Cadmium in PDB 4qe1: Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose

All present enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose:
5.3.1.5;

The structure of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose, PDB code: 4qe1 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 / 1.55
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.865, 99.869, 102.840, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19

The binding sites of Cadmium atom in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose (pdb code 4qe1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose, PDB code: 4qe1:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:16.2 occ:1.00 OE2 A:GLU217 2.2 17.2 1.0 OD1 A:ASP257 2.2 14.4 1.0 O A:HOH1001 2.4 18.7 1.0 OD1 A:ASP255 2.4 15.0 1.0 OD2 A:ASP255 2.4 16.6 1.0 NE2 A:HIS220 2.5 16.0 1.0 CG A:ASP255 2.8 16.8 1.0 OE1 A:GLU217 2.9 20.2 1.0 CD A:GLU217 2.9 19.9 1.0 CD2 A:HIS220 3.1 14.7 1.0 CG A:ASP257 3.2 23.1 1.0 OD2 A:ASP257 3.4 21.3 1.0 CE1 A:HIS220 3.5 16.7 1.0 O A:HOH1064 3.9 27.4 1.0 ND2 A:ASN247 4.1 16.5 1.0 O A:HOH1024 4.1 15.2 1.0 CB A:ASP255 4.3 13.5 1.0 CG A:HIS220 4.3 12.5 1.0 OD2 A:ASP287 4.3 17.0 1.0 O3 A:RUU403 4.4 20.5 1.0 CG A:GLU217 4.4 11.9 1.0 ND1 A:HIS220 4.4 13.4 1.0 CB A:ASP257 4.6 13.7 1.0 CD A:CD402 4.6 20.2 1.0 NZ A:LYS183 4.8 22.6 1.0 CE A:LYS183 4.8 17.4 1.0 O A:HOH1117 5.0 35.2 1.0 CG A:ASP287 5.0 24.8 1.0

Cadmium binding site 2 out of 2 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two CD2+ Ions and L-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:20.2 occ:1.00 OD2 A:ASP287 2.1 17.0 1.0 OD2 A:ASP245 2.2 20.0 1.0 OE2 A:GLU181 2.2 20.7 1.0 OE1 A:GLU217 2.3 20.2 1.0 O2 A:RUU403 2.3 22.1 1.0 O3 A:RUU403 2.5 20.5 1.0 CD A:GLU181 3.1 30.3 1.0 CG A:ASP287 3.1 24.8 1.0 OE1 A:GLU181 3.2 24.2 1.0 C2 A:RUU403 3.4 25.4 1.0 CG A:ASP245 3.4 23.7 1.0 CD A:GLU217 3.4 19.9 1.0 C3 A:RUU403 3.5 22.4 1.0 CB A:ASP287 3.6 15.4 1.0 O A:HOH1001 4.0 18.7 1.0 O5 A:RUU403 4.0 26.3 1.0 CB A:ASP245 4.0 12.5 1.0 CG A:GLU217 4.0 11.9 1.0 O A:HOH1078 4.1 29.3 1.0 CE1 A:HIS220 4.1 16.7 1.0 CB A:GLU217 4.2 14.9 1.0 OD1 A:ASP287 4.3 19.6 1.0 OD1 A:ASP245 4.3 20.6 1.0 C5 A:RUU403 4.3 24.8 1.0 OE2 A:GLU217 4.4 17.2 1.0 CG A:GLU181 4.4 18.4 1.0 C4 A:RUU403 4.6 29.4 1.0 C1 A:RUU403 4.6 22.0 1.0 CD A:CD401 4.6 16.2 1.0 NE2 A:HIS220 4.6 16.0 1.0 ND1 A:HIS220 4.8 13.4 1.0 O4 A:RUU403 5.0 31.0 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