Zinc in PDB 2d5m: Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F)

The structure of Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F), PDB code: 2d5m was solved by Y.Ueda, N.Shibata, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.346, 53.346, 116.224, 90.00, 90.00, 120.00
R / Rfree (%)	13.5 / 16.2

The binding sites of Zinc atom in the Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F) (pdb code 2d5m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F), PDB code: 2d5m:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:32.4 occ:1.00 O A:HOH3111 1.9 47.9 1.0 SG A:CYS40 2.3 14.0 0.3 O A:HOH3042 2.3 15.0 1.0 SG A:CYS40 2.8 9.2 0.7 O A:HOH3073 2.9 20.2 1.0 CB A:CYS40 3.2 8.5 0.7 CB A:CYS40 3.3 11.0 0.3 O A:HOH3220 3.5 22.2 1.0 CA A:CYS40 3.6 6.9 1.0 O A:CYS39 4.0 10.5 1.0 N A:SER41 4.2 6.8 1.0 O A:HOH3059 4.2 20.3 1.0 C A:CYS40 4.5 6.1 1.0 N A:CYS40 4.7 6.6 1.0 C A:CYS39 4.8 7.0 1.0 O A:GLN42 4.9 13.2 1.0 N A:GLN42 4.9 7.5 1.0

Zinc binding site 2 out of 3 in the Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:15.6 occ:1.00 O A:HOH3001 1.9 33.8 1.0 OD1 A:ASP150 2.0 22.3 1.0 O A:HOH3056 2.2 16.9 1.0 O A:HOH3048 2.3 19.1 1.0 OD2 A:ASP150 2.5 28.3 1.0 CG A:ASP150 2.6 18.6 1.0 CB A:ASP150 4.1 16.9 1.0 O A:HOH3138 4.2 35.2 1.0 O A:HOH3072 4.3 17.6 1.0 O A:HOH3197 4.4 52.6 1.0 CA A:ASP150 4.8 12.9 1.0 N A:ASP150 4.9 12.7 1.0

Zinc binding site 3 out of 3 in the Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:12.1 occ:1.00 O A:HOH3136 2.2 13.6 1.0 SG A:CYS40 2.3 9.2 0.7 SG A:CYS39 2.4 10.1 1.0 CB A:CYS40 3.0 11.0 0.3 CB A:CYS40 3.2 8.5 0.7 CB A:CYS39 3.3 9.4 1.0 C A:CYS39 3.7 7.0 1.0 N A:CYS40 3.7 6.6 1.0 CB A:SER45 3.9 8.0 1.0 CG2 A:ILE135 3.9 9.9 1.0 O A:CYS39 3.9 10.5 1.0 CA A:CYS40 4.0 6.9 1.0 O A:HOH3059 4.1 20.3 1.0 CA A:CYS39 4.1 7.0 1.0 SG A:CYS40 4.2 14.0 0.3 OG A:SER45 4.2 8.8 1.0 O A:HOH3042 4.7 15.0 1.0 CD1 A:ILE135 5.0 10.4 1.0 N A:CYS39 5.0 6.2 1.0

Y.Ueda, N.Shibata, Y.Higuchi. Flavoredoxin of Desulfovibrio Vulgaris (Miyazaki F) To Be Published.