Fluorine in PDB 7l07: Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases

Enzymatic activity of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases

All present enzymatic activity of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases:
2.7.1.49;

Protein crystallography data

The structure of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases, PDB code: 7l07 was solved by F.Gonzalez-Ordenes, P.Maturana, A.Herrera-Morande, G.Araya, S.Arizabalos, V.Castro-Fernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.58 / 2.00
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 65.644, 65.644, 243.726, 90, 90, 120
R / Rfree (%) 20.8 / 21.5

Other elements in 7l07:

The structure of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases also contains other interesting chemical elements:

Aluminium (Al) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases (pdb code 7l07). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases, PDB code: 7l07:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 7l07

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Fluorine binding site 1 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:38.4
occ:1.00
 F1 A:AF3301 0.0 38.4 1.0
AL A:AF3301 1.7 54.6 1.0
NZ A:LYS227 2.9 27.2 1.0
F2 A:AF3301 2.9 51.9 1.0
F3 A:AF3301 2.9 39.9 1.0
CD A:LYS227 3.5 26.3 1.0
CE A:LYS227 3.6 32.9 1.0
OH A:TYR229 4.0 27.5 1.0
CE2 A:TYR229 4.2 21.6 1.0
OE1 A:GLU224 4.5 23.7 1.0
CZ A:TYR229 4.6 24.4 1.0
CG A:LYS227 4.8 23.0 1.0
O A:LEU31 4.9 24.7 1.0

Fluorine binding site 2 out of 9 in 7l07

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Fluorine binding site 2 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:51.9
occ:1.00
 F2 A:AF3301 0.0 51.9 1.0
AL A:AF3301 1.7 54.6 1.0
F1 A:AF3301 2.9 38.4 1.0
F3 A:AF3301 2.9 39.9 1.0
OH A:TYR229 4.2 27.5 1.0

Fluorine binding site 3 out of 9 in 7l07

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Fluorine binding site 3 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:39.9
occ:1.00
 F3 A:AF3301 0.0 39.9 1.0
AL A:AF3301 1.7 54.6 1.0
OE1 A:GLU224 2.8 23.7 1.0
F2 A:AF3301 2.9 51.9 1.0
F1 A:AF3301 2.9 38.4 1.0
NZ A:LYS227 3.2 27.2 1.0
CD A:GLU224 3.4 27.0 1.0
OE2 A:GLU224 3.5 26.5 1.0
O A:HOH414 3.9 28.7 1.0
CG2 A:THR237 3.9 25.9 1.0
CE A:LYS227 4.2 32.9 1.0
CE2 A:TYR229 4.3 21.6 1.0
OH A:TYR229 4.5 27.5 1.0
CZ A:TYR229 4.6 24.4 1.0
CG A:GLU224 4.8 18.5 1.0

Fluorine binding site 4 out of 9 in 7l07

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Fluorine binding site 4 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:39.6
occ:1.00
 F1 A:AF3302 0.0 39.6 1.0
AL A:AF3302 1.7 53.0 1.0
O A:LYS101 2.9 31.6 1.0
F2 A:AF3302 2.9 53.2 1.0
F3 A:AF3302 2.9 56.1 1.0
OG1 A:THR135 3.1 17.7 1.0
CA A:THR135 3.7 18.7 1.0
CB A:THR135 3.8 21.2 1.0
O A:HOH419 3.9 26.1 1.0
N A:THR135 3.9 21.0 1.0
O A:HOH486 4.0 46.4 1.0
C A:LYS101 4.1 29.4 1.0
CG2 A:THR135 4.2 18.6 1.0
CD A:LYS172 4.3 34.7 1.0
O A:ALA134 4.3 17.1 1.0
C A:ALA134 4.3 22.7 1.0
O A:LEU133 4.6 21.1 1.0
O A:HOH433 4.6 32.1 1.0
CA A:LYS101 4.7 25.5 1.0
O A:HOH446 4.7 45.6 1.0
CB A:LYS172 4.8 23.4 1.0

Fluorine binding site 5 out of 9 in 7l07

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Fluorine binding site 5 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:53.2
occ:1.00
 F2 A:AF3302 0.0 53.2 1.0
AL A:AF3302 1.7 53.0 1.0
F3 A:AF3302 2.9 56.1 1.0
F1 A:AF3302 2.9 39.6 1.0
O A:HOH419 3.0 26.1 1.0
CD A:LYS101 3.4 40.7 1.0
O A:LYS101 3.4 31.6 1.0
CA A:LYS101 3.4 25.5 1.0
CB A:LYS101 3.7 32.6 1.0
C A:LYS101 3.9 29.4 1.0
CG A:LYS101 4.1 34.4 1.0
CE A:LYS101 4.4 42.9 1.0
NZ A:LYS101 4.4 43.8 1.0
O A:VAL100 4.5 18.4 1.0
N A:LYS101 4.6 22.8 1.0
C A:VAL100 5.0 19.2 1.0

