Aluminium in PDB 7l07: 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;

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

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

Fluorine

(F)

9 atoms

The binding sites of Aluminium 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 Aluminium atom.
In total 3 binding sites of Aluminium where determined in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases, PDB code: 7l07:
Jump to Aluminium binding site number: 1; 2; 3;

Aluminium binding site 1 out of 3 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al 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:Al301 b:54.6 occ:1.00 AL A:AF3301 0.0 54.6 1.0 F1 A:AF3301 1.7 38.4 1.0 F2 A:AF3301 1.7 51.9 1.0 F3 A:AF3301 1.7 39.9 1.0 NZ A:LYS227 3.6 27.2 1.0 OH A:TYR229 3.7 27.5 1.0 OE1 A:GLU224 4.0 23.7 1.0 CE2 A:TYR229 4.2 21.6 1.0 CZ A:TYR229 4.3 24.4 1.0 CE A:LYS227 4.5 32.9 1.0 O A:HOH414 4.8 28.7 1.0 CD A:LYS227 4.8 26.3 1.0 CD A:GLU224 4.8 27.0 1.0 OE2 A:GLU224 4.8 26.5 1.0

Aluminium binding site 2 out of 3 in the Last Common Ancestor of Hmppk and Plk/Hmppk Vitamin Kinases


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al 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:Al302 b:53.0 occ:1.00 AL A:AF3302 0.0 53.0 1.0 F2 A:AF3302 1.7 53.2 1.0 F3 A:AF3302 1.7 56.1 1.0 F1 A:AF3302 1.7 39.6 1.0 O A:HOH419 3.0 26.1 1.0 O A:LYS101 3.5 31.6 1.0 O A:LEU133 4.1 21.1 1.0 O A:HOH433 4.2 32.1 1.0 C A:LYS101 4.3 29.4 1.0 OG1 A:THR135 4.4 17.7 1.0 CA A:LYS101 4.5 25.5 1.0 C A:LEU133 4.8 22.7 1.0 N A:THR135 4.8 21.0 1.0 O A:ALA134 4.8 17.1 1.0 C A:ALA134 4.9 22.7 1.0 CB A:LYS101 5.0 32.6 1.0

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


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al 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:Al303 b:62.2 occ:1.00 AL A:AF3303 0.0 62.2 1.0 F3 A:AF3303 1.7 57.3 1.0 F1 A:AF3303 1.7 38.3 1.0 F2 A:AF3303 1.7 64.3 1.0 NZ A:LYS96 3.7 40.7 1.0 O A:GLU129 4.2 22.8 1.0 O A:GLU128 4.3 29.6 1.0 OE1 A:GLU129 4.3 39.7 1.0 CB A:PRO132 4.5 22.9 1.0 CD A:LYS96 4.6 28.6 1.0 CE A:LYS96 4.6 33.0 1.0 CA A:GLU129 4.7 26.6 1.0 CG A:PRO132 4.7 23.8 1.0 CD2 A:LEU133 4.8 17.9 1.0 C A:GLU129 4.9 20.6 1.0

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