Zinc in PDB 2d5n: Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis

All present enzymatic activity of Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis:
1.1.1.193; 3.5.4.26;

The structure of Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis, PDB code: 2d5n was solved by S.H.Liaw, S.J.Chen, Y.C.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.130, 107.952, 186.839, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27

The binding sites of Zinc atom in the Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis (pdb code 2d5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis, PDB code: 2d5n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Bifunctional Deaminase and Reductase Involved 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 Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1360 b:73.8 occ:1.00 SG A:CYS83 2.0 50.9 1.0 SG A:CYS74 2.5 56.3 1.0 CB A:CYS74 2.5 48.9 1.0 CD2 A:HIS49 2.5 56.3 1.0 CG A:HIS49 3.1 56.8 1.0 N A:CYS74 3.3 51.0 1.0 NE2 A:HIS49 3.3 57.8 1.0 CB A:CYS83 3.3 52.5 1.0 OE2 A:GLU51 3.3 49.5 1.0 CA A:CYS74 3.5 51.4 1.0 CB A:HIS49 3.5 57.4 1.0 CD A:GLU51 3.9 48.7 1.0 ND1 A:HIS49 4.0 58.7 1.0 OE1 A:GLU51 4.1 48.1 1.0 CE1 A:HIS49 4.1 57.3 1.0 C A:PRO73 4.5 48.3 1.0 N A:CYS83 4.6 53.2 1.0 CA A:CYS83 4.6 53.1 1.0 C A:CYS74 4.7 51.9 1.0 O A:CYS74 4.8 53.2 1.0 CA A:PRO73 4.8 47.1 1.0 CA A:HIS49 5.0 56.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Bifunctional Deaminase and Reductase Involved 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 Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1360 b:63.4 occ:1.00 SG B:CYS83 2.0 75.6 1.0 ND1 B:HIS49 2.1 59.5 1.0 CB B:CYS74 2.7 79.1 1.0 SG B:CYS74 2.7 85.5 1.0 OE1 B:GLU51 2.8 67.2 1.0 CG B:HIS49 3.0 59.9 1.0 CE1 B:HIS49 3.0 59.5 1.0 CB B:CYS83 3.3 78.9 1.0 CB B:HIS49 3.3 59.9 1.0 N B:CYS74 3.6 76.1 1.0 CA B:CYS74 3.8 78.7 1.0 CD B:GLU51 3.9 64.4 1.0 CD2 B:HIS49 4.0 59.4 1.0 NE2 B:HIS49 4.0 59.6 1.0 OE2 B:GLU51 4.3 66.5 1.0 O B:HOH1400 4.3 47.3 1.0 CA B:CYS83 4.6 80.2 1.0 N B:CYS83 4.6 82.7 1.0 CA B:HIS49 4.8 59.1 1.0 C B:PRO73 4.9 73.2 1.0 C B:CYS74 4.9 79.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Bifunctional Deaminase and Reductase Involved 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 Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1360 b:92.2 occ:1.00 SG C:CYS83 2.3 93.0 1.0 ND1 C:HIS49 2.5 83.5 1.0 OE2 C:GLU51 2.5 76.2 1.0 CB C:CYS74 2.6 90.5 1.0 OE1 C:GLU51 3.0 76.9 1.0 SG C:CYS74 3.0 93.5 1.0 N C:CYS74 3.0 86.5 1.0 CD C:GLU51 3.1 78.1 1.0 CB C:CYS83 3.2 97.3 1.0 CG C:HIS49 3.2 83.6 1.0 CB C:HIS49 3.3 80.9 1.0 CA C:CYS74 3.4 90.2 1.0 CE1 C:HIS49 3.5 84.4 1.0 C C:PRO73 4.2 84.3 1.0 CD2 C:HIS49 4.3 83.9 1.0 NE2 C:HIS49 4.4 83.9 1.0 CG C:GLU51 4.6 79.1 1.0 C C:CYS74 4.6 92.5 1.0 CA C:PRO73 4.6 83.3 1.0 CA C:CYS83 4.6 99.0 1.0 CA C:HIS49 4.8 79.4 1.0 O C:CYS74 4.9 92.7 1.0 N C:CYS83 5.0 0.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Bifunctional Deaminase and Reductase Involved 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 Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1360 b:78.6 occ:1.00 SG D:CYS74 2.0 49.6 1.0 SG D:CYS83 2.2 59.1 1.0 ND1 D:HIS49 2.6 51.7 1.0 CB D:CYS83 2.8 54.6 1.0 CB D:HIS49 3.1 52.8 1.0 CG D:HIS49 3.1 53.5 1.0 OE2 D:GLU51 3.4 51.3 1.0 OE1 D:GLU51 3.6 48.3 1.0 CD D:GLU51 3.6 50.3 1.0 CE1 D:HIS49 3.6 53.3 1.0 N D:CYS74 3.7 56.6 1.0 CB D:CYS74 3.7 53.4 1.0 CA D:CYS83 4.2 56.9 1.0 CD2 D:HIS49 4.3 54.1 1.0 CA D:CYS74 4.3 57.1 1.0 NE2 D:HIS49 4.5 55.0 1.0 N D:CYS83 4.5 59.1 1.0 CA D:HIS49 4.6 52.0 1.0 CG D:GLU51 4.6 48.7 1.0 C D:PRO73 4.7 55.5 1.0 CB D:GLU51 4.7 48.8 1.0 CA D:PRO73 4.7 53.9 1.0

S.J.Chen, Y.C.Chang, S.H.Liaw. Crystal Structure of A Bifunctional Deaminase and Reductase Involved in Riboflavin Biosynthesis To Be Published.