Zinc in PDB 4g3m: Complex Structure of Bacillus Subtilis Ribg: the Deamination Process in Riboflavin Biosynthesis

All present enzymatic activity of Complex Structure of Bacillus Subtilis Ribg: the Deamination Process in Riboflavin Biosynthesis:
1.1.1.193; 3.5.4.26;

The structure of Complex Structure of Bacillus Subtilis Ribg: the Deamination Process in Riboflavin Biosynthesis, PDB code: 4g3m was solved by S.C.Chen, C.Y.Shen, T.M.Yen, H.C.Yu, T.H.Chang, W.L.Lai, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.72 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.014, 109.190, 189.472, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 27

The binding sites of Zinc atom in the Complex Structure of Bacillus Subtilis Ribg: the Deamination Process in Riboflavin Biosynthesis (pdb code 4g3m). 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: the Deamination Process in Riboflavin Biosynthesis, PDB code: 4g3m:
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: the Deamination Process 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: the Deamination Process in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:39.5 occ:1.00 ND1 A:HIS49 2.0 43.9 1.0 SG A:CYS74 2.3 44.9 1.0 SG A:CYS83 2.3 43.5 1.0 CB A:CYS83 2.8 46.3 1.0 CE1 A:HIS49 2.9 45.5 1.0 CG A:HIS49 3.0 44.1 1.0 OE2 A:GLU51 3.1 47.2 1.0 CB A:CYS74 3.4 44.9 1.0 CB A:HIS49 3.4 44.4 1.0 N A:CYS83 3.8 51.0 1.0 N A:CYS74 3.8 42.2 1.0 CA A:CYS83 3.9 49.7 1.0 NE2 A:HIS49 4.0 45.6 1.0 CD2 A:HIS49 4.1 44.5 1.0 CD A:GLU51 4.2 46.3 1.0 CA A:CYS74 4.2 43.2 1.0 OE1 A:GLU51 4.8 46.6 1.0 C A:PRO73 4.9 39.7 1.0 CA A:HIS49 5.0 43.3 1.0 O A:CYS74 5.0 42.3 1.0 O A:HOH536 5.0 61.0 1.0 O A:HOH564 5.0 45.1 1.0 C A:PRO82 5.0 51.6 1.0

Zinc binding site 2 out of 4 in the Complex Structure of Bacillus Subtilis Ribg: the Deamination Process 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: the Deamination Process in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:63.3 occ:1.00 O2 B:AOF402 2.2 64.0 1.0 SG B:CYS83 2.2 68.0 1.0 ND1 B:HIS49 2.2 57.0 1.0 SG B:CYS74 2.4 61.9 1.0 CB B:CYS83 3.0 67.8 1.0 CE1 B:HIS49 3.2 54.9 1.0 CG B:HIS49 3.2 55.4 1.0 C2 B:AOF402 3.4 67.2 1.0 CB B:HIS49 3.5 53.1 1.0 N1 B:AOF402 3.6 66.5 1.0 CB B:CYS74 3.7 62.5 1.0 N B:CYS83 3.8 67.9 1.0 N3 B:AOF402 3.8 67.3 1.0 CA B:CYS83 4.0 68.0 1.0 N B:CYS74 4.0 60.7 1.0 C6 B:AOF402 4.3 66.2 1.0 OE2 B:GLU51 4.3 52.2 1.0 O B:PRO81 4.3 71.5 1.0 NE2 B:HIS49 4.3 54.6 1.0 CD2 B:HIS49 4.4 55.2 1.0 CA B:CYS74 4.4 62.3 1.0 C4 B:AOF402 4.4 66.9 1.0 C5 B:AOF402 4.6 66.2 1.0 O B:CYS74 4.7 62.1 1.0 CD B:GLU51 4.7 52.8 1.0 C B:PRO82 4.8 67.3 1.0 CG2 B:THR80 4.8 69.2 1.0 OE1 B:GLU51 4.9 55.2 1.0 C B:CYS74 5.0 63.7 1.0

