Manganese in PDB 3pif: Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese

The structure of Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese, PDB code: 3pif was solved by J.H.Chang, S.Xiang, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	116.267, 132.581, 144.066, 109.92, 105.81, 104.00
R / Rfree (%)	24.8 / 28.4

The binding sites of Manganese atom in the Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese (pdb code 3pif). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese, PDB code: 3pif:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant 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 the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1254 b:67.1 occ:1.00 OD2 A:ASP208 1.8 60.7 1.0 OD1 A:ASP206 2.2 56.6 1.0 OD1 A:ASP291 2.5 61.2 1.0 OE1 A:GLN178 2.9 60.0 1.0 CG A:ASP208 2.9 56.2 1.0 CG A:ASP206 3.2 55.8 1.0 CG A:ASP291 3.4 64.0 1.0 OD2 A:ASP206 3.4 56.4 1.0 CB A:ASP208 3.5 53.6 1.0 OD2 A:ASP291 4.0 71.7 1.0 CD A:GLN178 4.0 58.6 1.0 OD1 A:ASP208 4.0 57.8 1.0 CB A:ASP291 4.3 60.9 1.0 NE2 A:GLN178 4.4 57.6 1.0 OH A:TYR548 4.5 54.8 1.0 CB A:ASP206 4.5 55.1 1.0 CA A:ASP208 4.9 52.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1254 b:67.7 occ:1.00 OD2 B:ASP208 1.9 58.6 1.0 OD1 B:ASP206 2.3 58.5 1.0 OD1 B:ASP291 2.8 78.3 1.0 CG B:ASP208 3.0 58.2 1.0 CG B:ASP206 3.3 58.0 1.0 OD2 B:ASP291 3.4 78.8 1.0 CB B:ASP208 3.4 57.2 1.0 CG B:ASP291 3.4 78.1 1.0 NE2 B:GLN178 3.5 68.1 1.0 OD2 B:ASP206 3.6 56.8 1.0 OE1 B:GLN178 3.7 67.1 1.0 CD B:GLN178 4.0 65.9 1.0 OD1 B:ASP208 4.1 60.4 1.0 OH B:TYR548 4.5 58.2 1.0 CB B:ASP206 4.7 59.1 1.0 CB B:ASP291 4.8 78.4 1.0 CA B:ASP208 4.8 56.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1254 b:66.3 occ:1.00 OD1 C:ASP206 2.0 66.3 1.0 OD1 C:ASP291 2.0 72.1 1.0 OD2 C:ASP208 2.2 71.6 1.0 CG C:ASP206 3.0 66.1 1.0 CG C:ASP208 3.0 69.8 1.0 CG C:ASP291 3.1 70.5 1.0 CB C:ASP208 3.3 67.3 1.0 OD2 C:ASP206 3.4 62.0 1.0 NE2 C:GLN178 3.5 65.7 1.0 OD2 C:ASP291 3.6 71.6 1.0 OD1 C:ASP208 4.2 73.4 1.0 CB C:ASP206 4.3 67.3 1.0 CB C:ASP291 4.3 69.7 1.0 CD C:GLN178 4.5 66.4 1.0 OH C:TYR548 4.7 67.0 1.0 OE1 C:GLN178 4.8 68.5 1.0 CA C:ASP208 4.8 66.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the 5'->3' Exoribonuclease XRN1, E178Q Mutant in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1254 b:75.0 occ:1.00 OD2 D:ASP208 2.2 71.8 1.0 OD1 D:ASP206 2.2 69.9 1.0 OD1 D:ASP291 2.9 88.3 1.0 CG D:ASP206 3.0 71.5 1.0 OD2 D:ASP206 3.2 69.1 1.0 OD2 D:ASP291 3.2 88.3 1.0 CG D:ASP208 3.3 72.7 1.0 CG D:ASP291 3.4 86.9 1.0 OE1 D:GLN178 3.7 89.4 1.0 CB D:ASP208 3.8 73.8 1.0 NE2 D:GLN178 3.9 88.2 1.0 CD D:GLN178 4.1 87.5 1.0 CB D:ASP206 4.3 73.4 1.0 OD1 D:ASP208 4.4 72.2 1.0 OH D:TYR548 4.4 78.0 1.0 CB D:ASP291 4.9 86.2 1.0

J.H.Chang, S.Xiang, K.Xiang, J.L.Manley, L.Tong. Structural and Biochemical Studies of the 5' -> 3' Exoribonuclease XRN1. Nat.Struct.Mol.Biol. V. 18 270 2011.
ISSN: ISSN 1545-9993
PubMed: 21297639
DOI: 10.1038/NSMB.1984