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Cadmium in PDB 2zgd: Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold

Protein crystallography data

The structure of Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold, PDB code: 2zgd was solved by M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.29 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.887, 48.887, 67.088, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 22.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold (pdb code 2zgd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold, PDB code: 2zgd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 2zgd

Go back to Cadmium Binding Sites List in 2zgd
Cadmium binding site 1 out of 5 in the Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd410

b:12.9
occ:1.00
OE1 A:GLN36 2.1 11.7 1.0
OE1 A:GLU39 2.2 15.6 1.0
OE2 A:GLU30 2.3 13.1 1.0
OE2 A:GLU39 2.5 15.5 1.0
CD A:GLU39 2.7 16.6 1.0
OE1 A:GLU30 2.8 10.5 1.0
CD A:GLU30 2.9 12.9 1.0
CD A:GLN36 3.0 14.5 1.0
NE2 A:GLN36 3.4 11.8 1.0
O A:HOH1006 3.7 16.1 1.0
CG A:GLU39 4.2 19.5 1.0
CA A:ALA31 4.4 11.3 1.0
CG A:GLN36 4.4 17.0 1.0
CG A:GLU30 4.4 11.1 1.0
N A:ALA31 4.6 11.8 1.0
CB A:GLN36 4.7 11.8 1.0
O A:HOH1059 4.8 45.4 1.0
CB A:ALA31 4.8 12.2 1.0
O A:GLU30 4.8 9.5 1.0
C A:GLU30 4.8 10.0 1.0
CB A:ALA34 4.9 8.8 1.0
CB A:GLU39 4.9 18.1 1.0
O A:HOH1060 5.0 45.6 1.0
O A:HOH1002 5.0 35.9 1.0

Cadmium binding site 2 out of 5 in 2zgd

Go back to Cadmium Binding Sites List in 2zgd
Cadmium binding site 2 out of 5 in the Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd411

b:19.6
occ:1.00
O A:HOH1019 2.3 16.1 1.0
OE1 A:GLU107 2.4 18.9 1.0
OE2 A:GLU107 2.5 17.4 1.0
O A:HOH1018 2.5 20.9 1.0
CD A:GLU107 2.8 17.2 1.0
CG A:GLU107 4.3 16.0 1.0
OD1 A:ASP104 4.3 17.4 1.0
O A:HOH1058 5.0 41.5 1.0

Cadmium binding site 3 out of 5 in 2zgd

Go back to Cadmium Binding Sites List in 2zgd
Cadmium binding site 3 out of 5 in the Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd412

b:36.4
occ:0.50
O A:HOH1020 2.5 5.8 1.0
CL A:CL415 2.6 8.1 1.0
O A:HOH1066 2.6 14.9 1.0
O A:HOH1050 2.7 3.0 1.0
O A:HOH1065 2.7 25.0 1.0
CB A:GLU71 4.3 20.1 1.0
O A:GLY35 4.6 7.6 1.0
N A:GLU71 4.7 12.6 1.0
ND1 A:HIS69 4.8 6.3 1.0
CA A:HIS69 4.9 8.9 1.0
N A:LEU70 4.9 10.7 1.0

Cadmium binding site 4 out of 5 in 2zgd

Go back to Cadmium Binding Sites List in 2zgd
Cadmium binding site 4 out of 5 in the Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd413

b:63.2
occ:1.00
O A:HOH1046 2.1 26.7 1.0
OD2 A:ASP38 2.3 32.4 1.0
CL A:CL416 2.9 28.7 1.0
CG A:ASP38 3.0 30.0 1.0
OD1 A:ASP38 3.0 33.0 1.0
OD2 A:ASP37 3.0 31.4 1.0
CG A:ASP37 4.1 29.9 1.0
OD1 A:ASP37 4.4 36.8 1.0
O A:HOH1048 4.4 33.4 1.0
CB A:ASP38 4.4 23.8 1.0
NH1 A:ARG41 4.5 33.1 1.0
N A:ASP38 4.9 18.8 1.0

Cadmium binding site 5 out of 5 in 2zgd

Go back to Cadmium Binding Sites List in 2zgd
Cadmium binding site 5 out of 5 in the Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Asn-Hydroxylation Stabilises the Ankyrin Repeat Domain Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd414

b:65.8
occ:1.00
OD2 A:ASP23 2.4 37.5 1.0
OD1 A:ASP23 2.5 35.6 1.0
O A:HOH1039 2.6 25.1 1.0
CG A:ASP23 2.8 37.2 1.0
O A:HOH1045 3.1 41.6 1.0
CE A:LYS26 4.2 36.4 1.0
CB A:ASP23 4.3 36.4 1.0
CG A:LYS26 4.3 27.8 1.0
NZ A:LYS26 4.4 41.9 1.0
CA A:GLY25 4.4 21.4 1.0
N A:LYS26 4.5 19.9 1.0
N A:GLY25 4.6 21.7 1.0
O A:HOH1049 4.7 41.3 1.0
CD A:LYS26 4.8 34.5 1.0
C A:GLY25 4.9 19.5 1.0

Reference:

L.Kelly, M.A.Mcdonough, M.L.Coleman, P.J.Ratcliffe, C.J.Schofield. Asparagine Beta-Hydroxylation Stabilizes the Ankyrin Repeat Domain Fold Mol Biosyst V. 5 52 2009.
ISSN: ISSN 1742-206X
PubMed: 19081931
DOI: 10.1039/B815271C
Page generated: Fri Aug 28 13:19:52 2020
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