Nickel in PDB 4qe4: Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose

All present enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose:
5.3.1.5;

The structure of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose, PDB code: 4qe4 was solved by A.Y.Kovalevsky, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.876, 99.630, 102.968, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18

The binding sites of Nickel atom in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose (pdb code 4qe4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose, PDB code: 4qe4:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:22.0 occ:0.40 NI A:NI401 0.0 22.0 0.4 NI A:NI401 1.9 10.1 0.6 O A:HOH1001 1.9 21.6 1.0 NE2 A:HIS220 2.2 21.4 1.0 O1 A:34V404 2.5 10.8 0.5 OE2 A:GLU217 2.5 19.6 1.0 OE1 A:GLU217 2.5 18.4 1.0 CE1 A:HIS220 2.6 16.4 1.0 O A:HOH1063 2.7 23.0 1.0 CD A:GLU217 2.9 15.0 1.0 OD2 A:ASP255 3.1 20.9 1.0 CD2 A:HIS220 3.4 15.3 1.0 OD1 A:ASP257 3.5 16.4 1.0 C1 A:34V404 3.5 23.2 0.5 NI A:NI403 3.6 21.4 1.0 OD2 A:ASP257 3.7 19.6 1.0 OD2 A:ASP287 3.8 20.8 1.0 ND1 A:HIS220 3.9 16.6 1.0 CG A:ASP255 3.9 24.5 1.0 OD1 A:ASP255 4.0 17.6 1.0 CG A:ASP257 4.1 20.2 1.0 OE2 A:GLU181 4.2 24.8 1.0 CG A:HIS220 4.3 11.5 1.0 CG A:GLU217 4.3 9.4 1.0 O2 A:34V404 4.3 40.0 0.5 CG A:ASP287 4.5 20.6 1.0 C2 A:34V404 4.6 33.9 0.5 O A:HOH1244 4.8 45.6 1.0 ND2 A:ASN247 4.8 15.6 1.0 CB A:GLU217 4.9 11.3 1.0 O3 A:34V404 5.0 10.2 0.5 OD1 A:ASP287 5.0 18.8 1.0 CE A:LYS183 5.0 16.0 1.0

Nickel binding site 2 out of 3 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:10.1 occ:0.60 NI A:NI401 0.0 10.1 0.6 NI A:NI401 1.9 22.0 0.4 OE2 A:GLU217 1.9 19.6 1.0 OD2 A:ASP255 2.0 20.9 1.0 OD1 A:ASP257 2.1 16.4 1.0 OD1 A:ASP255 2.2 17.6 1.0 NE2 A:HIS220 2.3 21.4 1.0 CG A:ASP255 2.4 24.5 1.0 O A:HOH1001 2.7 21.6 1.0 CD2 A:HIS220 2.9 15.3 1.0 CD A:GLU217 3.0 15.0 1.0 CG A:ASP257 3.1 20.2 1.0 OD2 A:ASP257 3.3 19.6 1.0 CE1 A:HIS220 3.4 16.4 1.0 OE1 A:GLU217 3.4 18.4 1.0 O A:HOH1063 3.6 23.0 1.0 CB A:ASP255 4.0 16.9 1.0 ND2 A:ASN247 4.0 15.6 1.0 O A:HOH1038 4.0 17.0 1.0 CG A:HIS220 4.2 11.5 1.0 CG A:GLU217 4.3 9.4 1.0 O1 A:34V404 4.4 10.8 0.5 ND1 A:HIS220 4.4 16.6 1.0 O A:HOH1100 4.4 31.3 1.0 CB A:ASP257 4.5 12.4 1.0 CE A:LYS183 4.7 16.0 1.0 CA A:ASP257 4.9 10.8 1.0 CA A:ASP255 4.9 13.9 1.0 N A:ASP257 4.9 14.9 1.0 NZ A:LYS183 4.9 22.5 1.0

Nickel binding site 3 out of 3 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:21.4 occ:1.00 OE2 A:GLU181 2.1 24.8 1.0 OD2 A:ASP287 2.1 20.8 1.0 O3 A:34V404 2.1 10.2 0.5 OD2 A:ASP245 2.2 18.9 1.0 OE1 A:GLU217 2.2 18.4 1.0 O1 A:34V404 2.2 10.8 0.5 CD A:GLU181 3.0 27.0 1.0 CG A:ASP287 3.1 20.6 1.0 OE1 A:GLU181 3.2 26.4 1.0 CG A:ASP245 3.3 23.0 1.0 C3 A:34V404 3.3 24.8 0.5 C1 A:34V404 3.3 23.2 0.5 CD A:GLU217 3.4 15.0 1.0 CB A:ASP287 3.6 14.0 1.0 NI A:NI401 3.6 22.0 0.4 C2 A:34V404 3.7 33.9 0.5 CB A:ASP245 3.9 12.0 1.0 O2 A:34V404 3.9 40.0 0.5 O A:HOH1001 4.0 21.6 1.0 O A:HOH1101 4.0 29.9 1.0 CG A:GLU217 4.1 9.4 1.0 CE1 A:HIS220 4.2 16.4 1.0 CB A:GLU217 4.2 11.3 1.0 OD1 A:ASP287 4.2 18.8 1.0 OD1 A:ASP245 4.3 18.9 1.0 OE2 A:GLU217 4.3 19.6 1.0 CG A:GLU181 4.3 18.8 1.0 C4 A:34V404 4.6 22.2 0.5 O4 A:34V404 4.6 47.2 0.5 NE2 A:HIS220 4.8 21.4 1.0 ND2 A:ASN215 4.9 18.1 1.0 ND1 A:HIS220 4.9 16.6 1.0

P.Langan, A.K.Sangha, T.Wymore, J.M.Parks, Z.K.Yang, B.L.Hanson, Z.Fisher, S.A.Mason, M.P.Blakeley, V.T.Forsyth, J.P.Glusker, H.L.Carrell, J.C.Smith, D.A.Keen, D.E.Graham, A.Kovalevsky. L-Arabinose Binding, Isomerization, and Epimerization By D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Structure V. 22 1287 2014.
ISSN: ISSN 0969-2126
PubMed: 25132082
DOI: 10.1016/J.STR.2014.07.002