Manganese in PDB 4lt5: Structure of A Naegleria Tet-Like Dioxygenase in Complex with 5- Methylcytosine Dna

The structure of Structure of A Naegleria Tet-Like Dioxygenase in Complex with 5- Methylcytosine Dna, PDB code: 4lt5 was solved by H.Hashimoto, J.E.Pais, X.Zhang, L.Saleh, Z.Q.Fu, N.Dai, I.R.Correa, R.J.Roberts, Y.Zheng, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.55 / 2.89
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.954, 108.648, 166.384, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.5

The binding sites of Manganese atom in the Structure of A Naegleria Tet-Like Dioxygenase in Complex with 5- Methylcytosine Dna (pdb code 4lt5). 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 Structure of A Naegleria Tet-Like Dioxygenase in Complex with 5- Methylcytosine Dna, PDB code: 4lt5:

Manganese binding site 1 out of 1 in the Structure of A Naegleria Tet-Like Dioxygenase in Complex with 5- Methylcytosine Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Naegleria Tet-Like Dioxygenase in Complex with 5- Methylcytosine Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:31.9 occ:1.00 O2 A:OGA413 2.1 53.4 1.0 OD2 A:ASP231 2.2 31.3 1.0 O2' A:OGA413 2.2 42.8 1.0 NE2 A:HIS279 2.2 36.8 1.0 NE2 A:HIS229 2.2 49.7 1.0 O A:HOH414 2.4 67.6 0.5 C1 A:OGA413 2.8 40.9 1.0 C2 A:OGA413 2.8 37.9 1.0 CE1 A:HIS279 3.1 39.7 1.0 CG A:ASP231 3.2 40.8 1.0 CD2 A:HIS229 3.2 53.5 1.0 CE1 A:HIS229 3.2 40.6 1.0 CD2 A:HIS279 3.2 39.3 1.0 OD1 A:ASP231 3.5 36.3 1.0 O A:HOH414 3.6 55.4 0.5 O1 A:OGA413 4.1 42.3 1.0 N1 A:OGA413 4.1 38.5 1.0 ND1 A:HIS279 4.2 40.9 1.0 NH2 A:ARG224 4.2 37.7 1.0 ND1 A:HIS229 4.3 39.6 1.0 CG A:HIS229 4.3 44.9 1.0 CG A:HIS279 4.3 41.5 1.0 CB A:ASP231 4.5 46.7 1.0 NH1 A:ARG224 4.7 34.2 1.0 N A:ASP231 4.8 40.7 1.0 C4 A:OGA413 4.9 32.8 1.0 CZ A:ARG224 5.0 34.4 1.0

H.Hashimoto, J.E.Pais, X.Zhang, L.Saleh, Z.Q.Fu, N.Dai, I.R.Correa, Y.Zheng, X.Cheng. Structure of A Naegleria Tet-Like Dioxygenase in Complex with 5-Methylcytosine Dna. Nature V. 506 391 2014.
ISSN: ISSN 0028-0836
PubMed: 24390346
DOI: 10.1038/NATURE12905