Zinc in PDB 2x2p: The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State

The structure of The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State, PDB code: 2x2p was solved by A.K.Rohr, H.P.Hersleth, K.K.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.955, 45.485, 56.200, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 19.1

The structure of The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Zinc atom in the The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State (pdb code 2x2p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State, PDB code: 2x2p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1120 b:9.3 occ:1.00 O2 A:CAC1124 2.0 9.0 0.8 NE2 A:HIS17 2.0 8.5 1.0 O A:HOH2129 2.1 18.4 1.0 CE1 A:HIS17 2.9 9.1 1.0 CD2 A:HIS17 3.1 8.7 1.0 AS A:CAC1124 3.2 12.0 0.8 C1 A:CAC1124 3.6 16.2 0.8 O A:HOH2016 3.8 25.4 1.0 ND1 A:HIS17 4.1 9.2 1.0 C2 A:CAC1124 4.1 16.1 0.8 CG A:HIS17 4.2 8.2 1.0 CE A:LYS13 4.5 15.8 1.0 O1 A:CAC1124 4.6 14.8 0.8

Zinc binding site 2 out of 4 in the The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1121 b:21.7 occ:0.85 O A:HOH2130 1.9 14.9 1.0 OD1 A:ASP54 1.9 18.7 1.0 OE2 A:GLU50 2.2 21.7 1.0 OD2 A:ASP54 2.6 20.0 1.0 CG A:ASP54 2.7 14.9 1.0 O A:HOH2133 2.8 7.7 1.0 ZN A:ZN1123 2.8 19.4 0.3 CD A:GLU50 3.1 18.1 1.0 O A:HOH2134 3.4 5.0 1.0 CG A:GLU50 3.4 13.6 1.0 O A:HOH2135 3.5 25.6 1.0 O A:HOH2136 3.8 41.9 1.0 CB A:ASP54 4.1 11.1 1.0 OE1 A:GLU50 4.3 24.1 1.0 O A:GLU50 4.5 8.6 1.0 O A:HOH2062 4.5 33.2 1.0 CA A:ASP54 4.8 9.7 1.0 CB A:GLU50 4.9 11.2 1.0

Zinc binding site 3 out of 4 in the The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1122 b:21.3 occ:0.79 OD2 A:ASP76 1.9 23.8 1.0 CG A:ASP76 2.5 25.5 1.0 OD1 A:ASP76 2.5 34.8 1.0 O A:HOH2131 3.5 12.0 1.0 CB A:ASP76 4.0 21.7 1.0 N A:ASP76 4.5 18.5 1.0 CE A:MET77 4.6 30.1 1.0 CG A:MET77 4.6 23.7 1.0 CA A:ASP76 4.6 19.1 1.0 C A:ASP76 4.8 17.4 1.0 N A:MET77 4.9 15.3 1.0

Zinc binding site 4 out of 4 in the The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Flavoprotein Nrdi From Bacillus Cereus with the Initially Semiquinone Fmn Cofactor in An Intermediate Radiation Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1123 b:19.4 occ:0.33 O A:HOH2134 1.7 5.0 1.0 O A:HOH2133 2.0 7.7 1.0 O A:HOH2135 2.0 25.6 1.0 O A:HOH2136 2.6 41.9 1.0 ZN A:ZN1121 2.8 21.7 0.8 OD1 A:ASP54 2.9 18.7 1.0 O A:HOH2132 3.5 16.9 1.0 OE2 A:GLU50 3.7 21.7 1.0 OE1 A:GLU57 3.7 35.4 1.0 CD A:GLU57 3.9 33.5 1.0 CG A:ASP54 4.0 14.9 1.0 OE2 A:GLU57 4.1 35.0 1.0 O A:HOH2062 4.1 33.2 1.0 O A:HOH2130 4.3 14.9 1.0 CG A:GLU57 4.7 28.6 1.0 OD2 A:ASP54 4.7 20.0 1.0 CA A:ASP54 4.8 9.7 1.0 CD A:GLU50 4.9 18.1 1.0 CB A:ASP54 4.9 11.1 1.0

A.K.Rohr, H.P.Hersleth, K.K.Andersson. Tracking Flavin Conformations in Protein Crystal Structures with Raman Spectroscopy and Qm/Mm Calculations Angew.Chem.Int.Ed.Engl. V. 49 2324 2010.
ISSN: ISSN 1433-7851
PubMed: 20187055
DOI: 10.1002/ANIE.200907143