Nickel in PDB 6c8z: Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales

All present enzymatic activity of Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales:
2.7.1.146;

The structure of Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales, PDB code: 6c8z was solved by V.Castro-Fernandez, F.Gonzalez-Ordenes, S.Munoz, N.Fuentes, D.Leonardo, M.Fuentealba, A.Herrera-Morande, P.Maturana, P.Villalobos, R.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.99 / 2.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.081, 75.986, 82.442, 90.00, 94.92, 90.00
R / Rfree (%)	19.8 / 23.9

The structure of Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Nickel atom in the Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales (pdb code 6c8z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales, PDB code: 6c8z:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:75.7 occ:0.64 OE2 A:GLU230 2.1 0.9 1.0 NE2 A:HIS227 2.3 76.8 1.0 CD2 A:HIS227 2.9 75.3 1.0 CD A:GLU230 2.9 96.7 1.0 OE1 A:GLU230 3.2 94.5 1.0 CE1 A:HIS227 3.5 76.6 1.0 CG A:GLU230 4.1 70.5 1.0 CG A:HIS227 4.2 72.7 1.0 ND1 A:HIS227 4.4 75.8 1.0 O A:LEU163 4.7 80.7 1.0 CB A:GLU230 4.8 62.8 1.0

Nickel binding site 2 out of 3 in the Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni503 b:73.0 occ:1.00 OD2 A:ASP298 2.1 80.2 1.0 OD1 A:ASP298 2.1 68.9 1.0 CG A:ASP298 2.4 69.8 1.0 CB A:ASP298 3.9 61.7 1.0 CA A:ALA294 4.5 57.7 1.0 N A:ASP298 4.7 60.6 1.0 CA A:ASP298 4.7 60.5 1.0 CB A:ALA294 4.7 59.3 1.0

Nickel binding site 3 out of 3 in the Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Last Common Ancestor of Adp-Dependent Phosphofructokinases From Methanosarcinales within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni504 b:0.2 occ:1.00 OD2 A:ASP42 2.1 0.8 1.0 OD2 A:ASP44 2.1 0.1 1.0 OD1 A:ASP42 2.1 97.3 1.0 OD1 A:ASP45 2.1 96.2 1.0 CG A:ASP42 2.3 98.7 1.0 CG A:ASP45 2.9 90.7 1.0 CG A:ASP44 3.0 93.0 1.0 OD2 A:ASP45 3.3 99.3 1.0 OD1 A:ASP44 3.3 96.8 1.0 CB A:ASP42 3.7 81.5 1.0 N A:ASP45 4.0 69.2 1.0 CB A:ASP45 4.1 69.1 1.0 CB A:ASP44 4.2 72.5 1.0 N A:ASP42 4.3 75.4 1.0 CA A:ASP42 4.5 77.1 1.0 CA A:ASP45 4.5 67.7 1.0 C A:ASP44 4.7 71.3 1.0 N A:ASP44 4.8 69.8 1.0 CA A:ASP44 4.9 69.1 1.0 C A:ASP42 4.9 77.8 1.0

F.Gonzalez-Ordenes, P.A.Cea, N.Fuentes-Ugarte, S.M.Munoz, R.A.Zamora, D.Leonardo, R.C.Garratt, V.Castro-Fernandez, V.Guixe. Adp-Dependent Kinases From the Archaeal Ordermethanosarcinalesadapt to Salt By A Non-Canonical Evolutionarily Conserved Strategy. Front Microbiol V. 9 1305 2018.
ISSN: ESSN 1664-302X
PubMed: 29997580
DOI: 10.3389/FMICB.2018.01305