Manganese in PDB 5cg9: NGTET1 in Complex with 5MC Dna in Space Group P3221

The structure of NGTET1 in Complex with 5MC Dna in Space Group P3221, PDB code: 5cg9 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)	29.74 / 2.69
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	191.216, 191.216, 51.254, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.2

The binding sites of Manganese atom in the NGTET1 in Complex with 5MC Dna in Space Group P3221 (pdb code 5cg9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the NGTET1 in Complex with 5MC Dna in Space Group P3221, PDB code: 5cg9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the NGTET1 in Complex with 5MC Dna in Space Group P3221


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 5MC Dna in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:54.4 occ:1.00 O2 A:AKG402 2.1 54.3 1.0 NE2 A:HIS229 2.1 58.8 1.0 OD2 A:ASP231 2.2 51.1 1.0 O A:HOH501 2.2 72.7 1.0 O5 A:AKG402 2.2 73.7 1.0 NE2 A:HIS279 2.2 60.5 1.0 C2 A:AKG402 2.8 65.1 1.0 C1 A:AKG402 2.9 70.1 1.0 CE1 A:HIS229 3.0 51.1 1.0 CG A:ASP231 3.1 68.9 1.0 CD2 A:HIS229 3.1 56.6 1.0 CD2 A:HIS279 3.2 54.3 1.0 CE1 A:HIS279 3.2 64.6 1.0 OD1 A:ASP231 3.3 58.4 1.0 O1 A:AKG402 4.1 53.2 1.0 ND1 A:HIS229 4.1 51.5 1.0 CG A:HIS229 4.2 68.8 1.0 NH2 A:ARG224 4.3 59.3 1.0 C3 A:AKG402 4.3 51.6 1.0 ND1 A:HIS279 4.3 54.0 1.0 CG A:HIS279 4.3 52.3 1.0 CB A:ASP231 4.4 55.3 1.0 NH1 A:ARG224 4.6 55.3 1.0 N A:ASP231 4.8 58.5 1.0 CZ A:ARG224 4.9 55.2 1.0 C4 A:AKG402 4.9 46.6 1.0

Manganese binding site 2 out of 2 in the NGTET1 in Complex with 5MC Dna in Space Group P3221


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of NGTET1 in Complex with 5MC Dna in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn405 b:66.1 occ:1.00 O2 D:AKG404 1.9 57.9 1.0 OD2 D:ASP231 2.2 74.8 1.0 NE2 D:HIS279 2.2 69.3 1.0 O D:HOH501 2.2 85.3 1.0 O5 D:AKG404 2.2 66.0 1.0 NE2 D:HIS229 2.3 80.9 1.0 C1 D:AKG404 2.7 58.0 1.0 C2 D:AKG404 2.8 64.9 1.0 CD2 D:HIS279 3.0 67.6 1.0 CG D:ASP231 3.1 79.7 1.0 CD2 D:HIS229 3.2 78.6 1.0 CE1 D:HIS229 3.2 77.5 1.0 CE1 D:HIS279 3.3 77.0 1.0 OD1 D:ASP231 3.4 69.6 1.0 O1 D:AKG404 3.9 61.5 1.0 NH2 D:ARG224 4.2 69.5 1.0 CG D:HIS279 4.2 64.8 1.0 ND1 D:HIS229 4.3 77.2 1.0 C3 D:AKG404 4.3 61.4 1.0 CG D:HIS229 4.3 79.5 1.0 ND1 D:HIS279 4.3 60.4 1.0 CB D:ASP231 4.5 77.5 1.0 NH1 D:ARG224 4.8 66.8 1.0 C4 D:AKG404 4.9 56.7 1.0 CZ D:ARG224 4.9 73.1 1.0 O D:HOH502 4.9 49.5 1.0 N D:ASP231 5.0 74.4 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