Zinc in PDB 6jko: Crystal Structure of Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense

The structure of Crystal Structure of Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense, PDB code: 6jko was solved by Y.Zhou, T.Xu, L.Lin, Y.Zhang, Z.Yuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.30 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.468, 112.502, 93.406, 90.00, 107.33, 90.00
R / Rfree (%)	15.7 / 19.3

The binding sites of Zinc atom in the Crystal Structure of Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense (pdb code 6jko). 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 Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense, PDB code: 6jko:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense


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 Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.7 occ:0.47 NE2 A:HIS275 2.1 27.2 1.0 OD1 A:ASP192 2.2 27.5 1.0 NE2 A:HIS261 2.2 30.0 1.0 O A:HOH702 2.4 43.7 1.0 CD2 A:HIS275 2.9 21.6 1.0 O A:HOH582 2.9 33.8 1.0 CE1 A:HIS261 3.1 25.9 1.0 CE1 A:HIS275 3.1 24.8 1.0 CG A:ASP192 3.2 25.6 1.0 NE2 A:GLN196 3.2 37.7 1.0 CD2 A:HIS261 3.2 27.3 1.0 OD2 A:ASP192 3.5 29.4 1.0 CG A:GLN196 3.9 24.5 1.0 CD A:GLN196 3.9 37.1 1.0 CG A:HIS275 4.1 21.8 1.0 ND1 A:HIS275 4.2 20.6 1.0 ND1 A:HIS261 4.3 23.4 1.0 CG A:HIS261 4.3 26.9 1.0 SG A:CYS279 4.4 19.6 1.0 CB A:ASP192 4.5 14.8 1.0 O A:ASP192 4.8 12.3 1.0 CA A:ASP192 4.9 15.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense


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 Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:21.8 occ:0.48 NE2 B:HIS261 2.1 24.1 1.0 NE2 B:HIS275 2.2 21.3 1.0 OD1 B:ASP192 2.2 27.5 1.0 CD2 B:HIS261 2.9 24.9 1.0 CD2 B:HIS275 3.1 22.4 1.0 CG B:ASP192 3.1 25.7 1.0 CE1 B:HIS261 3.2 23.4 1.0 OD2 B:ASP192 3.3 30.4 1.0 CE1 B:HIS275 3.3 25.9 1.0 NE2 B:GLN196 3.4 38.1 1.0 CG B:GLN196 4.1 24.9 1.0 CG B:HIS261 4.1 24.6 1.0 ND1 B:HIS261 4.2 24.3 1.0 CD B:GLN196 4.2 35.7 1.0 CG B:HIS275 4.3 20.9 1.0 SG B:CYS279 4.3 18.7 1.0 ND1 B:HIS275 4.3 22.7 1.0 CB B:ASP192 4.5 13.6 1.0 O B:ASP192 4.8 13.8 1.0 CA B:ASP192 4.9 15.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense


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 Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:25.2 occ:0.48 OD1 C:ASP192 2.2 26.6 1.0 NE2 C:HIS261 2.2 24.8 1.0 NE2 C:HIS275 2.3 23.3 1.0 O C:HOH509 2.7 37.3 1.0 CD2 C:HIS275 2.9 21.2 1.0 CG C:ASP192 3.1 25.1 1.0 NE2 C:GLN196 3.1 37.5 1.0 CD2 C:HIS261 3.1 23.3 1.0 CE1 C:HIS261 3.3 24.4 1.0 OD2 C:ASP192 3.3 23.2 1.0 CE1 C:HIS275 3.5 24.2 1.0 CG C:GLN196 3.9 26.1 1.0 CD C:GLN196 4.0 33.0 1.0 CG C:HIS275 4.2 20.1 1.0 CG C:HIS261 4.3 23.9 1.0 ND1 C:HIS261 4.3 24.6 1.0 ND1 C:HIS275 4.4 22.8 1.0 SG C:CYS279 4.5 18.4 1.0 CB C:ASP192 4.5 15.1 1.0 O C:ASP192 4.7 11.8 1.0 O C:HOH732 4.8 37.3 1.0 CA C:ASP192 4.9 14.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense


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 Sulfoacetaldehyde Reductase From Bifidobacterium Kashiwanohense within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:29.8 occ:0.46 NE2 D:HIS275 2.2 22.8 1.0 OD1 D:ASP192 2.2 29.4 1.0 NE2 D:HIS261 2.2 31.7 1.0 O D:HOH557 2.8 34.3 1.0 CD2 D:HIS275 3.0 22.5 1.0 CG D:ASP192 3.0 25.3 1.0 CD2 D:HIS261 3.2 22.8 1.0 OD2 D:ASP192 3.2 28.8 1.0 CE1 D:HIS261 3.2 28.3 1.0 CE1 D:HIS275 3.3 26.7 1.0 NE2 D:GLN196 3.8 36.8 1.0 CG D:GLN196 4.2 25.3 1.0 CG D:HIS275 4.2 22.5 1.0 ND1 D:HIS261 4.3 32.5 1.0 CG D:HIS261 4.3 28.5 1.0 ND1 D:HIS275 4.3 25.5 1.0 SG D:CYS279 4.3 21.0 1.0 CD D:GLN196 4.4 36.0 1.0 CB D:ASP192 4.4 14.9 1.0 O D:ASP192 4.8 14.7 1.0 CA D:ASP192 4.8 14.4 1.0

Y.Zhou, Y.Wei, A.N.Nanjaraj Urs, L.Lin, T.Xu, Y.Hu, E.L.Ang, H.Zhao, Z.Yuchi, Y.Zhang. Identification and Characterization of A New Sulfoacetaldehyde Reductase From the Human Gut Bacteriumbifidobacterium Kashiwanohense. Biosci.Rep. V. 39 2019.
ISSN: ISSN 0144-8463
PubMed: 31123167
DOI: 10.1042/BSR20190715