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Cadmium in PDB 3kcl: Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM)

Enzymatic activity of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM)

All present enzymatic activity of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM):
5.3.1.5;

Protein crystallography data

The structure of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM), PDB code: 3kcl 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) N/A / 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 (%) 17.3 / 19.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM) (pdb code 3kcl). 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 Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM), PDB code: 3kcl:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3kcl

Go back to Cadmium Binding Sites List in 3kcl
Cadmium binding site 1 out of 2 in the Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd391

b:15.3
occ:1.00
 O A:DOD1001 2.3 25.6 1.0
OE2 A:GLU217 2.3 13.2 1.0
NE2 A:HIS220 2.4 13.0 1.0
OD2 A:ASP255 2.4 16.5 1.0
OD1 A:ASP257 2.4 17.0 1.0
OD1 A:ASP255 2.6 14.6 1.0
OE1 A:GLU217 2.6 13.2 1.0
D1 A:DOD1001 2.8 26.9 1.0
CG A:ASP255 2.8 17.2 1.0
CD A:GLU217 2.8 12.7 1.0
D2 A:DOD1001 2.9 28.1 1.0
CD2 A:HIS220 3.0 13.4 1.0
HD2 A:HIS220 3.1 14.5 1.0
D1 A:DOD1159 3.1 25.8 1.0
DO3 A:GLC401 3.3 22.2 1.0
CG A:ASP257 3.3 17.4 1.0
DD21 A:ASN247 3.4 14.1 1.0
CE1 A:HIS220 3.4 13.7 1.0
OD2 A:ASP257 3.5 17.5 1.0
D1 A:DOD1017 3.5 24.7 1.0
HE1 A:HIS220 3.8 12.7 1.0
O A:DOD1159 3.8 26.2 1.0
DD22 A:ASN247 4.0 15.1 0.7
ND2 A:ASN247 4.0 12.6 1.0
O3 A:GLC401 4.1 22.1 1.0
O A:DOD1017 4.1 21.6 1.0
D1 A:DOD1084 4.1 56.3 1.0
HE3 A:LYS183 4.1 17.5 1.0
CG A:HIS220 4.2 13.7 1.0
D2 A:DOD1159 4.3 26.8 1.0
CB A:ASP255 4.3 16.4 1.0
CG A:GLU217 4.4 11.0 1.0
ND1 A:HIS220 4.4 14.8 1.0
DZ2 A:LYS183 4.4 21.7 1.0
OD2 A:ASP287 4.4 18.8 1.0
CD A:CD392 4.6 18.4 1.0
HB2 A:ASP255 4.7 17.3 1.0
HG2 A:GLU217 4.7 11.5 1.0
HA A:ASP257 4.7 15.5 1.0
D A:ASP257 4.7 16.3 0.8
CB A:ASP257 4.8 15.7 1.0
HD2 A:LYS183 4.8 15.1 1.0
HB3 A:ASP255 4.8 16.3 1.0
HG3 A:GLU217 4.9 10.0 1.0
HB3 A:GLU217 4.9 15.2 1.0
HA3 A:GLY219 4.9 13.9 1.0
D1 A:DOD1163 4.9 42.0 1.0
D2 A:DOD1017 4.9 23.6 1.0
DZ1 A:LYS183 4.9 20.9 1.0
D A:HIS220 4.9 21.1 1.0
CE A:LYS183 5.0 17.9 1.0
O A:DOD1084 5.0 55.5 1.0
NZ A:LYS183 5.0 20.2 1.0

Cadmium binding site 2 out of 2 in 3kcl

Go back to Cadmium Binding Sites List in 3kcl
Cadmium binding site 2 out of 2 in the Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Room Temperature Neutron Structure of D-Xylose Isomerase in Complex with Two CD2+ Cations and D12-D-Alpha-Glucose in the Ring Form (Refined Jointly with X-Ray Structure 3KBM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd392

b:18.4
occ:1.00
 OE2 A:GLU181 2.2 17.6 1.0
OD2 A:ASP245 2.2 18.1 1.0
OD2 A:ASP287 2.2 18.8 1.0
OE1 A:GLU217 2.4 13.2 1.0
O3 A:GLC401 2.4 22.1 1.0
O4 A:GLC401 2.5 21.4 1.0
DO4 A:GLC401 2.9 22.7 1.0
DO3 A:GLC401 3.0 22.2 1.0
CD A:GLU181 3.0 18.9 1.0
C3 A:GLC401 3.2 23.6 1.0
OE1 A:GLU181 3.2 20.1 1.0
D2 A:DOD1001 3.2 28.1 1.0
HB2 A:GLU217 3.3 14.7 1.0
CG A:ASP287 3.3 15.6 1.0
D3 A:GLC401 3.3 23.0 1.0
C4 A:GLC401 3.3 23.2 1.0
CG A:ASP245 3.4 20.4 1.0
HB3 A:ASP287 3.5 13.8 1.0
CD A:GLU217 3.5 12.7 1.0
D2 A:DOD1095 3.5 35.0 1.0
HE1 A:HIS220 3.5 12.7 1.0
HB3 A:ASP245 3.6 19.3 1.0
D1 A:DOD1095 3.6 36.0 1.0
HB2 A:ASP287 3.6 13.2 1.0
CB A:ASP287 3.7 14.9 1.0
HG3 A:GLU217 3.7 10.0 1.0
D4 A:GLC401 3.7 23.9 1.0
O A:DOD1001 3.8 25.6 1.0
CB A:ASP245 3.9 18.4 1.0
HB2 A:ASP245 3.9 20.1 1.0
CG A:GLU217 3.9 11.0 1.0
CE1 A:HIS220 4.0 13.7 1.0
O A:DOD1095 4.0 35.8 1.0
CB A:GLU217 4.1 13.8 1.0
OD1 A:ASP245 4.4 18.7 1.0
OD1 A:ASP287 4.4 18.1 1.0
HB3 A:GLU217 4.4 15.2 1.0
CG A:GLU181 4.4 17.2 1.0
DD21 A:ASN215 4.4 18.1 1.0
NE2 A:HIS220 4.6 13.0 1.0
CD A:CD391 4.6 15.3 1.0
OE2 A:GLU217 4.6 13.2 1.0
D1 A:DOD1001 4.6 26.9 1.0
C2 A:GLC401 4.7 24.9 1.0
HG3 A:GLU181 4.7 18.2 1.0
HZ2 A:TRP16 4.7 19.0 1.0
C5 A:GLC401 4.7 25.2 1.0
D5 A:GLC401 4.7 25.0 1.0
ND1 A:HIS220 4.7 14.8 1.0
HG2 A:GLU181 4.8 18.0 1.0
D2 A:GLC401 4.9 25.6 1.0
DD22 A:ASN215 4.9 14.9 0.6
DD1 A:HIS220 4.9 15.4 1.0
ND2 A:ASN215 5.0 17.2 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 Jul 19 16:09:36 2024

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