Zinc in PDB 2xoe: Crystal Structure of Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form

The structure of Crystal Structure of Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form, PDB code: 2xoe was solved by R.Johansson, J.Sprenger, E.Torrents, M.Sahlin, B.M.Sjoberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.71 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.830, 45.260, 55.660, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 19.2

The structure of Crystal Structure of Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form (pdb code 2xoe). 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 Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form, PDB code: 2xoe:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form


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 Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1120 b:15.9 occ:1.00 O1 A:CAC1124 2.0 16.9 0.7 NE2 A:HIS17 2.1 14.3 1.0 O A:ACT1123 2.1 35.6 1.0 OXT A:ACT1123 2.7 40.4 1.0 C A:ACT1123 2.8 37.9 1.0 CE1 A:HIS17 2.9 14.5 1.0 CD2 A:HIS17 3.2 13.1 1.0 AS A:CAC1124 3.2 22.1 0.7 O2 A:CAC1124 3.5 24.4 0.7 O A:HOH2120 3.7 43.9 1.0 ND1 A:HIS17 4.1 14.1 1.0 C2 A:CAC1124 4.2 23.1 0.7 CG A:HIS17 4.2 12.8 1.0 CH3 A:ACT1123 4.3 39.2 1.0 CE A:LYS13 4.4 23.2 1.0 C1 A:CAC1124 4.7 17.6 0.7 NZ A:LYS13 5.0 26.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form


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 Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1121 b:19.1 occ:0.64 OE2 A:GLU50 1.9 22.1 1.0 OE2 A:GLU54 2.1 27.7 1.0 O A:HOH2115 2.2 34.5 1.0 O A:HOH2116 2.3 45.7 1.0 O A:HOH2114 2.6 28.8 1.0 CD A:GLU50 2.9 20.9 1.0 CD A:GLU54 3.1 25.4 1.0 OE1 A:GLU50 3.3 23.7 1.0 O A:HOH2051 3.4 53.3 1.0 O A:HOH2118 3.6 41.3 1.0 O A:HOH2119 3.6 35.6 1.0 CG A:GLU54 3.7 21.3 1.0 ZN A:ZN1122 3.7 23.5 0.6 CG A:GLU50 4.2 18.8 1.0 OE1 A:GLU54 4.2 25.4 1.0 O A:HOH2055 4.7 40.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form


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 Flavoprotein Nrdi From Bacillus Anthracis in the Semiquinone Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1122 b:23.5 occ:0.62 O A:HOH2117 1.8 45.5 1.0 OE1 A:GLU54 2.1 25.4 1.0 OE2 A:GLU54 2.2 27.7 1.0 O A:HOH2055 2.2 40.4 1.0 O A:HOH2118 2.3 41.3 1.0 CD A:GLU54 2.5 25.4 1.0 O A:HOH2119 2.6 35.6 1.0 O A:HOH2051 3.1 53.3 1.0 O A:HOH2114 3.3 28.8 1.0 O A:HOH2116 3.5 45.7 1.0 ZN A:ZN1121 3.7 19.1 0.6 OE1 A:GLU57 3.9 34.2 1.0 OE2 A:GLU57 4.0 36.6 1.0 CG A:GLU54 4.0 21.3 1.0 CD A:GLU57 4.1 33.5 1.0 O A:HOH2052 4.6 45.6 1.0 O A:HOH2115 4.7 34.5 1.0 CB A:GLU54 4.9 17.6 1.0

R.Johansson, E.Torrents, D.Lundin, J.Sprenger, M.Sahlin, B.M.Sjoberg, D.T.Logan. High Resolution Crystal Structures of Nrdi in the Oxidised and Reduced States: An Unusual Flavodoxin Febs J. V. 277 4265 2010.
ISSN: ISSN 1742-464X
PubMed: 20831589
DOI: 10.1111/J.1742-4658.2010.07815.X