Zinc in PDB 6ekb: Crystal Structure of the BSD2 Homolog of Arabidopsis Thaliana

The structure of Crystal Structure of the BSD2 Homolog of Arabidopsis Thaliana, PDB code: 6ekb was solved by H.Aigner, R.H.Wilson, A.Bracher, L.Calisse, J.Y.Bhat, F.U.Hartl, M.Hayer-Hartl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.708, 55.708, 48.131, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.6

The binding sites of Zinc atom in the Crystal Structure of the BSD2 Homolog of Arabidopsis Thaliana (pdb code 6ekb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the BSD2 Homolog of Arabidopsis Thaliana, PDB code: 6ekb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the BSD2 Homolog of 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 the BSD2 Homolog of Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:55.0 occ:1.00 SG A:CYS121 2.4 44.2 1.0 SG A:CYS75 2.4 41.0 1.0 SG A:CYS118 2.4 46.2 1.0 SG A:CYS72 2.5 47.9 1.0 CB A:CYS72 3.1 45.4 1.0 CB A:CYS118 3.1 44.2 1.0 CB A:CYS121 3.3 49.1 1.0 CB A:CYS75 3.4 41.2 1.0 N A:CYS75 3.8 44.8 1.0 N A:CYS121 3.9 52.5 1.0 CA A:CYS75 4.2 41.2 1.0 CA A:CYS121 4.2 51.6 1.0 CA A:CYS72 4.5 48.1 1.0 CB A:ASP120 4.6 57.5 1.0 CB A:ASN74 4.6 50.9 1.0 CA A:CYS118 4.6 47.2 1.0 CA A:GLY125 4.7 42.7 1.0 C A:ASN74 4.8 48.7 1.0 C A:ASP120 4.8 55.8 1.0 ND2 A:ASN74 4.9 48.5 1.0 N A:GLY125 4.9 44.0 1.0 C A:CYS118 4.9 49.6 1.0 C A:CYS72 4.9 50.7 1.0 N A:ASP120 4.9 54.6 1.0 O A:CYS118 4.9 48.4 1.0 O A:CYS72 5.0 49.3 1.0 C A:GLY125 5.0 43.7 1.0 N A:ASN74 5.0 52.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the BSD2 Homolog of 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 the BSD2 Homolog of Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:44.6 occ:1.00 SG A:CYS86 2.3 35.7 1.0 SG A:CYS83 2.3 35.1 1.0 SG A:CYS110 2.4 35.0 1.0 SG A:CYS107 2.4 32.9 1.0 CB A:CYS83 3.0 35.7 1.0 CB A:CYS107 3.1 33.7 1.0 CB A:CYS86 3.3 37.8 1.0 CB A:CYS110 3.3 32.9 1.0 N A:CYS86 3.7 36.7 1.0 N A:CYS110 3.8 33.4 1.0 CA A:CYS86 4.1 36.9 1.0 CA A:CYS110 4.1 35.1 1.0 CA A:CYS83 4.4 36.7 1.0 CA A:CYS107 4.6 32.8 1.0 CB A:GLN85 4.6 34.9 1.0 C A:GLN85 4.7 37.1 1.0 CB A:LEU109 4.8 33.5 1.0 CA A:GLY90 4.8 38.0 1.0 C A:CYS83 4.8 36.7 1.0 C A:LEU109 4.9 33.5 1.0 C A:CYS110 4.9 36.0 1.0 O A:HOH308 4.9 31.5 1.0 O A:CYS83 4.9 37.7 1.0 CA A:LYS114 4.9 37.6 1.0 C A:CYS86 4.9 38.0 1.0 N A:GLN85 4.9 38.2 1.0 N A:GLY90 4.9 38.9 1.0 CA A:GLN85 5.0 36.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the BSD2 Homolog of Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the BSD2 Homolog of Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:46.7 occ:1.00 OE2 A:GLU115 2.1 38.4 1.0 OE1 A:GLU78 2.1 36.1 1.0 SG A:CYS80 2.3 34.9 1.0 CD A:GLU115 2.9 37.5 1.0 CD A:GLU78 3.1 34.5 1.0 OE1 A:GLU115 3.1 36.9 1.0 CG A:GLU78 3.3 34.6 1.0 CB A:CYS80 3.4 34.7 1.0 C A:CYS80 3.9 38.8 1.0 O A:CYS80 4.0 38.9 1.0 O A:HOH311 4.1 41.3 1.0 CA A:CYS80 4.1 36.5 1.0 OE2 A:GLU78 4.2 35.2 1.0 CG A:GLU115 4.3 35.5 1.0 N A:VAL81 4.5 35.8 1.0 N A:CYS80 4.7 36.2 1.0 O A:HOH307 4.8 39.5 1.0 CB A:GLU78 4.8 34.3 1.0 CA A:VAL81 4.9 36.8 1.0 CB A:GLU115 4.9 36.0 1.0 O A:GLU78 5.0 35.7 1.0

H.Aigner, R.H.Wilson, A.Bracher, L.Calisse, J.Y.Bhat, F.U.Hartl, M.Hayer-Hartl. Plant Rubisco Assembly in E. Coli with Five Chloroplast Chaperones Including BSD2. Science V. 358 1272 2017.
ISSN: ESSN 1095-9203
PubMed: 29217567
DOI: 10.1126/SCIENCE.AAP9221