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Cadmium in PDB 3wo6: Crystal Structure of Yidc From Bacillus Halodurans (Form I)

Protein crystallography data

The structure of Crystal Structure of Yidc From Bacillus Halodurans (Form I), PDB code: 3wo6 was solved by K.Kumazaki, T.Tsukazaki, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.30 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.926, 60.631, 58.903, 90.00, 100.35, 90.00
R / Rfree (%) 24.2 / 25.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Yidc From Bacillus Halodurans (Form I) (pdb code 3wo6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Crystal Structure of Yidc From Bacillus Halodurans (Form I), PDB code: 3wo6:

Cadmium binding site 1 out of 1 in 3wo6

Go back to Cadmium Binding Sites List in 3wo6
Cadmium binding site 1 out of 1 in the Crystal Structure of Yidc From Bacillus Halodurans (Form I)


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 Yidc From Bacillus Halodurans (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:51.8
occ:1.00
O A:HOH401 2.8 34.6 1.0
ND1 A:HIS162 2.8 39.4 1.0
CG A:HIS162 3.6 37.4 1.0
CE1 A:HIS162 3.8 38.9 1.0
CB A:HIS162 3.8 39.8 1.0
O A:HOH406 3.8 47.9 1.0
O A:GLU158 4.2 60.4 1.0
CA A:HIS162 4.3 43.7 1.0
O A:GLY58 4.8 45.0 1.0
CD2 A:HIS162 4.8 38.8 1.0
NE2 A:HIS162 4.8 38.5 1.0
CD2 A:TYR60 4.9 41.4 1.0

Reference:

K.Kumazaki, S.Chiba, M.Takemoto, A.Furukawa, K.Nishiyama, Y.Sugano, T.Mori, N.Dohmae, K.Hirata, Y.Nakada-Nakura, A.D.Maturana, Y.Tanaka, H.Mori, Y.Sugita, F.Arisaka, K.Ito, R.Ishitani, T.Tsukazaki, O.Nureki. Structural Basis of Sec-Independent Membrane Protein Insertion By Yidc Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13167
Page generated: Sun Jan 24 09:56:21 2021

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