Fluorine binding site 6 out of 9 in 7l07

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Fluorine binding site 6 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:56.1
occ:1.00
 F3 A:AF3302 0.0 56.1 1.0
AL A:AF3302 1.7 53.0 1.0
O A:HOH433 2.9 32.1 1.0
F2 A:AF3302 2.9 53.2 1.0
F1 A:AF3302 2.9 39.6 1.0
O A:HOH419 3.7 26.1 1.0
O A:LEU133 4.0 21.1 1.0
C A:LEU133 4.2 22.7 1.0
O A:PRO132 4.3 20.2 1.0
O A:ALA134 4.4 17.1 1.0
CA A:LEU133 4.5 18.5 1.0
C A:ALA134 4.8 22.7 1.0
N A:ALA134 4.8 16.1 1.0

Fluorine binding site 7 out of 9 in 7l07

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Fluorine binding site 7 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:38.3
occ:1.00
 F1 A:AF3303 0.0 38.3 1.0
AL A:AF3303 1.7 62.2 1.0
O A:GLU129 2.7 22.8 1.0
F3 A:AF3303 3.0 57.3 1.0
F2 A:AF3303 3.0 64.3 1.0
NZ A:LYS96 3.5 40.7 1.0
C A:GLU129 3.6 20.6 1.0
CA A:GLU129 3.8 26.6 1.0
CG A:LEU133 3.9 22.2 1.0
CD2 A:LEU133 3.9 17.9 1.0
OE1 A:GLU129 4.0 39.7 1.0
CD1 A:LEU133 4.0 17.7 1.0
CE A:LYS96 4.1 33.0 1.0
CD A:LYS96 4.1 28.6 1.0
O A:GLU128 4.4 29.6 1.0
CB A:PRO132 4.5 22.9 1.0
CB A:GLU129 4.6 26.8 1.0
CG A:PRO132 4.7 23.8 1.0
O A:HOH444 4.7 41.4 1.0
N A:LEU130 4.8 17.6 1.0
CB A:ALA92 4.8 15.5 1.0
N A:GLU129 4.9 22.6 1.0
CG A:LYS96 4.9 17.9 1.0
CD A:PRO132 5.0 21.3 1.0
CD A:GLU129 5.0 43.0 1.0

Fluorine binding site 8 out of 9 in 7l07

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Fluorine binding site 8 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:64.3
occ:1.00
 F2 A:AF3303 0.0 64.3 1.0
AL A:AF3303 1.7 62.2 1.0
F1 A:AF3303 3.0 38.3 1.0
F3 A:AF3303 3.0 57.3 1.0
CB A:PRO132 3.4 22.9 1.0
CG A:PRO132 3.8 23.8 1.0
O A:GLU128 4.3 29.6 1.0
CA A:PRO132 4.9 19.7 1.0
O A:GLU129 4.9 22.8 1.0
CD A:PRO132 4.9 21.3 1.0

Fluorine binding site 9 out of 9 in 7l07

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Fluorine binding site 9 out of 9 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:57.3
occ:1.00
 F3 A:AF3303 0.0 57.3 1.0
AL A:AF3303 1.7 62.2 1.0
F1 A:AF3303 3.0 38.3 1.0
F2 A:AF3303 3.0 64.3 1.0
NZ A:LYS96 3.0 40.7 1.0
CE A:LYS96 4.2 33.0 1.0
CD A:LYS96 4.4 28.6 1.0
OE1 A:GLU129 4.4 39.7 1.0

Reference:

F.Gonzalez-Ordenes, F.Bravo-Moraga, E.Gonzalez, L.Hernandez-Cabello, J.Alzate-Morales, G.Victoria, V.Castro-Fernandez. Crystal Structure and Molecular Dynamics Simulations of A Promiscuous Ancestor Reveal Residues and An Epistatic Interaction Involved in Substrate Binding and Catalysis in the Atp-Dependent Vitamin Kinase Family Members Protein Sci. 2021.
ISSN: ESSN 1469-896X
DOI: 10.1002/PRO.4040
Page generated: Fri Aug 2 08:39:12 2024

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