Zinc in PDB 7ds1: Crystal Structure of Aspergillus Oryzae RIB2 Deaminase in Complex with Daripp (C-Terminal Deletion Mutant at pH 6.5)

The structure of Crystal Structure of Aspergillus Oryzae RIB2 Deaminase in Complex with Daripp (C-Terminal Deletion Mutant at pH 6.5), PDB code: 7ds1 was solved by S.C.Chen, S.H.Liaw, C.H.Hsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.54 / 1.58
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.32, 90.778, 40.833, 90, 90, 90
R / Rfree (%)	18.3 / 20.8

The binding sites of Zinc atom in the Crystal Structure of Aspergillus Oryzae RIB2 Deaminase in Complex with Daripp (C-Terminal Deletion Mutant at pH 6.5) (pdb code 7ds1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Aspergillus Oryzae RIB2 Deaminase in Complex with Daripp (C-Terminal Deletion Mutant at pH 6.5), PDB code: 7ds1:

Zinc binding site 1 out of 1 in the Crystal Structure of Aspergillus Oryzae RIB2 Deaminase in Complex with Daripp (C-Terminal Deletion Mutant at pH 6.5)


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 Aspergillus Oryzae RIB2 Deaminase in Complex with Daripp (C-Terminal Deletion Mutant at pH 6.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:10.2 occ:1.00 ND1 A:HIS61 2.0 10.2 1.0 O A:HOH304 2.2 12.3 1.0 SG A:CYS102 2.3 9.2 1.0 SG A:CYS112 2.3 10.6 1.0 CE1 A:HIS61 2.9 11.1 1.0 CB A:CYS112 3.1 9.8 1.0 CG A:HIS61 3.1 10.4 1.0 CB A:CYS102 3.4 9.9 1.0 CB A:HIS61 3.5 9.7 1.0 N A:CYS112 3.8 8.8 1.0 N A:CYS102 3.8 10.8 1.0 O A:HOH319 3.9 11.9 1.0 OE2 A:GLU63 3.9 11.8 1.0 CA A:CYS112 4.0 8.9 1.0 NE2 A:HIS61 4.1 11.8 1.0 C2 A:HJL202 4.1 19.1 1.0 N1 A:HJL202 4.2 19.8 1.0 CD2 A:HIS61 4.2 11.4 1.0 CA A:CYS102 4.2 9.6 1.0 OE1 A:GLU63 4.2 9.9 1.0 N3 A:HJL202 4.3 17.8 1.0 CD A:GLU63 4.3 9.7 1.0 N2 A:HJL202 4.5 17.7 1.0 C6 A:HJL202 4.5 19.7 1.0 CD A:ARG105 4.5 11.7 1.0 C4 A:HJL202 4.6 19.0 1.0 C5 A:HJL202 4.7 17.0 1.0 CG A:ARG105 4.8 11.4 1.0 O A:HOH346 4.8 20.9 1.0 O A:CYS102 4.8 10.0 1.0 C A:PRO111 4.9 10.5 1.0 C A:PRO101 4.9 10.4 1.0 C A:CYS102 5.0 9.5 1.0

S.C.Chen, L.C.Ye, T.M.Yen, R.X.Zhu, C.Y.Li, S.C.Chang, S.H.Liaw, C.H.Hsu. Crystal Structures of Aspergillus Oryzae RIB2 Deaminase: the Functional Mechanism Involved in Riboflavin Biosynthesis. Iucrj V. 8 549 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S205225252100275X