Zinc in PDB 5xn8: Structure of Glycerol Dehydrogenase Crystallised As A Contaminant

The structure of Structure of Glycerol Dehydrogenase Crystallised As A Contaminant, PDB code: 5xn8 was solved by K.Hatti, Y.K.Mathiharan, N.Srinivasan, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.46 / 2.33
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	178.550, 178.550, 80.090, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 25.1

The binding sites of Zinc atom in the Structure of Glycerol Dehydrogenase Crystallised As A Contaminant (pdb code 5xn8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Glycerol Dehydrogenase Crystallised As A Contaminant, PDB code: 5xn8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Glycerol Dehydrogenase Crystallised As A Contaminant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Glycerol Dehydrogenase Crystallised As A Contaminant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:32.6 occ:1.00 OD1 A:ASP171 2.1 27.5 1.0 O A:HOH515 2.1 23.6 1.0 NE2 A:HIS254 2.2 19.8 1.0 NE2 A:HIS271 2.2 23.0 1.0 CG A:ASP171 2.9 28.9 1.0 CD2 A:HIS271 3.0 22.9 1.0 OD2 A:ASP171 3.0 33.4 1.0 CE1 A:HIS254 3.1 20.0 1.0 CD2 A:HIS254 3.2 20.5 1.0 CE1 A:HIS271 3.3 23.9 1.0 OD1 A:ASP121 3.7 31.1 1.0 ND1 A:HIS254 4.2 19.9 1.0 CG A:HIS271 4.2 23.3 1.0 CG2 A:VAL275 4.3 22.7 1.0 CG A:HIS254 4.3 20.2 1.0 ND1 A:HIS271 4.4 23.7 1.0 CB A:ASP171 4.4 29.0 1.0 CG A:ASP121 4.6 30.8 1.0 OG1 A:THR120 4.7 29.2 1.0 OD2 A:ASP121 4.7 32.0 1.0 O A:HOH501 5.0 9.0 1.0 CA A:ASP171 5.0 28.5 1.0

Zinc binding site 2 out of 4 in the Structure of Glycerol Dehydrogenase Crystallised As A Contaminant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Glycerol Dehydrogenase Crystallised As A Contaminant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:31.4 occ:1.00 OD1 B:ASP171 2.0 24.0 1.0 NE2 B:HIS254 2.4 24.8 1.0 NE2 B:HIS271 2.6 23.9 1.0 CG B:ASP171 2.8 23.6 1.0 OD2 B:ASP171 2.8 24.0 1.0 CD2 B:HIS271 3.2 23.3 1.0 CE1 B:HIS254 3.3 25.4 1.0 OD1 B:ASP121 3.3 30.6 1.0 CD2 B:HIS254 3.5 25.0 1.0 O B:HOH539 3.8 17.0 1.0 CE1 B:HIS271 3.8 24.4 1.0 O B:HOH511 4.0 8.6 1.0 CG B:ASP121 4.2 32.4 1.0 CB B:ASP171 4.2 23.1 1.0 OD2 B:ASP121 4.4 33.5 1.0 ND1 B:HIS254 4.5 25.2 1.0 CG B:HIS271 4.5 24.2 1.0 CG B:HIS254 4.6 25.2 1.0 CG2 B:VAL275 4.6 29.8 1.0 ND1 B:HIS271 4.8 24.2 1.0 O B:ASP171 4.9 23.5 1.0 CA B:ASP171 4.9 22.8 1.0

Zinc binding site 3 out of 4 in the Structure of Glycerol Dehydrogenase Crystallised As A Contaminant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Glycerol Dehydrogenase Crystallised As A Contaminant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:32.1 occ:1.00 NE2 C:HIS254 2.0 26.3 1.0 OD1 C:ASP171 2.0 30.8 1.0 NE2 C:HIS271 2.3 23.8 1.0 CE1 C:HIS254 2.9 28.7 1.0 CG C:ASP171 2.9 30.2 1.0 CD2 C:HIS271 3.1 23.9 1.0 OD2 C:ASP171 3.1 30.1 1.0 CD2 C:HIS254 3.1 27.5 1.0 CE1 C:HIS271 3.4 24.8 1.0 OD1 C:ASP121 3.8 22.6 1.0 ND1 C:HIS254 4.1 28.4 1.0 CG2 C:VAL275 4.2 24.0 1.0 CG C:HIS254 4.2 28.2 1.0 CG C:HIS271 4.3 23.9 1.0 CB C:ASP171 4.4 28.4 1.0 ND1 C:HIS271 4.4 24.4 1.0 CG C:ASP121 4.7 24.6 1.0 OD2 C:ASP121 4.8 23.1 1.0 O C:ASP171 4.9 28.9 1.0 CA C:ASP171 4.9 27.9 1.0

Zinc binding site 4 out of 4 in the Structure of Glycerol Dehydrogenase Crystallised As A Contaminant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Glycerol Dehydrogenase Crystallised As A Contaminant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:34.0 occ:1.00 OD1 D:ASP171 1.9 24.0 1.0 O D:HOH501 2.1 21.3 1.0 NE2 D:HIS271 2.3 26.4 1.0 NE2 D:HIS254 2.4 27.5 1.0 CG D:ASP171 2.7 24.0 1.0 OD2 D:ASP171 2.8 23.6 1.0 O D:HOH528 3.0 23.3 1.0 CD2 D:HIS271 3.0 26.2 1.0 CE1 D:HIS254 3.3 27.2 1.0 CD2 D:HIS254 3.4 27.8 1.0 CE1 D:HIS271 3.5 26.7 1.0 OD1 D:ASP121 3.6 31.2 1.0 O D:HOH523 4.1 16.0 1.0 CB D:ASP171 4.2 24.2 1.0 CG D:HIS271 4.3 26.6 1.0 CG2 D:VAL275 4.4 29.9 1.0 CG D:ASP121 4.4 33.8 1.0 ND1 D:HIS271 4.4 26.6 1.0 ND1 D:HIS254 4.5 27.6 1.0 CG D:HIS254 4.6 27.7 1.0 OD2 D:ASP121 4.6 34.1 1.0 CA D:ASP171 4.8 24.0 1.0 O D:ASP171 4.9 24.3 1.0

K.Hatti, Y.K.Mathiharan, N.Srinivasan, M.R.N.Murthy. Seeing But Not Believing: the Structure of Glycerol Dehydrogenase Initially Assumed to Be the Structure of A Survival Protein From Salmonella Typhimurium Acta Crystallogr.,Sect.D V. 73 609 2017.
ISSN: ISSN 0907-4449
DOI: 10.1107/S2059798317007677