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Zinc in PDB 2dge: Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana

Protein crystallography data

The structure of Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana, PDB code: 2dge was solved by H.Chida, T.Yokoyama, F.Kawai, A.Nakazawa, H.Akazaki, Y.Takayama, T.Hirano, K.Suruga, T.Satoh, S.Yamada, R.Kawachi, S.Unzai, T.Nishio, S.-Y.Park, T.Oku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.47 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.443, 51.843, 53.685, 82.51, 62.08, 63.26
R / Rfree (%) 18.6 / 21.5

Other elements in 2dge:

The structure of Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana (pdb code 2dge). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana, PDB code: 2dge:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2dge

Go back to Zinc Binding Sites List in 2dge
Zinc binding site 1 out of 2 in the Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:13.7
occ:1.00
OE2 C:GLU159 2.0 13.0 1.0
OD2 C:ASP74 2.0 13.1 1.0
OD1 A:ASP74 2.0 12.9 1.0
OE2 A:GLU159 2.0 13.7 1.0
CD A:GLU159 2.7 14.6 1.0
CD C:GLU159 2.7 13.7 1.0
OE1 A:GLU159 2.8 15.1 1.0
OE1 C:GLU159 2.8 14.2 1.0
CG C:ASP74 2.9 12.7 1.0
CG A:ASP74 2.9 13.8 1.0
CB A:ASP74 3.2 12.9 1.0
CB C:ASP74 3.2 11.9 1.0
NZ C:LYS155 3.7 19.9 1.0
O C:HOH206 3.9 17.2 1.0
O C:HOH205 3.9 17.1 1.0
O A:HOH1059 4.0 41.0 1.0
OD1 C:ASP74 4.0 14.6 1.0
OD2 A:ASP74 4.1 15.9 1.0
CG A:GLU159 4.2 12.6 1.0
CG C:GLU159 4.2 10.8 1.0
O C:HOH201 4.6 14.2 1.0
O A:HOH1003 4.6 16.3 1.0
CA A:ASP74 4.7 13.9 1.0
CA C:ASP74 4.7 12.4 1.0
CE C:LYS155 4.9 20.1 1.0

Zinc binding site 2 out of 2 in 2dge

Go back to Zinc Binding Sites List in 2dge
Zinc binding site 2 out of 2 in the Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:12.3
occ:1.00
OE2 D:GLU159 2.0 12.5 1.0
OE2 B:GLU159 2.0 11.2 1.0
OD1 D:ASP74 2.0 11.5 1.0
OD2 B:ASP74 2.0 12.9 1.0
CD D:GLU159 2.8 13.1 1.0
CD B:GLU159 2.8 12.9 1.0
CG B:ASP74 2.9 12.4 1.0
OE1 D:GLU159 2.9 13.7 1.0
OE1 B:GLU159 2.9 12.7 1.0
CG D:ASP74 2.9 12.0 1.0
CB B:ASP74 3.2 12.8 1.0
CB D:ASP74 3.2 11.8 1.0
NZ D:LYS155 3.6 20.4 1.0
O B:HOH1005 3.9 14.7 1.0
O B:HOH1054 4.0 33.5 1.0
OD1 B:ASP74 4.0 15.5 1.0
O B:HOH1008 4.0 16.3 1.0
OD2 D:ASP74 4.1 14.2 1.0
CG B:GLU159 4.2 11.7 1.0
CG D:GLU159 4.2 11.1 1.0
O D:HOH201 4.6 14.0 1.0
O B:HOH1006 4.7 15.5 1.0
CE D:LYS155 4.7 21.4 1.0
CA B:ASP74 4.7 13.0 1.0
CA D:ASP74 4.8 11.8 1.0

Reference:

H.Chida, T.Yokoyama, F.Kawai, A.Nakazawa, H.Akazaki, Y.Takayama, T.Hirano, K.Suruga, T.Satoh, S.Yamada, R.Kawachi, S.Unzai, T.Nishio, S.-Y.Park, T.Oku. Crystal Structure of Oxidized Cytochrome C(6A) From Arabidopsis Thaliana Febs Lett. V. 580 3763 2006.
ISSN: ISSN 0014-5793
PubMed: 16777100
DOI: 10.1016/J.FEBSLET.2006.05.067
Page generated: Wed Dec 16 03:21:00 2020

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