Zinc in PDB 6sch: Nadh-Dependent Variant of Cbadh

All present enzymatic activity of Nadh-Dependent Variant of Cbadh:
1.1.1.80;

The structure of Nadh-Dependent Variant of Cbadh, PDB code: 6sch was solved by L.Selles Vidal, J.W.Murray, J.T.Heap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.01 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.812, 99.570, 114.089, 90.00, 102.77, 90.00
R / Rfree (%)	16.4 / 20.8

The structure of Nadh-Dependent Variant of Cbadh also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Nadh-Dependent Variant of Cbadh (pdb code 6sch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Nadh-Dependent Variant of Cbadh, PDB code: 6sch:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Nadh-Dependent Variant of Cbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nadh-Dependent Variant of Cbadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:40.1 occ:1.00 OD2 A:ASP150 2.0 47.7 1.0 NE2 A:HIS59 2.0 41.8 1.0 SG A:CYS37 2.4 38.9 1.0 N7N A:NAD401 2.6 45.1 0.8 CE1 A:HIS59 3.0 38.1 1.0 C4N A:NAD401 3.0 88.1 0.8 CG A:ASP150 3.1 37.7 1.0 CD2 A:HIS59 3.1 36.6 1.0 CB A:CYS37 3.2 36.9 1.0 C3N A:NAD401 3.3 82.5 0.8 C7N A:NAD401 3.4 62.8 0.8 OG A:SER39 3.4 50.0 1.0 OD1 A:ASP150 3.5 40.3 1.0 C5N A:NAD401 3.7 87.5 0.8 ND1 A:HIS59 4.1 38.1 1.0 OE2 A:GLU60 4.1 45.5 1.0 CG A:HIS59 4.2 34.5 1.0 CB A:SER39 4.3 45.2 1.0 CB A:ASP150 4.3 31.1 1.0 C2N A:NAD401 4.3 84.6 0.8 CE A:MET151 4.5 32.5 1.0 O7N A:NAD401 4.5 65.3 0.8 CD A:GLU60 4.6 46.7 1.0 C6N A:NAD401 4.6 86.7 0.8 CA A:CYS37 4.7 32.0 1.0 CG A:GLU60 4.8 37.5 1.0 N1N A:NAD401 4.8 86.2 0.8

Zinc binding site 2 out of 4 in the Nadh-Dependent Variant of Cbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nadh-Dependent Variant of Cbadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:45.6 occ:1.00 OD2 B:ASP150 2.0 47.4 1.0 NE2 B:HIS59 2.1 45.9 1.0 SG B:CYS37 2.4 42.5 1.0 O7N B:NAD401 2.5 67.5 0.8 CE1 B:HIS59 2.8 41.9 1.0 CG B:ASP150 3.0 34.8 1.0 CD2 B:HIS59 3.2 39.4 1.0 CB B:CYS37 3.2 40.5 1.0 C7N B:NAD401 3.3 71.3 0.8 OD1 B:ASP150 3.3 36.5 1.0 C3N B:NAD401 3.4 92.0 0.8 C4N B:NAD401 3.4 98.0 0.8 OG B:SER39 3.5 46.2 1.0 OE2 B:GLU60 4.0 57.4 1.0 ND1 B:HIS59 4.0 39.8 1.0 C2N B:NAD401 4.2 0.0 0.8 CG B:HIS59 4.2 40.5 1.0 C5N B:NAD401 4.2 99.6 0.8 CB B:SER39 4.3 39.7 1.0 CB B:ASP150 4.3 30.3 1.0 CE B:MET151 4.4 39.4 1.0 CD B:GLU60 4.5 52.2 1.0 N7N B:NAD401 4.5 62.4 0.8 CA B:CYS37 4.7 42.4 1.0 CG B:GLU60 4.8 40.0 1.0 N1N B:NAD401 4.9 0.4 0.8 C6N B:NAD401 4.9 99.8 0.8 O B:HOH536 5.0 39.4 1.0

Zinc binding site 3 out of 4 in the Nadh-Dependent Variant of Cbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nadh-Dependent Variant of Cbadh within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:48.8 occ:1.00 OD2 C:ASP150 1.9 50.4 1.0 NE2 C:HIS59 2.0 48.7 1.0 SG C:CYS37 2.5 44.3 1.0 CE1 C:HIS59 2.9 45.6 1.0 CG C:ASP150 3.0 39.1 1.0 CD2 C:HIS59 3.1 33.4 1.0 CB C:CYS37 3.1 35.5 1.0 OD1 C:ASP150 3.4 36.5 1.0 C4N C:NAD401 3.4 88.1 0.8 C7N C:NAD401 3.7 63.5 0.8 C3N C:NAD401 3.7 84.9 0.8 O7N C:NAD401 3.8 58.7 0.8 OG C:SER39 3.8 51.1 1.0 OE2 C:GLU60 3.9 55.1 1.0 ND1 C:HIS59 4.1 41.1 1.0 CG C:HIS59 4.2 34.5 1.0 C5N C:NAD401 4.2 88.2 0.8 N7N C:NAD401 4.2 51.5 0.8 CB C:ASP150 4.2 30.8 1.0 CD C:GLU60 4.5 45.4 1.0 CE C:MET151 4.5 31.3 1.0 C2N C:NAD401 4.6 89.6 0.8 CA C:CYS37 4.6 37.8 1.0 CB C:SER39 4.7 49.2 1.0 CG C:GLU60 4.8 38.2 1.0 C6N C:NAD401 5.0 89.4 0.8

Zinc binding site 4 out of 4 in the Nadh-Dependent Variant of Cbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nadh-Dependent Variant of Cbadh within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn404 b:44.3 occ:1.00 OD2 D:ASP150 1.9 45.2 1.0 NE2 D:HIS59 2.0 46.6 1.0 SG D:CYS37 2.4 39.5 1.0 CE1 D:HIS59 2.9 40.2 1.0 CG D:ASP150 3.0 34.8 1.0 CD2 D:HIS59 3.1 39.2 1.0 O7N D:NAD401 3.2 57.0 0.8 CB D:CYS37 3.2 30.9 1.0 C4N D:NAD401 3.3 85.6 0.8 OD1 D:ASP150 3.4 41.7 1.0 C3N D:NAD401 3.5 82.1 0.8 OG D:SER39 3.5 49.3 1.0 C7N D:NAD401 3.5 64.4 0.8 C5N D:NAD401 4.0 87.3 0.8 ND1 D:HIS59 4.1 40.9 1.0 OE2 D:GLU60 4.1 51.8 1.0 CG D:HIS59 4.2 39.3 1.0 CB D:ASP150 4.2 31.6 1.0 C2N D:NAD401 4.3 87.2 0.8 CB D:SER39 4.3 43.6 1.0 CE D:MET151 4.4 48.2 1.0 N7N D:NAD401 4.5 61.3 0.8 CD D:GLU60 4.6 47.4 1.0 CA D:CYS37 4.7 35.2 1.0 C6N D:NAD401 4.7 85.6 0.8 CG D:GLU60 4.7 38.2 1.0 N1N D:NAD401 4.8 83.9 0.8

L.Selles Vidal, J.W.Murray, J.T.Heap. Nadh-Dependent Variant of Cbadh To Be Published.