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

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

The structure of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribose, PDB code: 4qee 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 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.958, 99.613, 103.035, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 19.1

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-Ribose (pdb code 4qee). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 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-Ribose, PDB code: 4qee:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two NI2+ Ions and L-Ribose


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-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:16.5 occ:1.00 OE2 A:GLU217 1.9 18.9 1.0 OD1 A:ASP257 2.1 15.5 1.0 OD2 A:ASP255 2.1 18.0 1.0 O A:HOH1001 2.1 15.7 1.0 NE2 A:HIS220 2.2 16.6 1.0 OD1 A:ASP255 2.3 14.6 1.0 CG A:ASP255 2.5 18.6 1.0 CD2 A:HIS220 2.9 13.6 1.0 CD A:GLU217 2.9 16.5 1.0 CG A:ASP257 3.0 21.4 1.0 CE1 A:HIS220 3.3 15.0 1.0 OD2 A:ASP257 3.3 21.6 1.0 OE1 A:GLU217 3.3 19.8 1.0 O A:HOH1050 3.8 22.6 1.0 ND2 A:ASN247 4.0 16.9 1.0 CB A:ASP255 4.0 14.1 1.0 O A:HOH1024 4.0 17.4 1.0 CG A:HIS220 4.1 11.7 1.0 ND1 A:HIS220 4.2 13.9 1.0 CG A:GLU217 4.3 11.6 1.0 CB A:ASP257 4.5 12.3 1.0 O4 A:Z6J403 4.5 13.2 0.5 O A:HOH1098 4.5 31.3 1.0 CA A:ASP257 4.8 11.7 1.0 N A:ASP257 4.9 13.9 1.0 CE A:LYS183 4.9 16.1 1.0 NZ A:LYS183 4.9 17.9 1.0 CA A:ASP255 5.0 12.7 1.0 OD2 A:ASP287 5.0 22.1 1.0

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


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-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:22.6 occ:1.00 OD2 A:ASP287 2.0 22.1 1.0 OD2 A:ASP245 2.2 20.9 1.0 O5 A:Z6J403 2.2 14.4 0.5 O4 A:Z6J403 2.3 13.2 0.5 OE1 A:GLU217 2.3 19.8 1.0 OE2 A:GLU181 2.3 31.9 1.0 CD A:GLU181 2.9 34.5 1.0 OE1 A:GLU181 3.0 39.7 1.0 C4 A:Z6J403 3.1 15.9 0.5 CG A:ASP287 3.1 21.3 1.0 C5 A:Z6J403 3.2 24.0 0.5 CG A:ASP245 3.3 22.9 1.0 CD A:GLU217 3.5 16.5 1.0 CB A:ASP287 3.6 15.6 1.0 O3 A:Z6J403 3.7 46.8 0.5 C3 A:Z6J403 3.8 12.0 0.5 O A:HOH1001 3.8 15.7 1.0 O A:HOH1167 3.9 40.2 1.0 CB A:ASP245 3.9 13.3 1.0 CG A:GLU217 4.2 11.6 1.0 OD1 A:ASP287 4.2 18.8 1.0 CB A:GLU217 4.2 14.4 1.0 CE1 A:HIS220 4.3 15.0 1.0 OD1 A:ASP245 4.3 19.6 1.0 CG A:GLU181 4.3 19.2 1.0 O2 A:Z6J403 4.3 29.7 0.5 OE2 A:GLU217 4.4 18.9 1.0 C2 A:Z6J403 4.7 16.7 0.5 ND2 A:ASN215 4.9 20.9 1.0 NE2 A:HIS220 4.9 16.6 1.0 ND1 A:HIS220 5.0 13.9 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