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Cadmium in PDB 2fu4: Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)

Protein crystallography data

The structure of Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator), PDB code: 2fu4 was solved by L.Pecqueur, B.D'autreaux, J.Dupuy, Y.Nicolet, L.Jacquamet, B.Brutscher, I.Michaud-Soret, B.Bersch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.42 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 38.500, 159.270, 28.650, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.5

Other elements in 2fu4:

The structure of Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) (pdb code 2fu4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator), PDB code: 2fu4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 2fu4

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Cadmium binding site 1 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


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 Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd84

b:13.8
occ:1.00
NE2 A:HIS33 2.3 9.6 1.0
OE2 A:GLU81 2.5 11.0 1.0
OE1 A:GLU81 2.5 12.6 1.0
CL A:CL92 2.5 41.6 1.0
CL A:CL91 2.6 14.1 1.0
CD A:GLU81 2.8 10.7 1.0
CE1 A:HIS33 3.3 10.1 1.0
CD2 A:HIS33 3.3 10.0 1.0
CG A:GLU81 4.3 11.2 1.0
NE2 A:HIS32 4.4 15.6 1.0
ND1 A:HIS33 4.4 9.3 1.0
O A:HOH158 4.4 32.4 1.0
CD2 A:HIS32 4.4 14.9 1.0
CG A:HIS33 4.5 9.2 1.0
NE2 A:HIS71 4.7 12.7 1.0
CB A:GLU81 5.0 11.3 1.0

Cadmium binding site 2 out of 8 in 2fu4

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Cadmium binding site 2 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


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 Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd85

b:14.3
occ:1.00
ND1 A:HIS71 2.3 13.7 1.0
O A:HOH124 2.5 15.8 1.0
CL A:CL93 2.6 14.1 1.0
CE1 A:HIS71 3.2 12.1 1.0
CG A:HIS71 3.4 12.5 1.0
CB A:HIS71 3.7 13.4 1.0
CA A:HIS71 4.0 13.8 1.0
O A:HOH107 4.3 24.8 1.0
NE2 A:HIS71 4.4 12.7 1.0
CD2 A:HIS71 4.5 11.3 1.0
O A:ARG70 4.5 15.7 1.0
O A:HOH172 4.6 52.8 1.0
N A:ASN72 4.9 13.5 1.0
C A:HIS71 5.0 14.0 1.0
N A:HIS71 5.0 14.2 1.0

Cadmium binding site 3 out of 8 in 2fu4

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Cadmium binding site 3 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


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 Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd86

b:13.6
occ:1.00
O A:HOH128 2.4 7.6 1.0
OD1 A:ASP30 2.4 14.0 1.0
CL A:CL94 2.5 12.8 1.0
CL A:CL95 2.6 13.2 1.0
CG A:ASP30 3.5 14.2 1.0
O A:HOH178 4.2 14.0 1.0
CA A:ASP30 4.2 11.3 1.0
OD2 A:ASP30 4.2 17.1 1.0
O A:HOH133 4.2 17.9 1.0
CL A:CL96 4.2 24.1 1.0
CB A:ASP30 4.3 11.6 1.0
O A:HOH100 4.6 15.2 1.0
O A:HOH130 4.6 18.3 1.0
N A:ASP30 4.7 10.3 1.0

Cadmium binding site 4 out of 8 in 2fu4

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Cadmium binding site 4 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


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 Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd87

b:14.6
occ:1.00
OE1 A:GLU74 2.4 14.0 1.0
OE2 A:GLU74 2.4 15.1 1.0
CL B:CL85 2.5 14.8 1.0
CL A:CL97 2.6 14.2 1.0
CD A:GLU74 2.7 15.1 1.0
CG A:GLU74 4.2 15.7 1.0
CB B:ALA53 4.3 8.8 1.0
CA B:GLY51 4.5 12.8 1.0
O B:HOH198 4.5 14.2 1.0
N B:ALA53 4.5 8.8 1.0
O A:HOH106 4.6 13.3 1.0
N B:LEU52 4.7 10.1 1.0
CA A:GLU74 4.8 15.4 1.0
C B:GLY51 4.8 11.6 1.0
CB A:GLU74 4.9 15.6 1.0

Cadmium binding site 5 out of 8 in 2fu4

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Cadmium binding site 5 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


