Manganese in PDB 4gpu: Crystal Structure of K. Lactis DXO1 (YDR370C) in Complex with Manganese

The structure of Crystal Structure of K. Lactis DXO1 (YDR370C) in Complex with Manganese, PDB code: 4gpu was solved by J.H.Chang, K.Chiba, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 2.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.130, 82.130, 260.730, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 25.7

The binding sites of Manganese atom in the Crystal Structure of K. Lactis DXO1 (YDR370C) in Complex with Manganese (pdb code 4gpu). 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 Crystal Structure of K. Lactis DXO1 (YDR370C) in Complex with Manganese, PDB code: 4gpu:

Manganese binding site 1 out of 1 in the Crystal Structure of K. Lactis DXO1 (YDR370C) in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of K. Lactis DXO1 (YDR370C) in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:74.2 occ:1.00 O A:ILE274 2.2 65.7 1.0 OE2 A:GLU273 2.4 89.3 1.0 OD2 A:ASP262 2.4 75.6 1.0 O A:HOH601 2.9 66.4 1.0 OE1 A:GLU223 3.0 0.9 1.0 O A:HOH633 3.1 55.8 1.0 CG A:ASP262 3.4 77.3 1.0 C A:ILE274 3.4 65.6 1.0 CD A:GLU273 3.5 89.8 1.0 OD1 A:ASP262 3.6 87.2 1.0 O A:HOH602 3.7 58.6 1.0 NZ A:LYS275 3.8 60.2 1.0 N A:ILE274 4.0 64.3 1.0 CD A:GLU223 4.1 0.2 1.0 CA A:ILE274 4.2 66.0 1.0 OE1 A:GLU273 4.3 95.7 1.0 CB A:ILE274 4.5 63.8 1.0 N A:LYS275 4.5 62.4 1.0 CG A:GLU273 4.5 82.5 1.0 CE A:LYS275 4.5 62.5 1.0 CD A:LYS275 4.5 61.7 1.0 CB A:ASP262 4.7 69.0 1.0 CA A:LYS275 4.7 63.1 1.0 CG A:GLU223 4.8 94.3 1.0 C A:GLU273 4.9 68.7 1.0 OE2 A:GLU223 5.0 0.1 1.0

J.H.Chang, X.Jiao, K.Chiba, C.Oh, C.E.Martin, M.Kiledjian, L.Tong. DXO1 Is A New Type of Eukaryotic Enzyme with Both Decapping and 5'-3' Exoribonuclease Activity. Nat.Struct.Mol.Biol. V. 19 1011 2012.
ISSN: ISSN 1545-9993
PubMed: 22961381
DOI: 10.1038/NSMB.2381