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Cadmium in PDB 3o39: Crystal Structure of Spy

Protein crystallography data

The structure of Crystal Structure of Spy, PDB code: 3o39 was solved by K.M.Ruane, R.Shi, M.Cygler, Montreal-Kingston Bacterial Structuralgenomics Initiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.06 / 2.60
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 68.971, 68.971, 124.281, 90.00, 90.00, 120.00
R / Rfree (%) 24.3 / 28.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Spy (pdb code 3o39). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of Spy, PDB code: 3o39:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3o39

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Cadmium binding site 1 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1

b:74.0
occ:0.50
OD1 A:ASP66 2.6 71.1 1.0
CG A:ASP66 3.6 73.0 1.0
OD2 A:ASP66 3.9 78.1 1.0
NH2 A:ARG62 4.6 46.6 0.5
CB A:ASP66 4.9 62.6 1.0

Cadmium binding site 2 out of 9 in 3o39

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Cadmium binding site 2 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2

b:30.0
occ:0.50
OD1 A:ASP74 2.8 38.8 1.0
OD2 A:ASP74 3.0 27.4 1.0
CG A:ASP74 3.3 32.0 1.0
O A:HOH5 4.0 43.5 1.0
CB A:ALA76 4.5 18.1 1.0
CG A:LYS77 4.7 43.5 1.0
CB A:ASP74 4.7 24.2 1.0

Cadmium binding site 3 out of 9 in 3o39

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Cadmium binding site 3 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd6

b:0.8
occ:1.00
OD2 A:ASP36 2.6 0.7 1.0
OD1 A:ASP36 3.1 0.8 1.0
CG A:ASP36 3.2 0.4 1.0
CB A:ASP36 4.7 0.0 1.0

Cadmium binding site 4 out of 9 in 3o39

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Cadmium binding site 4 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd8

b:97.8
occ:0.50
O A:HOH130 2.8 56.8 1.0
O A:HOH131 3.0 68.1 1.0
CB A:ALA76 4.0 18.1 1.0
O A:HOH5 4.0 43.5 1.0
CA A:ALA76 4.5 25.6 1.0
O A:HOH129 4.6 57.8 1.0
OE1 A:GLU79 4.6 48.9 1.0
N A:ALA76 4.7 29.2 1.0

Cadmium binding site 5 out of 9 in 3o39

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Cadmium binding site 5 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3

b:95.3
occ:0.50
OE2 A:GLU86 2.4 0.3 1.0
CD B:GLU86 2.5 99.4 1.0
OE2 B:GLU86 2.7 0.0 1.0
CD A:GLU86 2.7 98.3 1.0
OE1 B:GLU86 2.8 0.7 1.0
OE1 A:GLU86 3.0 0.3 1.0
CG B:GLU86 3.1 83.7 1.0
CG A:GLU86 3.8 81.2 1.0
O A:HOH7 4.0 61.2 1.0
CB B:GLU86 4.2 69.3 1.0
NZ B:LYS90 4.3 72.0 1.0
CD B:LYS90 4.9 61.8 1.0

Cadmium binding site 6 out of 9 in 3o39

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Cadmium binding site 6 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd4

b:72.7
occ:0.50
OD1 B:ASP66 2.8 82.5 1.0
CG B:ASP66 3.8 80.4 1.0
OD2 B:ASP66 4.3 87.4 1.0
OE2 A:GLU120 4.3 0.4 1.0

Cadmium binding site 7 out of 9 in 3o39

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Cadmium binding site 7 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd5

b:25.5
occ:0.50
OD1 B:ASP74 2.8 39.3 1.0
OD2 B:ASP74 2.9 34.5 1.0
CG B:ASP74 3.2 33.4 1.0
CG B:LYS77 4.5 66.5 1.0
CB B:ALA76 4.6 24.4 1.0
CB B:ASP74 4.7 27.5 1.0

Cadmium binding site 8 out of 9 in 3o39

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Cadmium binding site 8 out of 9 in the Crystal Structure of Spy


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 Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd7

b:0.7
occ:1.00
OD2 B:ASP36 3.0 0.1 1.0
OD1 B:ASP36 3.1 0.9 1.0
CG B:ASP36 3.4 0.5 1.0
CB B:ASP36 4.9 0.8 1.0

Cadmium binding site 9 out of 9 in 3o39

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Cadmium binding site 9 out of 9 in the Crystal Structure of Spy


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Spy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9

b:87.6
occ:0.50
O B:HOH130 2.8 75.7 1.0
CB B:ALA76 3.9 24.4 1.0
CA B:ALA76 4.4 34.6 1.0
N B:ALA76 4.6 38.2 1.0
OE1 B:GLU79 4.7 58.9 1.0

Reference:

S.Quan, P.Koldewey, T.Tapley, N.Kirsch, K.M.Ruane, J.Pfizenmaier, R.Shi, S.Hofmann, L.Foit, G.Ren, U.Jakob, Z.Xu, M.Cygler, J.C.Bardwell. Genetic Selection Designed to Stabilize Proteins Uncovers A Chaperone Called Spy. Nat.Struct.Mol.Biol. V. 18 262 2011.
ISSN: ISSN 1545-9993
PubMed: 21317898
DOI: 10.1038/NSMB.2016
Page generated: Fri Aug 28 13:50:56 2020
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