Zinc binding site 3 out of 4 in the Complex Structure of Bacillus Subtilis Ribg: the Deamination Process 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: the Deamination Process in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:69.3 occ:1.00 ND1 C:HIS49 1.9 57.4 1.0 SG C:CYS83 2.1 74.9 1.0 O2 C:AOF402 2.2 67.1 1.0 SG C:CYS74 2.3 74.6 1.0 CE1 C:HIS49 2.8 58.1 1.0 CG C:HIS49 3.0 57.8 1.0 CB C:CYS83 3.3 73.2 1.0 CB C:HIS49 3.4 56.6 1.0 C2 C:AOF402 3.4 70.0 1.0 CB C:CYS74 3.5 69.3 1.0 N3 C:AOF402 3.8 70.1 1.0 N1 C:AOF402 3.8 70.5 1.0 NE2 C:HIS49 3.9 58.8 1.0 N C:CYS74 3.9 66.1 1.0 CD2 C:HIS49 4.0 58.6 1.0 N C:CYS83 4.1 73.9 1.0 OE1 C:GLU51 4.2 60.8 1.0 CA C:CYS74 4.3 68.9 1.0 CA C:CYS83 4.3 73.6 1.0 O C:PRO81 4.4 78.8 1.0 C4 C:AOF402 4.4 69.9 1.0 C6 C:AOF402 4.5 71.1 1.0 CD C:GLU51 4.6 62.4 1.0 OE2 C:GLU51 4.6 63.5 1.0 O C:CYS74 4.7 68.8 1.0 C5 C:AOF402 4.8 70.2 1.0 OG1 C:THR80 4.9 77.7 1.0 CA C:HIS49 4.9 55.7 1.0 C C:CYS74 4.9 69.2 1.0

Zinc binding site 4 out of 4 in the Complex Structure of Bacillus Subtilis Ribg: the Deamination Process 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: the Deamination Process in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:54.0 occ:1.00 ND1 D:HIS49 1.9 55.0 1.0 SG D:CYS83 2.1 63.5 1.0 SG D:CYS74 2.2 61.4 1.0 O2 D:AOF402 2.4 73.1 1.0 CE1 D:HIS49 2.8 53.6 1.0 CG D:HIS49 3.0 53.4 1.0 CB D:CYS83 3.2 57.6 1.0 CB D:CYS74 3.2 57.0 1.0 CB D:HIS49 3.5 51.5 1.0 C2 D:AOF402 3.6 73.9 1.0 N D:CYS74 3.8 53.6 1.0 N1 D:AOF402 3.9 73.8 1.0 NE2 D:HIS49 3.9 52.8 1.0 N3 D:AOF402 3.9 73.1 1.0 N D:CYS83 4.0 59.0 1.0 CD2 D:HIS49 4.1 53.9 1.0 CA D:CYS74 4.1 57.0 1.0 CA D:CYS83 4.2 56.5 1.0 OE1 D:GLU51 4.3 49.8 1.0 C6 D:AOF402 4.4 73.4 1.0 OE2 D:GLU51 4.4 54.7 1.0 C4 D:AOF402 4.5 73.1 1.0 CD D:GLU51 4.6 50.7 1.0 O D:PRO81 4.7 77.5 1.0 C5 D:AOF402 4.7 73.6 1.0 C D:PRO73 4.9 51.2 1.0 C D:CYS74 5.0 59.3 1.0 O D:CYS74 5.0 59.1 1.0

S.C.Chen, C.Y.Shen, T.M.Yen, H.C.Yu, T.H.Chang, W.L.Lai, S.H.Liaw. Evolution of Vitamin B(2) Biosynthesis: Eubacterial Ribg and Fungal RIB2 Deaminases. Acta Crystallogr.,Sect.D V. 69 227 2013.
ISSN: ISSN 0907-4449
PubMed: 23385458
DOI: 10.1107/S0907444912044903