Nickel in PDB 6vlo: X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus

All present enzymatic activity of X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus:
4.2.1.46;

The structure of X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus, PDB code: 6vlo was solved by J.B.Thoden, J.D.Ferek, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.88 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.883, 111.083, 133.385, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.9

The binding sites of Nickel atom in the X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus (pdb code 6vlo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus, PDB code: 6vlo:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni403 b:70.7 occ:1.00 NE2 D:HIS66 2.3 36.3 1.0 NE2 B:HIS66 2.7 45.2 1.0 NE2 B:HIS71 3.0 53.7 1.0 CD2 B:HIS66 3.0 43.7 1.0 CD2 D:HIS66 3.3 35.0 1.0 CE1 D:HIS66 3.3 36.5 1.0 CD2 B:HIS71 3.6 54.7 1.0 CE1 B:HIS66 3.9 44.2 1.0 CG D:GLU70 4.0 69.9 1.0 CE1 B:HIS71 4.1 49.7 1.0 CB B:GLU70 4.1 49.3 1.0 CG B:HIS66 4.3 41.5 1.0 ND1 D:HIS66 4.4 38.8 1.0 CG D:HIS66 4.4 31.0 1.0 CB D:GLU70 4.5 58.6 1.0 CG B:GLU70 4.6 59.6 1.0 ND1 B:HIS66 4.7 42.5 1.0 CG B:HIS71 4.9 48.7 1.0

Nickel binding site 2 out of 2 in the X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Structure of the R141 Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Minivirus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni403 b:48.0 occ:1.00 OE2 C:GLU70 2.1 32.0 1.0 OE1 C:GLU70 2.1 43.3 1.0 NE2 C:HIS66 2.2 31.3 1.0 CD C:GLU70 2.4 47.6 1.0 NE2 A:HIS66 2.4 43.8 1.0 NE2 A:HIS71 2.6 40.8 1.0 CD2 A:HIS66 3.0 35.6 1.0 CE1 C:HIS66 3.1 31.2 1.0 CD2 C:HIS66 3.2 32.3 1.0 CD2 A:HIS71 3.4 41.9 1.0 CE1 A:HIS66 3.6 41.4 1.0 CE1 A:HIS71 3.7 39.9 1.0 CG C:GLU70 3.9 47.9 1.0 ND1 C:HIS66 4.3 30.0 1.0 CG A:HIS66 4.3 34.4 1.0 CG C:HIS66 4.3 28.9 1.0 CB A:GLU70 4.4 42.9 1.0 ND1 A:HIS66 4.5 36.3 1.0 CG A:HIS71 4.6 36.9 1.0 CB C:GLU70 4.7 45.8 1.0 ND1 A:HIS71 4.7 42.3 1.0 CG A:GLU70 4.9 51.0 1.0 O A:HIS66 5.0 30.8 1.0

J.D.Ferek, J.B.Thoden, H.M.Holden. Biochemical Analysis of A Sugar 4,6-Dehydratase From Acanthamoeba Polyphaga Mimivirus. Protein Sci. 2020.
ISSN: ESSN 1469-896X
PubMed: 32083779
DOI: 10.1002/PRO.3843