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Cadmium in PDB 2iy2: Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg, PDB code: 2iy2 was solved by S.-M.Yeh, P.Metcalf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.79 / 1.9
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 56.842, 56.842, 42.049, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg (pdb code 2iy2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg, PDB code: 2iy2:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 2iy2

Go back to Cadmium Binding Sites List in 2iy2
Cadmium binding site 1 out of 4 in the Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1072

b:33.2
occ:1.00
O A:HOH2024 2.1 31.4 1.0
O A:HOH2023 2.3 19.4 1.0
NE2 A:HIS49 2.3 9.4 1.0
CE1 A:HIS49 3.0 14.0 1.0
CD2 A:HIS49 3.5 12.7 1.0
ND1 A:HIS49 4.2 12.9 1.0
CB B:ASN57 4.3 15.5 1.0
CG A:HIS49 4.5 13.0 1.0
CB B:PRO24 4.6 23.0 1.0
O A:LYS48 5.0 15.5 1.0

Cadmium binding site 2 out of 4 in 2iy2

Go back to Cadmium Binding Sites List in 2iy2
Cadmium binding site 2 out of 4 in the Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1073

b:22.1
occ:0.70
OD1 A:ASP46 2.3 12.1 1.0
CG A:ASP46 3.1 16.4 1.0
CB A:ASP46 3.3 18.9 1.0
OD2 A:ASP46 4.3 14.2 1.0
CA B:GLY25 4.4 23.4 1.0
N B:GLY25 4.4 22.8 1.0
CD A:LYS48 4.5 23.0 1.0
CE1 A:HIS49 4.6 14.0 1.0
CA A:ASP46 4.9 19.2 1.0
ND1 A:HIS49 4.9 12.9 1.0

Cadmium binding site 3 out of 4 in 2iy2

Go back to Cadmium Binding Sites List in 2iy2
Cadmium binding site 3 out of 4 in the Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1072

b:25.8
occ:1.00
O B:HOH2022 2.3 18.1 1.0
NE2 B:HIS49 2.3 6.2 1.0
O A:HOH2026 2.3 27.9 1.0
CE1 B:HIS49 3.1 9.1 1.0
CD2 B:HIS49 3.5 8.7 1.0
ND1 B:HIS49 4.3 9.3 1.0
CB A:ASN57 4.3 15.0 1.0
CB A:PRO24 4.4 17.0 1.0
CG B:HIS49 4.5 12.5 1.0
CG A:PRO24 4.7 17.0 1.0
ND2 A:ASN57 4.9 15.8 1.0

Cadmium binding site 4 out of 4 in 2iy2

Go back to Cadmium Binding Sites List in 2iy2
Cadmium binding site 4 out of 4 in the Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the N-Terminal Dimer Domain of E.Coli Dsbg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1073

b:20.6
occ:0.80
OD2 B:ASP46 2.3 12.7 1.0
O B:HOH2020 2.4 16.7 1.0
CG B:ASP46 3.2 15.6 1.0
CB B:ASP46 3.4 17.3 1.0
OD1 B:ASP46 4.3 15.0 1.0
CA A:GLY25 4.4 16.0 1.0
N A:GLY25 4.4 15.6 1.0
CE1 B:HIS49 4.5 9.1 1.0
O B:HOH2019 4.7 26.9 1.0
CD B:LYS48 4.8 14.9 1.0
ND1 B:HIS49 4.9 9.3 1.0
CA B:ASP46 4.9 17.3 1.0

Reference:

S.-M.Yeh, N.Koon, C.Squire, P.Metcalf. Structures of the Dimerization Domains of the Escherichia Coli Disulfide-Bond Isomerase Enzymes Dsbc and Dsbg Acta Crystallogr.,Sect.D V. 63 465 2007.
ISSN: ISSN 0907-4449
PubMed: 17372350
DOI: 10.1107/S0907444907003320
Page generated: Sat Dec 12 08:17:17 2020

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