Zinc in PDB 6ijm: Apo Structure of the N6-Methyl-Amp Deaminase From Arabidopsis Thaliana

The structure of Apo Structure of the N6-Methyl-Amp Deaminase From Arabidopsis Thaliana, PDB code: 6ijm was solved by W.Xie, Q.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.74 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.625, 79.862, 86.853, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.2

The binding sites of Zinc atom in the Apo Structure of the N6-Methyl-Amp Deaminase From Arabidopsis Thaliana (pdb code 6ijm). 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 Apo Structure of the N6-Methyl-Amp Deaminase From Arabidopsis Thaliana, PDB code: 6ijm:

Zinc binding site 1 out of 1 in the Apo Structure of the N6-Methyl-Amp Deaminase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Structure of the N6-Methyl-Amp Deaminase From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.2 occ:1.00 OD1 A:ASP295 2.1 20.4 1.0 NE2 A:HIS15 2.2 18.4 1.0 NE2 A:HIS217 2.2 17.2 1.0 NE2 A:HIS13 2.2 18.7 1.0 O A:HOH506 2.2 18.9 1.0 O A:HOH656 2.4 26.8 1.0 CD2 A:HIS15 3.0 21.4 1.0 CE1 A:HIS217 3.1 16.5 1.0 CG A:ASP295 3.1 22.1 1.0 CE1 A:HIS13 3.2 21.9 1.0 CD2 A:HIS217 3.2 18.5 1.0 CD2 A:HIS13 3.2 18.6 1.0 CE1 A:HIS15 3.2 14.9 1.0 OD2 A:ASP295 3.5 21.2 1.0 O A:HOH524 3.8 40.6 1.0 O A:HOH667 3.8 29.7 1.0 NE2 A:HIS240 3.9 36.0 1.0 CG A:HIS15 4.2 18.9 1.0 ND1 A:HIS217 4.2 19.3 1.0 ND1 A:HIS13 4.3 18.1 1.0 ND1 A:HIS15 4.3 21.2 1.0 CG A:HIS217 4.3 21.4 1.0 CG A:HIS13 4.3 16.1 1.0 CB A:ASP295 4.5 20.0 1.0 CE1 A:HIS240 4.5 33.9 1.0 CA A:ASP295 4.8 16.8 1.0 OD2 A:ASP296 4.9 31.0 1.0 CD2 A:HIS240 5.0 29.7 1.0

Q.Jia, W.Xie. Alternative Conformation Induced By Substrate Binding For Arabidopsis THALIANAN6-Methyl-Amp Deaminase. Nucleic Acids Res. V. 47 3233 2019.
ISSN: ESSN 1362-4962
PubMed: 30721978
DOI: 10.1093/NAR/GKZ070