Zinc in PDB 3ex8: Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis

All present enzymatic activity of Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis:
1.1.1.193; 3.5.4.26;

The structure of Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis, PDB code: 3ex8 was solved by S.C.Chen, Y.H.Lin, H.C.Yu, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.078, 108.367, 187.394, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.3

The binding sites of Zinc atom in the Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis (pdb code 3ex8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis, PDB code: 3ex8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn362 b:49.5 occ:1.00 ND1 A:HIS49 2.2 40.1 1.0 SG A:CYS83 2.3 34.9 1.0 SG A:CYS74 2.4 41.4 1.0 CE1 A:HIS49 3.1 37.1 1.0 CG A:HIS49 3.2 40.5 1.0 CB A:CYS83 3.2 37.1 1.0 CB A:CYS74 3.5 33.9 1.0 CB A:HIS49 3.6 42.1 1.0 N A:CYS74 3.8 35.4 1.0 OE1 A:GLU51 4.1 43.5 1.0 N A:CYS83 4.2 40.8 1.0 NE2 A:HIS49 4.2 37.2 1.0 CA A:CYS74 4.3 35.1 1.0 CD2 A:HIS49 4.3 40.4 1.0 CA A:CYS83 4.3 39.4 1.0 OE2 A:GLU51 4.4 48.3 1.0 CD A:GLU51 4.5 44.1 1.0 O A:HOH410 4.7 60.2 1.0 C A:PRO73 4.9 34.8 1.0

Zinc binding site 2 out of 4 in the Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn362 b:60.9 occ:1.00 ND1 B:HIS49 2.3 56.9 1.0 O B:HOH400 2.5 45.5 1.0 SG B:CYS74 2.5 72.1 1.0 SG B:CYS83 2.6 84.1 1.0 CE1 B:HIS49 3.0 55.5 1.0 CB B:CYS83 3.1 85.5 1.0 CG B:HIS49 3.1 56.0 1.0 CB B:CYS74 3.3 71.1 1.0 CB B:HIS49 3.5 53.0 1.0 OE1 B:GLU51 3.6 53.1 1.0 N B:CYS74 3.7 69.1 1.0 OE2 B:GLU51 3.8 56.6 1.0 CD B:GLU51 4.0 55.3 1.0 NE2 B:HIS49 4.1 56.3 1.0 CA B:CYS74 4.1 71.2 1.0 CD2 B:HIS49 4.1 55.3 1.0 N B:CYS83 4.2 87.7 1.0 CA B:CYS83 4.2 85.8 1.0 C B:PRO73 4.8 67.1 1.0 O B:HOH398 4.9 52.4 1.0 C B:CYS74 4.9 73.0 1.0

Zinc binding site 3 out of 4 in the Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn362 b:55.1 occ:1.00 ND1 C:HIS49 2.0 43.2 1.0 SG C:CYS83 2.3 60.2 1.0 SG C:CYS74 2.5 61.0 1.0 CE1 C:HIS49 2.8 43.1 1.0 O C:HOH383 2.8 35.6 1.0 CB C:CYS83 3.1 64.4 1.0 CG C:HIS49 3.2 43.3 1.0 CB C:CYS74 3.4 57.8 1.0 CB C:HIS49 3.7 43.1 1.0 N C:CYS74 3.7 57.0 1.0 NE2 C:HIS49 4.0 44.0 1.0 N C:CYS83 4.0 66.5 1.0 OE2 C:GLU51 4.1 56.8 1.0 CA C:CYS74 4.2 58.9 1.0 CA C:CYS83 4.2 65.5 1.0 CD2 C:HIS49 4.2 43.0 1.0 OE1 C:GLU51 4.3 56.3 1.0 CD C:GLU51 4.5 53.7 1.0 C C:PRO73 4.8 54.7 1.0 O C:CYS74 5.0 60.6 1.0

Zinc binding site 4 out of 4 in the Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex Structure of Bacillus Subtilis Ribg Reduction Mechanism in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn362 b:52.6 occ:1.00 ND1 D:HIS49 2.2 38.6 1.0 SG D:CYS74 2.3 46.6 1.0 SG D:CYS83 2.4 43.4 1.0 CE1 D:HIS49 3.1 36.8 1.0 CG D:HIS49 3.1 41.2 1.0 CB D:CYS83 3.3 42.9 1.0 CB D:CYS74 3.3 46.2 1.0 CB D:HIS49 3.4 42.3 1.0 N D:CYS74 3.7 46.6 1.0 CA D:CYS74 4.1 48.0 1.0 N D:CYS83 4.1 46.4 1.0 NE2 D:HIS49 4.1 36.3 1.0 CD2 D:HIS49 4.2 38.2 1.0 CA D:CYS83 4.3 44.6 1.0 OE1 D:GLU51 4.3 42.2 1.0 OE2 D:GLU51 4.7 46.9 1.0 CD D:GLU51 4.7 43.6 1.0 C D:PRO73 4.8 44.0 1.0 O D:CYS74 4.9 51.4 1.0 C D:CYS74 4.9 51.0 1.0 CA D:HIS49 5.0 44.0 1.0 CA D:PRO73 5.0 44.7 1.0

S.C.Chen, Y.H.Lin, H.C.Yu, S.H.Liaw. Complex Structure of Bacillus Subtilis Ribg: the Reduction Mechanism During Riboflavin Biosynthesis. J.Biol.Chem. V. 284 1725 2009.
ISSN: ISSN 0021-9258
PubMed: 18986985
DOI: 10.1074/JBC.M805820200