.0
P A:C5P196 3.9 18.8 1.0
O A:GLY14 3.9 19.9 1.0
O2B A:ADP195 4.1 17.1 1.0
C A:PRO15 4.2 17.7 1.0
CZ A:ARG148 4.2 22.6 1.0
N A:PRO15 4.3 19.5 1.0
CZ A:ARG93 4.3 20.9 1.0
NH1 A:ARG148 4.4 21.6 1.0
C A:GLY14 4.4 19.3 1.0
MG A:MG500 4.5 19.8 1.0
CB A:PRO15 4.5 18.9 1.0
O A:HOH712 4.6 25.5 1.0
NH1 A:ARG93 4.7 18.9 1.0
O5' A:C5P196 4.8 15.8 1.0
CA A:GLY16 4.9 15.2 1.0
O1P A:C5P196 4.9 18.6 1.0
O3A A:ADP195 5.0 18.3 1.0
CD A:LYS19 5.0 16.3 1.0

Fluorine binding site 3 out of 3 in 3ukd

Go back to Fluorine Binding Sites List in 3ukd
Fluorine binding site 3 out of 3 in the Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ump/Cmp Kinase From Slime Mold Complexed with Adp, Cmp, and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:25.6
occ:1.00
F3 A:AF3501 0.0 25.6 1.0
AL A:AF3501 1.6 27.3 1.0
MG A:MG500 2.1 19.8 1.0
O3B A:ADP195 2.5 14.8 1.0
O3P A:C5P196 2.6 17.6 1.0
O A:HOH198 2.7 24.1 1.0
F1 A:AF3501 2.8 25.1 1.0
F2 A:AF3501 2.9 28.9 1.0
O A:HOH215 3.0 13.7 1.0
O2B A:ADP195 3.0 17.1 1.0
NH1 A:ARG137 3.1 23.8 1.0
P A:C5P196 3.2 18.8 1.0
O A:HOH220 3.3 21.8 1.0
PB A:ADP195 3.3 17.0 1.0
O1P A:C5P196 3.3 18.6 1.0
O2P A:C5P196 3.4 18.1 1.0
NH1 A:ARG131 3.8 19.1 1.0
NH2 A:ARG137 4.0 19.9 1.0
CZ A:ARG137 4.0 23.0 1.0
O A:HOH227 4.3 18.9 1.0
O1B A:ADP195 4.3 18.0 1.0
O3A A:ADP195 4.3 18.3 1.0
NH2 A:ARG131 4.6 19.3 1.0
CZ A:ARG131 4.6 21.9 1.0
NH2 A:ARG148 4.6 21.1 1.0
O5' A:C5P196 4.7 15.8 1.0
O2A A:ADP195 4.7 17.7 1.0
NZ A:LYS19 4.8 14.5 1.0
NH2 A:ARG42 4.8 29.5 1.0
O A:HOH553 4.9 32.6 1.0

Reference:

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
Page generated: Sun Dec 13 11:56:31 2020

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