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Cadmium in PDB 1y47: Structural Studies of Designed Alpha-Helical Hairpins

Protein crystallography data

The structure of Structural Studies of Designed Alpha-Helical Hairpins, PDB code: 1y47 was solved by S.J.Lahr, D.E.Engel, S.E.Stayrook, O.Maglio, B.North, S.Geremia, A.Lombardi, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.274, 39.017, 46.891, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 25.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structural Studies of Designed Alpha-Helical Hairpins (pdb code 1y47). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structural Studies of Designed Alpha-Helical Hairpins, PDB code: 1y47:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1y47

Go back to Cadmium Binding Sites List in 1y47
Cadmium binding site 1 out of 3 in the Structural Studies of Designed Alpha-Helical Hairpins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural Studies of Designed Alpha-Helical Hairpins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd60

b:41.5
occ:1.00
OE1 A:GLU36 2.3 35.2 1.0
ND1 A:HIS39 2.4 32.2 1.0
OE1 A:GLU10 2.5 52.8 1.0
OE2 A:GLU10 2.6 41.7 1.0
CD A:GLU10 2.9 38.6 1.0
CE1 A:HIS39 3.2 33.5 1.0
CD A:GLU36 3.2 41.5 1.0
CG A:HIS39 3.4 34.4 1.0
OE2 A:GLU36 3.6 44.8 1.0
CB A:HIS39 3.8 36.0 1.0
O A:HOH61 3.8 38.4 0.5
CA A:GLU36 4.2 48.5 1.0
CG A:GLU10 4.4 42.2 1.0
NE2 A:HIS39 4.4 38.4 1.0
CG A:GLU36 4.4 39.9 1.0
CB A:GLU36 4.5 45.8 1.0
CD2 A:HIS39 4.5 24.7 1.0
N A:GLU36 4.9 50.2 1.0

Cadmium binding site 2 out of 3 in 1y47

Go back to Cadmium Binding Sites List in 1y47
Cadmium binding site 2 out of 3 in the Structural Studies of Designed Alpha-Helical Hairpins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural Studies of Designed Alpha-Helical Hairpins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd61

b:41.9
occ:1.00
ND1 B:HIS39 2.4 37.2 1.0
OE1 B:GLU36 2.5 51.0 1.0
OE2 B:GLU10 2.5 43.3 1.0
OE1 B:GLU10 2.6 48.5 1.0
CD B:GLU10 2.9 46.4 1.0
CE1 B:HIS39 3.1 36.4 1.0
O B:HOH63 3.4 24.8 0.5
CD B:GLU36 3.4 49.9 1.0
CG B:HIS39 3.5 41.1 1.0
OE2 B:GLU36 3.9 46.3 1.0
CB B:HIS39 4.0 36.9 1.0
CA B:GLU36 4.3 48.1 1.0
NE2 B:HIS39 4.3 34.3 1.0
CG B:GLU10 4.4 44.8 1.0
CB B:GLU36 4.5 47.4 1.0
CD2 B:HIS39 4.6 26.5 1.0
CG B:GLU36 4.6 45.7 1.0
N B:GLU36 5.0 46.6 1.0

Cadmium binding site 3 out of 3 in 1y47

Go back to Cadmium Binding Sites List in 1y47
Cadmium binding site 3 out of 3 in the Structural Studies of Designed Alpha-Helical Hairpins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural Studies of Designed Alpha-Helical Hairpins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd62

b:92.0
occ:1.00
OE1 B:GLU19 2.6 77.8 1.0
CD B:GLU19 3.8 73.7 1.0
NH2 B:ARG23 3.8 86.1 1.0
OE2 B:GLU22 4.1 61.5 1.0
OE2 B:GLU19 4.4 78.8 1.0
NZ B:LYS15 4.5 81.8 1.0
CB B:GLU19 4.7 74.3 1.0
CG B:GLU19 4.9 72.5 1.0
OE1 B:GLU22 4.9 74.5 1.0
CD B:GLU22 4.9 70.4 1.0

Reference:

S.J.Lahr, D.E.Engel, S.E.Stayrook, O.Maglio, B.North, S.Geremia, A.Lombardi, W.F.Degrado. Analysis and Design of Turns in Alpha-Helical Hairpins J.Mol.Biol. V. 346 1441 2005.
ISSN: ISSN 0022-2836
PubMed: 15713492
DOI: 10.1016/J.JMB.2004.12.016
Page generated: Fri Aug 28 12:39:45 2020
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