Zinc in PDB 7drz: Crystal Structure of Aspergillus Oryzae RIB2 Deaminase (C-Terminal Deletion Mutant) at pH 4.6

Protein crystallography data

The structure of Crystal Structure of Aspergillus Oryzae RIB2 Deaminase (C-Terminal Deletion Mutant) at pH 4.6, PDB code: 7drz 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) 25.12 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.093, 87.093, 61.215, 90, 90, 90
R / Rfree (%) 19.5 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aspergillus Oryzae RIB2 Deaminase (C-Terminal Deletion Mutant) at pH 4.6 (pdb code 7drz). 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 (C-Terminal Deletion Mutant) at pH 4.6, PDB code: 7drz:

Zinc binding site 1 out of 1 in 7drz

Go back to Zinc Binding Sites List in 7drz
Zinc binding site 1 out of 1 in the Crystal Structure of Aspergillus Oryzae RIB2 Deaminase (C-Terminal Deletion Mutant) at pH 4.6


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 (C-Terminal Deletion Mutant) at pH 4.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:12.6
occ:1.00
ND1 A:HIS61 2.0 9.6 1.0
SG A:CYS112 2.3 11.3 1.0
SG A:CYS102 2.3 12.5 1.0
CE1 A:HIS61 2.9 13.2 1.0
CG A:HIS61 3.1 11.2 1.0
CB A:CYS112 3.2 11.5 1.0
CB A:CYS102 3.4 14.1 1.0
CB A:HIS61 3.5 11.2 1.0
N A:CYS102 3.8 12.9 1.0
O A:HOH424 3.9 15.1 1.0
N A:CYS112 3.9 11.7 1.0
NE2 A:HIS61 4.0 13.2 1.0
CD2 A:HIS61 4.2 11.2 1.0
CA A:CYS112 4.2 11.0 1.0
CA A:CYS102 4.2 13.0 1.0
OE1 A:GLU63 4.4 10.4 1.0
O A:HOH463 4.4 22.4 1.0
CD A:ARG105 4.7 27.1 1.0
CD A:GLU63 4.8 14.5 1.0
O A:CYS102 4.8 14.2 1.0
O A:HOH479 4.9 14.1 1.0
C A:PRO101 4.9 13.7 1.0
C A:CYS102 4.9 16.2 1.0
OE2 A:GLU63 4.9 15.7 1.0
CG2 A:THR139 5.0 16.3 1.0
O A:HOH407 5.0 14.4 1.0

Reference:

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
Page generated: Sat Aug 21 18:01:25 2021

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