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Cadmium in PDB 5czu: Crystal Structure of Fecat-Fn

Protein crystallography data

The structure of Crystal Structure of Fecat-Fn, PDB code: 5czu was solved by S.Abe, H.Nakajima, M.Kondo, T.Nakane, T.Nakao, T.Ueno, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.96 / 1.60
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.070, 181.070, 181.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.8

Other elements in 5czu:

The structure of Crystal Structure of Fecat-Fn also contains other interesting chemical elements:

Iron (Fe) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Fecat-Fn (pdb code 5czu). 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 Fecat-Fn, PDB code: 5czu:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 5czu

Go back to Cadmium Binding Sites List in 5czu
Cadmium binding site 1 out of 4 in the Crystal Structure of Fecat-Fn


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 Fecat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:25.1
occ:0.50
OD1 A:ASP80 2.3 11.4 1.0
OD2 A:ASP80 2.5 31.0 1.0
CG A:ASP80 2.9 13.8 1.0
O A:HOH384 4.2 22.5 1.0
CB A:ASP80 4.4 15.6 1.0

Cadmium binding site 2 out of 4 in 5czu

Go back to Cadmium Binding Sites List in 5czu
Cadmium binding site 2 out of 4 in the Crystal Structure of Fecat-Fn


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 Fecat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:37.6
occ:0.10
O A:HOH319 2.1 22.9 1.0
CD A:CD206 2.2 34.8 0.3
O A:HOH438 2.4 42.7 1.0
OG A:SER131 3.6 27.2 1.0
OD2 A:ASP127 4.0 24.6 1.0
OD1 A:ASP127 4.5 20.2 1.0
CG A:ASP127 4.7 22.5 1.0
CB A:SER131 4.8 19.7 1.0

Cadmium binding site 3 out of 4 in 5czu

Go back to Cadmium Binding Sites List in 5czu
Cadmium binding site 3 out of 4 in the Crystal Structure of Fecat-Fn


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 Fecat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:54.4
occ:0.33
OE1 A:GLU130 2.5 23.9 1.0
OE2 A:GLU130 3.2 23.7 1.0
CD A:GLU130 3.3 25.0 1.0
OD2 A:ASP127 4.2 24.6 1.0
O A:HOH309 4.3 26.5 1.0
CG A:GLU130 4.8 16.0 1.0
CD A:CD206 4.8 34.8 0.3
CG A:ASP127 5.0 22.5 1.0

Cadmium binding site 4 out of 4 in 5czu

Go back to Cadmium Binding Sites List in 5czu
Cadmium binding site 4 out of 4 in the Crystal Structure of Fecat-Fn


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 Fecat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:34.8
occ:0.33
CD A:CD204 2.2 37.6 0.1
O A:HOH319 2.3 22.9 1.0
OD2 A:ASP127 2.5 24.6 1.0
CG A:ASP127 3.5 22.5 1.0
OD1 A:ASP127 3.8 20.2 1.0
OG A:SER131 3.9 27.2 1.0
OE1 A:GLU130 4.3 23.9 1.0
O A:HOH438 4.3 42.7 1.0
CD A:CD205 4.8 54.4 0.3
CB A:ASP127 4.9 17.0 1.0

Reference:

H.Nakajima, M.Kondo, T.Nakane, S.Abe, T.Nakao, Y.Watanabe, T.Ueno. Construction of An Enterobactin Analogue with Symmetrically Arranged Monomer Subunits of Ferritin Chem.Commun.(Camb.) V. 51 16609 2015.
ISSN: ESSN 1364-548X
PubMed: 26404005
DOI: 10.1039/C5CC06904A
Page generated: Sat Dec 12 08:26:31 2020

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