Zinc in PDB 6iv5: Crystal Structure of Arabidopsis N6-Mamp Deaminase Mapda

The structure of Crystal Structure of Arabidopsis N6-Mamp Deaminase Mapda, PDB code: 6iv5 was solved by B.X.Wu, D.Zhang, H.B.Nie, S.L.Shen, S.S.Li, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.904, 82.352, 86.686, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.8

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis N6-Mamp Deaminase Mapda (pdb code 6iv5). 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 Arabidopsis N6-Mamp Deaminase Mapda, PDB code: 6iv5:

Zinc binding site 1 out of 1 in the Crystal Structure of Arabidopsis N6-Mamp Deaminase Mapda


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 Arabidopsis N6-Mamp Deaminase Mapda within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:21.3 occ:1.00 NE2 A:HIS15 2.0 20.4 1.0 NE2 A:HIS13 2.0 16.3 1.0 O A:HOH530 2.0 24.1 1.0 NE2 A:HIS217 2.1 20.5 1.0 OD1 A:ASP295 2.3 19.2 1.0 CE1 A:HIS13 3.0 20.0 1.0 CD2 A:HIS15 3.0 21.8 1.0 CE1 A:HIS15 3.0 21.2 1.0 CE1 A:HIS217 3.1 24.9 1.0 CD2 A:HIS13 3.1 18.6 1.0 CD2 A:HIS217 3.2 22.2 1.0 CG A:ASP295 3.3 21.4 1.0 OD2 A:ASP295 3.7 24.3 1.0 O A:HOH542 3.7 34.6 1.0 NE2 A:HIS240 3.8 27.8 1.0 O A:HOH614 4.1 31.3 1.0 ND1 A:HIS13 4.1 19.3 1.0 ND1 A:HIS15 4.1 18.7 1.0 CG A:HIS15 4.2 18.4 1.0 CG A:HIS13 4.2 18.1 1.0 ND1 A:HIS217 4.2 24.0 1.0 CG A:HIS217 4.3 21.7 1.0 CB A:ASP295 4.6 19.6 1.0 CE1 A:HIS240 4.6 26.1 1.0 CD2 A:HIS240 4.8 27.1 1.0 OD2 A:ASP296 4.9 25.1 1.0 CA A:ASP295 4.9 18.2 1.0 NH1 A:ARG96 4.9 17.6 1.0

B.Wu, D.Zhang, H.Nie, S.Shen, Y.Li, S.Li. Structure Ofarabidopsis Thaliana N6-Methyl-Amp Deaminase Adal with Bound Gmp and Imp and Implications FORN6-Methyl-Amp Recognition and Processing. Rna Biol. V. 16 1504 2019.
ISSN: ESSN 1555-8584
PubMed: 31318636
DOI: 10.1080/15476286.2019.1642712