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Cadmium in PDB 4qdp: Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose

Enzymatic activity of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose

All present enzymatic activity of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose:
5.3.1.5;

Protein crystallography data

The structure of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose, PDB code: 4qdp 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 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.930, 99.693, 102.973, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 24.7

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 2 in 4qdp

Go back to Cadmium Binding Sites List in 4qdp
Cadmium binding site 1 out of 2 in the Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:20.8
occ:1.00
OE2 A:GLU217 2.3 21.7 1.0
OD1 A:ASP257 2.4 22.1 1.0
O A:DOD1001 2.4 25.4 1.0
OD2 A:ASP255 2.4 24.0 1.0
NE2 A:HIS220 2.4 20.3 1.0
OD1 A:ASP255 2.5 21.4 1.0
CG A:ASP255 2.8 22.0 1.0
D1 A:DOD1150 2.9 35.4 1.0
D1 A:DOD1001 2.9 31.4 1.0
OE1 A:GLU217 2.9 21.8 1.0
CD A:GLU217 2.9 20.5 1.0
CD2 A:HIS220 3.1 19.2 1.0
HD2 A:HIS220 3.2 18.6 1.0
D2 A:DOD1001 3.2 29.4 1.0
CG A:ASP257 3.2 22.5 1.0
OD2 A:ASP257 3.4 24.4 1.0
DO3 A:ARB403 3.4 40.8 1.0
DD21 A:ASN247 3.4 18.1 0.9
HD21 A:ASN247 3.4 18.1 0.1
CE1 A:HIS220 3.5 20.0 1.0
D1 A:DOD1017 3.6 24.3 1.0
O A:DOD1150 3.8 35.8 1.0
HE1 A:HIS220 3.8 21.5 1.0
HE3 A:LYS183 4.0 23.9 1.0
DD22 A:ASN247 4.0 18.9 1.0
ND2 A:ASN247 4.1 20.1 1.0
D2 A:DOD1150 4.1 37.2 1.0
CG A:HIS220 4.3 18.3 1.0
CB A:ASP255 4.3 21.6 1.0
O3 A:ARB403 4.3 38.2 1.0
D2 A:DOD1084 4.4 37.6 1.0
OD2 A:ASP287 4.4 23.8 1.0
DZ1 A:LYS183 4.4 27.1 1.0
CG A:GLU217 4.4 19.7 1.0
ND1 A:HIS220 4.4 20.6 1.0
O A:DOD1017 4.5 23.5 1.0
D1 A:DOD1292 4.5 50.0 1.0
DZ3 A:LYS183 4.5 25.2 1.0
HA A:ASP257 4.6 20.9 1.0
CB A:ASP257 4.7 19.9 1.0
HG2 A:GLU217 4.7 20.6 1.0
HB2 A:ASP255 4.7 22.2 1.0
CD A:CD402 4.7 23.1 1.0
H A:ASP257 4.7 20.4 0.3
D A:ASP257 4.7 20.4 0.7
HB3 A:ASP255 4.7 21.5 1.0
NZ A:LYS183 4.8 26.3 1.0
HD2 A:LYS183 4.8 21.5 1.0
CE A:LYS183 4.8 23.7 1.0
DO2 A:ARB403 4.8 53.1 1.0
HA3 A:GLY219 5.0 20.3 1.0
HG3 A:GLU217 5.0 20.4 1.0

Cadmium binding site 2 out of 2 in 4qdp

Go back to Cadmium Binding Sites List in 4qdp
Cadmium binding site 2 out of 2 in the Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Joint X-Ray and Neutron Structure of Streptomyces Rubiginosus D-Xylose Isomerase in Complex with Two CD2+ Ions and Cyclic Beta-L-Arabinose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:23.1
occ:1.00
OD2 A:ASP287 2.2 23.8 1.0
OD2 A:ASP245 2.2 25.1 1.0
OE2 A:GLU181 2.3 27.1 1.0
OE1 A:GLU217 2.3 21.8 1.0
O4 A:ARB403 2.3 37.2 1.0
DO4 A:ARB403 2.6 38.2 1.0
O3 A:ARB403 2.6 38.2 1.0
DO3 A:ARB403 2.7 40.8 1.0
CD A:GLU181 3.1 25.8 1.0
C3 A:ARB403 3.2 42.6 1.0
H3 A:ARB403 3.2 43.1 1.0
D1 A:DOD1095 3.2 40.8 1.0
C4 A:ARB403 3.2 41.4 1.0
CG A:ASP287 3.2 22.2 1.0
OE1 A:GLU181 3.3 26.7 1.0
CG A:ASP245 3.4 21.4 1.0
HB3 A:ASP287 3.4 22.0 1.0
HB2 A:GLU217 3.4 20.8 1.0
CD A:GLU217 3.5 20.5 1.0
D2 A:DOD1001 3.5 29.4 1.0
HB2 A:ASP287 3.6 21.9 1.0
CB A:ASP287 3.6 21.4 1.0
HB3 A:ASP245 3.6 20.4 1.0
HE1 A:HIS220 3.6 21.5 1.0
H4 A:ARB403 3.7 40.7 1.0
CB A:ASP245 3.9 20.6 1.0
HB2 A:ASP245 3.9 21.5 1.0
O A:DOD1095 3.9 39.5 1.0
HG3 A:GLU217 3.9 20.4 1.0
O A:DOD1001 4.0 25.4 1.0
CG A:GLU217 4.1 19.7 1.0
D2 A:DOD1095 4.1 40.0 1.0
CE1 A:HIS220 4.1 20.0 1.0
CB A:GLU217 4.2 19.7 1.0
OD1 A:ASP287 4.3 23.1 1.0
DD21 A:ASN215 4.3 25.0 1.0
HD21 A:ASN215 4.3 25.0 0.0
OD1 A:ASP245 4.4 23.5 1.0
H51 A:ARB403 4.4 42.5 1.0
C5 A:ARB403 4.5 42.2 1.0
OE2 A:GLU217 4.5 21.7 1.0
CG A:GLU181 4.5 23.0 1.0
C2 A:ARB403 4.6 46.0 1.0
HB3 A:GLU217 4.6 19.6 1.0
HZ2 A:TRP16 4.6 23.5 1.0
NE2 A:HIS220 4.7 20.3 1.0
CD A:CD401 4.7 20.8 1.0
HG3 A:GLU181 4.7 23.4 1.0
H2 A:ARB403 4.8 46.1 1.0
D1 A:DOD1001 4.8 31.4 1.0
H52 A:ARB403 4.9 42.7 1.0
HG2 A:GLU181 4.9 23.3 1.0
ND1 A:HIS220 4.9 20.6 1.0
DD22 A:ASN215 4.9 23.8 0.9
HD22 A:ASN215 4.9 23.8 0.1
ND2 A:ASN215 4.9 24.7 1.0

Reference:

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
Page generated: Sat Dec 12 08:25:37 2020

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