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Cadmium in PDB 1y1l: Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics

Protein crystallography data

The structure of Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics, PDB code: 1y1l was solved by Y.Patskovsky, S.C.Almo, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.390, 48.510, 66.370, 100.00, 90.70, 100.00
R / Rfree (%) 25.2 / 29.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics (pdb code 1y1l). 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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics, PDB code: 1y1l:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 1y1l

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Cadmium binding site 1 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd125

b:2.7
occ:1.00
OE2 D:GLU35 2.2 70.2 1.0
ND1 A:HIS8 2.3 40.6 1.0
OE1 D:GLU35 2.3 61.2 1.0
CD D:GLU35 2.3 65.9 1.0
CG A:HIS8 2.3 40.1 1.0
CE1 A:HIS8 2.3 38.3 1.0
CD2 A:HIS8 2.3 31.7 1.0
NE2 A:HIS8 2.4 32.7 1.0
CB A:HIS8 3.3 41.5 1.0
CG D:GLU35 3.4 60.5 1.0
ND2 A:ASN98 4.3 36.6 1.0
N A:HIS8 4.4 43.8 1.0
CB D:GLU35 4.5 54.0 1.0
CA A:HIS8 4.5 43.2 1.0
CG2 A:ILE7 4.9 28.0 1.0
CB A:ILE7 5.0 27.6 1.0

Cadmium binding site 2 out of 8 in 1y1l

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Cadmium binding site 2 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd125

b:3.1
occ:1.00
NE2 B:HIS95 2.3 63.3 1.0
OD1 A:ASP88 2.3 45.0 1.0
CE1 B:HIS95 2.3 59.8 1.0
OD2 A:ASP88 2.4 48.7 1.0
CG A:ASP88 2.6 43.8 1.0
ND1 B:HIS95 3.4 57.1 1.0
CD2 B:HIS95 3.5 59.9 1.0
CB A:ASP88 4.0 39.1 1.0
CG B:HIS95 4.0 52.0 1.0

Cadmium binding site 3 out of 8 in 1y1l

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Cadmium binding site 3 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd126

b:2.2
occ:1.00
CG B:HIS8 2.2 42.1 1.0
OE2 C:GLU35 2.3 67.6 1.0
ND1 B:HIS8 2.3 40.7 1.0
CD2 B:HIS8 2.3 36.0 1.0
OE1 C:GLU35 2.4 52.1 1.0
CE1 B:HIS8 2.5 33.2 1.0
NE2 B:HIS8 2.5 36.2 1.0
CD C:GLU35 2.6 58.6 1.0
CB B:HIS8 3.2 46.3 1.0
CG C:GLU35 4.1 56.5 1.0
CA B:HIS8 4.3 49.5 1.0
N B:HIS8 4.4 48.6 1.0
ND2 B:ASN98 4.5 45.4 1.0
CB C:GLU35 5.0 49.0 1.0

Cadmium binding site 4 out of 8 in 1y1l

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Cadmium binding site 4 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd127

b:2.6
occ:1.00
OD2 B:ASP88 2.3 41.7 1.0
OD1 B:ASP88 2.3 29.1 1.0
NE2 A:HIS95 2.4 65.8 1.0
CE1 A:HIS95 2.6 67.0 1.0
CG B:ASP88 2.7 33.6 1.0
CD2 A:HIS95 3.7 60.6 1.0
ND1 A:HIS95 3.9 65.7 1.0
CB B:ASP88 4.1 28.2 1.0
CG A:HIS95 4.4 56.1 1.0

Cadmium binding site 5 out of 8 in 1y1l

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Cadmium binding site 5 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd125

b:3.4
occ:1.00
OE1 B:GLU35 2.2 48.9 1.0
OE2 B:GLU35 2.3 62.2 1.0
CE1 C:HIS8 2.3 39.8 1.0
NE2 C:HIS8 2.3 39.0 1.0
ND1 C:HIS8 2.4 37.5 1.0
CD2 C:HIS8 2.4 36.5 1.0
CD B:GLU35 2.4 54.5 1.0
CG C:HIS8 2.5 43.5 1.0
CB C:HIS8 3.5 46.0 1.0
CG B:GLU35 3.8 52.9 1.0
ND2 C:ASN98 4.1 47.0 1.0
N C:HIS8 4.6 49.4 1.0
CA C:HIS8 4.6 49.1 1.0
OD1 C:ASN98 4.7 50.1 1.0
CB B:GLU35 4.8 40.0 1.0
CB C:ALA100 4.8 56.7 1.0
CG C:ASN98 4.8 48.4 1.0

Cadmium binding site 6 out of 8 in 1y1l

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Cadmium binding site 6 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd126

b:11.1
occ:1.00
OD1 C:ASP88 2.4 33.8 1.0
OD2 C:ASP88 2.4 43.2 1.0
NE2 D:HIS95 2.4 60.3 1.0
CG C:ASP88 2.7 37.1 1.0
CE1 D:HIS95 2.9 60.7 1.0
CD2 D:HIS95 3.6 57.5 1.0
ND1 D:HIS95 4.1 59.4 1.0
CB C:ASP88 4.2 35.6 1.0
CG D:HIS95 4.5 54.3 1.0

Cadmium binding site 7 out of 8 in 1y1l

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Cadmium binding site 7 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd125

b:7.5
occ:1.00
CG D:HIS8 2.2 56.2 1.0
ND1 D:HIS8 2.2 52.2 1.0
OE2 A:GLU35 2.3 58.8 1.0
OE1 A:GLU35 2.3 46.7 1.0
CD2 D:HIS8 2.3 46.1 1.0
CE1 D:HIS8 2.4 48.3 1.0
NE2 D:HIS8 2.4 50.5 1.0
CD A:GLU35 2.5 50.7 1.0
CB D:HIS8 3.2 58.6 1.0
CG A:GLU35 3.9 49.2 1.0
N D:HIS8 4.2 58.7 1.0
CA D:HIS8 4.3 59.4 1.0
ND2 D:ASN98 4.4 53.5 1.0
CB A:GLU35 4.8 38.6 1.0
CG2 D:ILE7 4.9 39.3 1.0

Cadmium binding site 8 out of 8 in 1y1l

Go back to Cadmium Binding Sites List in 1y1l
Cadmium binding site 8 out of 8 in the Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics


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 Arsenate Reductase From Archaeoglobus Fulgidus Dsm 4304, Structural Genomics within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd126

b:8.6
occ:1.00
OD2 D:ASP88 2.4 42.4 1.0
NE2 C:HIS95 2.4 70.6 1.0
OD1 D:ASP88 2.5 27.1 1.0
CE1 C:HIS95 2.5 73.0 1.0
CG D:ASP88 2.8 33.4 1.0
CD2 C:HIS95 3.7 66.6 1.0
ND1 C:HIS95 3.8 69.7 1.0
CB D:ASP88 4.3 32.8 1.0
CG C:HIS95 4.4 61.6 1.0

Reference:

Y.Patskovsky, S.C.Almo. Crystal Structure of Arsenate Reductase From Archaeoglobus Fulgidus To Be Published.
Page generated: Fri Aug 28 12:39:28 2020
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