Manganese in PDB 5cg8: NGTET1 in Complex with 5HMC Dna

The structure of NGTET1 in Complex with 5HMC Dna, PDB code: 5cg8 was solved by H.Hashimoto, J.E.Pais, N.Dai, X.Zhang, Y.Zheng, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.55 / 2.70
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.802, 107.360, 167.671, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23

The binding sites of Manganese atom in the NGTET1 in Complex with 5HMC Dna (pdb code 5cg8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the NGTET1 in Complex with 5HMC Dna, PDB code: 5cg8:

Manganese binding site 1 out of 1 in the NGTET1 in Complex with 5HMC Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of NGTET1 in Complex with 5HMC Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:69.8 occ:1.00 O2 A:AKG401 1.9 78.3 1.0 NE2 A:HIS279 2.1 69.5 1.0 OD2 A:ASP231 2.2 71.9 1.0 O A:HOH501 2.2 0.6 1.0 NE2 A:HIS229 2.2 95.1 1.0 O5 A:AKG401 2.3 85.0 1.0 C1 A:AKG401 2.7 81.7 1.0 C2 A:AKG401 2.8 83.0 1.0 CE1 A:HIS279 2.9 75.3 1.0 CG A:ASP231 3.0 85.6 1.0 CE1 A:HIS229 3.1 87.0 1.0 CD2 A:HIS229 3.2 87.4 1.0 OD1 A:ASP231 3.2 97.8 1.0 CD2 A:HIS279 3.3 80.6 1.0 O1 A:AKG401 3.8 82.1 1.0 ND1 A:HIS279 4.1 77.0 1.0 NH2 A:ARG224 4.1 74.1 1.0 ND1 A:HIS229 4.2 79.7 1.0 O5 C:5HC20 4.2 78.8 1.0 C3 A:AKG401 4.3 73.5 1.0 CG A:HIS229 4.3 93.4 1.0 CG A:HIS279 4.3 80.0 1.0 CB A:ASP231 4.5 88.8 1.0 N A:ASP231 4.8 83.6 1.0 NH1 A:ARG224 4.8 79.3 1.0 CZ A:ARG224 4.9 77.9 1.0 C4 A:AKG401 4.9 71.9 1.0

H.Hashimoto, J.E.Pais, N.Dai, I.R.Correa, X.Zhang, Y.Zheng, X.Cheng. Structure of Naegleria Tet-Like Dioxygenase (NGTET1) in Complexes with A Reaction Intermediate 5-Hydroxymethylcytosine Dna. Nucleic Acids Res. V. 43 10713 2015.
ISSN: ESSN 1362-4962
PubMed: 26323320
DOI: 10.1093/NAR/GKV870