Cadmium in PDB 3kbs: Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2CD(2+) Co-Factors

All present enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2CD(2+) Co-Factors:
5.3.1.5;

The structure of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2CD(2+) Co-Factors, PDB code: 3kbs was solved by A.Y.Kovalevsky, L.Hanson, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.630, 99.540, 102.900, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 28.4

The binding sites of Cadmium atom in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2CD(2+) Co-Factors (pdb code 3kbs). 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 2CD(2+) Co-Factors, PDB code: 3kbs:
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 2CD(2+) Co-Factors


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 2CD(2+) Co-Factors within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd390 b:5.4 occ:1.00 OD2 A:ASP257 2.3 1.1 1.0 OE1 A:GLU217 2.3 5.3 1.0 OD1 A:ASP255 2.3 4.6 1.0 O A:HOH1015 2.4 6.1 1.0 NE2 A:HIS220 2.4 6.3 1.0 OD2 A:ASP255 2.4 0.0 1.0 OE2 A:GLU217 2.7 0.5 1.0 CG A:ASP255 2.7 1.1 1.0 CD A:GLU217 2.9 1.9 1.0 CD2 A:HIS220 3.1 3.0 1.0 CG A:ASP257 3.2 1.2 1.0 OD1 A:ASP257 3.3 4.1 1.0 CE1 A:HIS220 3.4 0.1 1.0 O A:HOH1148 3.8 13.5 1.0 ND2 A:ASN247 4.1 2.9 1.0 O A:HOH1018 4.1 3.0 1.0 CB A:ASP255 4.2 0.0 1.0 CG A:HIS220 4.3 5.9 1.0 CG A:GLU217 4.3 5.1 1.0 ND1 A:HIS220 4.4 8.9 1.0 CB A:ASP257 4.6 2.1 1.0 CD A:CD391 4.6 10.4 1.0 NZ A:LYS183 4.7 8.5 1.0 O A:HOH1186 4.8 23.1 1.0 CE A:LYS183 4.8 3.5 1.0 OD2 A:ASP287 4.9 18.2 1.0 O A:HOH1109 4.9 11.9 1.0 CA A:ASP257 5.0 0.0 1.0

Cadmium binding site 2 out of 2 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2CD(2+) Co-Factors


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 2CD(2+) Co-Factors within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd391 b:10.4 occ:1.00 OE1 A:GLU181 2.1 27.3 1.0 OD2 A:ASP287 2.2 18.2 1.0 OD1 A:ASP245 2.2 8.6 1.0 OE2 A:GLU217 2.4 0.5 1.0 O A:HOH1109 2.4 11.9 1.0 CD A:GLU181 3.0 17.8 1.0 CG A:ASP287 3.2 14.5 1.0 OE2 A:GLU181 3.3 12.1 1.0 CG A:ASP245 3.4 12.1 1.0 CD A:GLU217 3.5 1.9 1.0 CB A:ASP287 3.5 5.7 1.0 O A:HOH1285 3.7 23.3 1.0 CG A:GLU217 3.9 5.1 1.0 CB A:ASP245 3.9 8.0 1.0 O A:HOH1015 4.0 6.1 1.0 CE1 A:HIS220 4.0 0.1 1.0 CB A:GLU217 4.1 3.7 1.0 OD1 A:ASP287 4.3 15.6 1.0 CG A:GLU181 4.4 6.6 1.0 OD2 A:ASP245 4.4 16.2 1.0 OE1 A:GLU217 4.5 5.3 1.0 CD A:CD390 4.6 5.4 1.0 NE2 A:HIS220 4.6 6.3 1.0 ND1 A:HIS220 4.7 8.9 1.0

A.Y.Kovalevsky, L.Hanson, S.Z.Fisher, M.Mustyakimov, S.A.Mason, V.T.Forsyth, M.P.Blakeley, D.A.Keen, T.Wagner, H.L.Carrell, A.K.Katz, J.P.Glusker, P.Langan. Metal Ion Roles and the Movement of Hydrogen During Reaction Catalyzed By D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study. Structure V. 18 688 2010.
ISSN: ISSN 0969-2126
PubMed: 20541506
DOI: 10.1016/J.STR.2010.03.011