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Cadmium in PDB 1oyr: Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis

Enzymatic activity of Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis:
2.7.7.56;

Protein crystallography data

The structure of Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis, PDB code: 1oyr was solved by L.S.Harlow, A.Kadziola, K.F.Jensen, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.92 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.790, 146.490, 152.250, 90.00, 90.00, 90.00
R / Rfree (%) 27.8 / 28.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis (pdb code 1oyr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis, PDB code: 1oyr:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1oyr

Go back to Cadmium Binding Sites List in 1oyr
Cadmium binding site 1 out of 3 in the Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis


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 Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:36.2
occ:1.00
ND1 A:HIS3 2.4 34.5 1.0
OE1 A:GLU179 2.5 36.8 1.0
OE2 A:GLU179 2.6 38.9 1.0
CD A:GLU179 2.8 37.2 1.0
CE1 A:HIS3 3.1 35.0 1.0
CG A:HIS3 3.6 36.0 1.0
CB A:HIS3 4.1 38.8 1.0
CG A:GLU179 4.2 34.0 1.0
NE2 A:HIS3 4.3 34.2 1.0
CD2 A:HIS3 4.5 35.3 1.0

Cadmium binding site 2 out of 3 in 1oyr

Go back to Cadmium Binding Sites List in 1oyr
Cadmium binding site 2 out of 3 in the Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis


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 Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd502

b:62.3
occ:1.00
CE1 E:HIS3 2.7 45.9 1.0
NE2 E:HIS3 3.2 47.2 1.0
ND1 E:HIS3 3.8 51.1 1.0
OG E:SER183 4.5 34.0 1.0
CD2 E:HIS3 4.6 49.3 1.0
CG E:HIS3 4.8 50.0 1.0

Cadmium binding site 3 out of 3 in 1oyr

Go back to Cadmium Binding Sites List in 1oyr
Cadmium binding site 3 out of 3 in the Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis


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 Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd503

b:43.2
occ:1.00
OE2 D:GLU179 2.3 38.1 1.0
OE1 D:GLU179 2.4 35.5 1.0
CD D:GLU179 2.5 37.1 1.0
CD2 D:HIS3 2.9 49.1 1.0
NE2 D:HIS3 3.1 48.3 1.0
CG D:HIS3 3.3 49.1 1.0
CE1 D:HIS3 3.5 50.4 1.0
ND1 D:HIS3 3.6 51.4 1.0
CG D:GLU179 3.8 33.9 1.0
CB D:HIS3 4.1 49.8 1.0
CB D:GLU179 4.9 29.9 1.0

Reference:

L.S.Harlow, A.Kadziola, K.F.Jensen, S.Larsen. Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis and Implications For Its Quaternary Structure and Trna Binding. Protein Sci. V. 13 668 2004.
ISSN: ISSN 0961-8368
PubMed: 14767080
DOI: 10.1110/PS.03477004
Page generated: Fri Aug 28 12:18:34 2020
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