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 the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd88

b:25.9
occ:1.00
O B:HOH233 2.1 32.2 1.0
OD2 A:ASP63 2.2 13.6 1.0
OD2 B:ASP64 2.3 18.4 1.0
O A:HOH118 2.3 5.2 1.0
OD1 B:ASP64 2.6 19.5 1.0
OD1 A:ASP63 2.7 15.4 1.0
CG B:ASP64 2.8 17.2 1.0
CG A:ASP63 2.8 13.0 1.0
O B:HOH210 3.0 14.8 1.0
O B:HOH234 3.1 11.8 1.0
O A:HOH163 3.9 17.7 1.0
CB B:ASP64 4.3 16.4 1.0
CB A:ASP63 4.3 11.0 1.0
O A:HOH125 4.3 20.0 1.0
NH2 A:ARG70 4.5 13.5 1.0
O B:ASN60 4.6 10.5 1.0
NE A:ARG70 4.6 13.8 1.0
O A:ASP63 4.7 13.6 1.0
C A:ASP63 4.8 12.4 1.0
O A:HOH120 4.9 12.6 1.0
OD1 A:ASP64 5.0 19.1 1.0

Cadmium binding site 6 out of 8 in 2fu4

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Cadmium binding site 6 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd89

b:27.1
occ:1.00
OD2 B:ASP63 2.2 15.7 1.0
O B:HOH186 2.3 7.9 1.0
OD2 A:ASP64 2.5 19.9 1.0
OD1 A:ASP64 2.5 19.1 1.0
OD1 B:ASP63 2.7 16.4 1.0
CG B:ASP63 2.8 14.8 1.0
CG A:ASP64 2.9 17.1 1.0
O A:HOH120 2.9 12.6 1.0
O B:HOH234 3.1 11.8 1.0
CB B:ASP63 4.3 13.3 1.0
CB A:ASP64 4.4 14.9 1.0
O A:ASN60 4.5 9.2 1.0
NH2 B:ARG70 4.5 16.6 1.0
NE B:ARG70 4.5 14.8 1.0
O B:HOH208 4.6 30.4 1.0
O A:HOH144 4.6 48.0 1.0
O B:ASP63 4.7 14.5 1.0
OD1 B:ASP64 4.8 19.5 1.0
C B:ASP63 4.8 14.4 1.0
O B:HOH210 5.0 14.8 1.0

Cadmium binding site 7 out of 8 in 2fu4

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Cadmium binding site 7 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd90

b:28.8
occ:0.75
OE1 A:GLU49 2.3 22.8 1.0
O A:HOH143 2.6 33.8 1.0
OE2 A:GLU49 2.6 24.3 1.0
CD A:GLU49 2.8 21.3 1.0
CG A:GLU49 4.3 17.1 1.0
CB A:GLU49 5.0 15.2 1.0

Cadmium binding site 8 out of 8 in 2fu4

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Cadmium binding site 8 out of 8 in the Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the Dna Binding Domain of E.Coli Fur (Ferric Uptake Regulator) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd84

b:26.0
occ:0.75
O A:HOH150 2.3 12.3 1.0
O B:HOH200 2.4 18.0 1.0
O B:HOH203 2.5 14.2 1.0
O A:HOH117 2.7 9.9 1.0
O B:HOH243 3.5 14.3 1.0
NH1 A:ARG70 4.3 12.6 1.0
CE2 B:TYR56 4.3 11.9 1.0
NH1 B:ARG70 4.4 15.1 1.0
OG B:SER78 4.4 24.9 0.5
CD2 B:TYR56 4.6 11.8 1.0
CE2 A:TYR56 4.7 13.6 1.0
OG B:SER78 4.7 25.3 0.5
CB B:SER78 4.7 24.5 0.5
CB B:SER78 4.7 24.4 0.2
OG A:SER78 4.8 17.8 0.5
OG A:SER78 4.9 19.2 0.5
OD1 B:ASN60 4.9 18.0 1.0
O B:HOH201 4.9 20.2 1.0

Reference:

L.Pecqueur, B.D'autreaux, J.Dupuy, Y.Nicolet, L.Jacquamet, B.Brutscher, I.Michaud-Soret, B.Bersch. Structural Changes of Escherichia Coli Ferric Uptake Regulator During Metal-Dependent Dimerization and Activation Explored By uc(Nmr) and X-Ray Crystallography J.Biol.Chem. V. 281 21286 2006.
ISSN: ISSN 0021-9258
PubMed: 16690618
DOI: 10.1074/JBC.M601278200
Page generated: Sat Dec 12 08:17:09 2020

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