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Cadmium in PDB 5axs: Crystal Structure of Cdcat-Fn

Protein crystallography data

The structure of Crystal Structure of Cdcat-Fn, PDB code: 5axs 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) 34.81 / 1.67
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.878, 180.878, 180.878, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Cdcat-Fn (pdb code 5axs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Cdcat-Fn, PDB code: 5axs:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5axs

Go back to Cadmium Binding Sites List in 5axs
Cadmium binding site 1 out of 5 in the Crystal Structure of Cdcat-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 Cdcat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:24.0
occ:0.50
OD1 A:ASP80 2.3 8.4 1.0
OD2 A:ASP80 2.4 26.0 1.0
CG A:ASP80 2.7 14.9 1.0
CB A:ASP80 4.1 14.9 1.0
O A:HOH325 4.4 19.8 1.0

Cadmium binding site 2 out of 5 in 5axs

Go back to Cadmium Binding Sites List in 5axs
Cadmium binding site 2 out of 5 in the Crystal Structure of Cdcat-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 Cdcat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:34.8
occ:0.33
CD A:CD206 2.2 36.1 0.1
O A:HOH311 2.3 22.9 1.0
OD1 A:ASP127 2.7 20.5 1.0
CG A:ASP127 3.8 19.0 1.0
OG A:SER131 4.1 23.2 1.0
OD2 A:ASP127 4.2 17.6 1.0
OE1 A:GLU130 4.3 20.2 1.0
CD A:CD205 4.7 44.5 0.3

Cadmium binding site 3 out of 5 in 5axs

Go back to Cadmium Binding Sites List in 5axs
Cadmium binding site 3 out of 5 in the Crystal Structure of Cdcat-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 Cdcat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:43.7
occ:0.33
O6 A:4LF201 2.2 23.9 1.0
O5 A:4LF201 2.2 24.0 1.0
C15 A:4LF201 3.0 24.2 1.0
C16 A:4LF201 3.0 26.5 1.0
O A:HOH305 3.9 25.5 1.0
O A:HOH411 4.0 27.4 1.0
C14 A:4LF201 4.3 22.3 1.0
C11 A:4LF201 4.3 26.8 1.0
N3 A:4LF201 4.6 33.9 1.0

Cadmium binding site 4 out of 5 in 5axs

Go back to Cadmium Binding Sites List in 5axs
Cadmium binding site 4 out of 5 in the Crystal Structure of Cdcat-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 Cdcat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:44.5
occ:0.33
O A:HOH316 1.6 20.9 1.0
OE1 A:GLU130 2.5 20.2 1.0
CD A:GLU130 3.3 18.1 1.0
OE2 A:GLU130 3.3 19.6 1.0
OD1 A:ASP127 4.2 20.5 1.0
O A:HOH305 4.4 25.5 1.0
CD A:CD203 4.7 34.8 0.3
CG A:GLU130 4.7 13.0 1.0
CG A:ASP127 5.0 19.0 1.0

Cadmium binding site 5 out of 5 in 5axs

Go back to Cadmium Binding Sites List in 5axs
Cadmium binding site 5 out of 5 in the Crystal Structure of Cdcat-Fn


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Cdcat-Fn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:36.1
occ:0.10
O A:HOH311 2.0 22.9 1.0
CD A:CD203 2.2 34.8 0.3
OG A:SER131 3.5 23.2 1.0
OD1 A:ASP127 4.0 20.5 1.0
OD2 A:ASP127 4.6 17.6 1.0
CG A:ASP127 4.7 19.0 1.0
CB A:SER131 4.7 15.7 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 08:26:15 2020

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