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Cadmium in PDB 3kbm: Room Temperature X-Ray Structure of D-Xylose Isomerase Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form

Enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form

All present enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form:
5.3.1.5;

Protein crystallography data

The structure of Room Temperature X-Ray Structure of D-Xylose Isomerase Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form, PDB code: 3kbm 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) 20.00 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.196, 99.430, 102.986, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Room Temperature X-Ray Structure of D-Xylose Isomerase Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form (pdb code 3kbm). 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 Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form, PDB code: 3kbm:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3kbm

Go back to Cadmium Binding Sites List in 3kbm
Cadmium binding site 1 out of 2 in the Room Temperature X-Ray Structure of D-Xylose Isomerase Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form


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 Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd391

b:22.7
occ:1.00
O A:HOH1001 2.0 23.0 1.0
OD2 A:ASP255 2.3 19.6 1.0
OD1 A:ASP257 2.4 17.6 1.0
NE2 A:HIS220 2.4 19.2 1.0
OE2 A:GLU217 2.4 22.2 1.0
OD1 A:ASP255 2.5 20.6 1.0
OE1 A:GLU217 2.7 24.3 1.0
CG A:ASP255 2.7 20.7 1.0
CD A:GLU217 2.9 22.4 1.0
CD2 A:HIS220 3.0 17.4 1.0
CG A:ASP257 3.3 20.8 1.0
CE1 A:HIS220 3.4 14.0 1.0
OD2 A:ASP257 3.5 22.0 1.0
O A:HOH1159 3.8 31.7 1.0
ND2 A:ASN247 4.0 21.3 1.0
O3 A:GLC401 4.1 28.4 1.0
O A:HOH1017 4.1 20.3 1.0
CG A:HIS220 4.2 18.7 1.0
CB A:ASP255 4.2 25.4 1.0
ND1 A:HIS220 4.4 17.3 1.0
OD2 A:ASP287 4.4 28.5 1.0
CG A:GLU217 4.4 16.2 1.0
CD A:CD392 4.6 25.8 1.0
CB A:ASP257 4.7 14.0 1.0
O A:HOH1084 4.8 40.1 1.0

Cadmium binding site 2 out of 2 in 3kbm

Go back to Cadmium Binding Sites List in 3kbm
Cadmium binding site 2 out of 2 in the Room Temperature X-Ray Structure of D-Xylose Isomerase Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form


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 Complexed with 2CD(2+) Co-Factors and D12-D-Alpha-Glucose in the Cyclic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd392

b:25.8
occ:1.00
OD2 A:ASP287 2.1 28.5 1.0
OE2 A:GLU181 2.2 24.8 1.0
OD2 A:ASP245 2.2 29.9 1.0
OE1 A:GLU217 2.4 24.3 1.0
O3 A:GLC401 2.4 28.4 1.0
O4 A:GLC401 2.5 35.4 1.0
CD A:GLU181 3.1 24.7 1.0
CG A:ASP287 3.2 24.6 1.0
C3 A:GLC401 3.2 31.6 1.0
C4 A:GLC401 3.3 36.6 1.0
OE1 A:GLU181 3.4 27.3 1.0
CG A:ASP245 3.4 22.0 1.0
CD A:GLU217 3.5 22.4 1.0
CB A:ASP287 3.6 23.2 1.0
O A:HOH1001 3.9 23.0 1.0
CE1 A:HIS220 3.9 14.0 1.0
CB A:ASP245 3.9 20.4 1.0
CG A:GLU217 4.0 16.2 1.0
CB A:GLU217 4.1 24.5 1.0
OD1 A:ASP287 4.3 29.8 1.0
OD1 A:ASP245 4.4 29.2 1.0
O A:HOH1095 4.4 40.0 1.0
NE2 A:HIS220 4.5 19.2 1.0
CG A:GLU181 4.5 25.6 1.0
CD A:CD391 4.6 22.7 1.0
OE2 A:GLU217 4.6 22.2 1.0
C2 A:GLC401 4.7 37.1 1.0
ND1 A:HIS220 4.7 17.3 1.0
C5 A:GLC401 4.7 40.1 1.0

Reference:

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
Page generated: Fri Aug 28 13:45:54 2020
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