Manganese in PDB 2a8q: 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp

The structure of 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp, PDB code: 2a8q was solved by J.N.Scarsdale, B.A.Peculis, H.T.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.60 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.828, 82.284, 111.860, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.8

The binding sites of Manganese atom in the 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp (pdb code 2a8q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp, PDB code: 2a8q:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:59.6 occ:0.50 O3 A:POP1307 2.3 55.9 0.5 O A:GLY72 2.4 58.8 1.0 OE2 A:GLU93 2.5 71.1 1.0 O6 A:POP1307 2.5 54.4 0.5 MN A:MN301 3.3 69.7 0.5 CD A:GLU93 3.3 62.9 1.0 P2 A:POP1307 3.4 57.0 0.5 P1 A:POP1307 3.5 54.0 0.5 OE1 A:GLU93 3.5 65.3 1.0 C A:GLY72 3.5 58.9 1.0 O A:POP1307 3.6 55.0 0.5 O4 A:POP1307 3.6 53.2 0.5 CA A:GLY73 4.1 59.6 1.0 N A:GLY73 4.3 58.7 1.0 NH1 A:ARG63 4.3 50.7 1.0 O2 A:POP1307 4.3 56.1 0.5 N A:GLY72 4.4 55.6 1.0 CE1 A:HIS37 4.5 59.8 1.0 O1 A:POP1307 4.6 51.3 0.5 CA A:GLY72 4.6 57.5 1.0 CG A:GLU93 4.6 60.8 1.0 O5 A:POP1307 4.8 55.6 0.5 OE2 A:GLU89 4.8 72.1 1.0

Manganese binding site 2 out of 5 in the 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:69.7 occ:0.50 O3 A:POP1307 2.2 55.9 0.5 OE2 A:GLU89 2.2 72.1 1.0 OE2 A:GLU93 2.3 71.1 1.0 MN A:MN300 3.3 59.6 0.5 CD A:GLU93 3.4 62.9 1.0 P1 A:POP1307 3.4 54.0 0.5 MN A:MN302 3.4 65.0 0.2 CD A:GLU89 3.4 64.3 1.0 O1 A:POP1307 3.5 51.3 0.5 O A:GLY72 3.6 58.8 1.0 CG A:GLU93 3.8 60.8 1.0 OD2 A:ASP146 3.8 69.3 1.0 OE1 A:GLU89 4.2 66.3 1.0 O2 A:POP1307 4.2 56.1 0.5 CG A:GLU89 4.4 60.8 1.0 OE1 A:GLU93 4.5 65.3 1.0 C A:GLY72 4.6 58.9 1.0 O A:POP1307 4.6 55.0 0.5 CB A:GLU89 4.6 61.1 1.0 CA A:GLY73 4.8 59.6 1.0 CG A:GLU150 4.9 62.3 1.0 CG A:ASP146 5.0 63.9 1.0

Manganese binding site 3 out of 5 in the 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:65.0 occ:0.25 O1 A:POP1307 2.2 51.3 0.5 OE1 A:GLU89 2.3 66.3 1.0 CD A:GLU89 2.6 64.3 1.0 OE2 A:GLU89 2.6 72.1 1.0 MN A:MN301 3.4 69.7 0.5 P1 A:POP1307 3.5 54.0 0.5 O3 A:POP1307 3.7 55.9 0.5 CG A:GLU89 3.8 60.8 1.0 N A:PHE74 4.0 63.1 1.0 O A:PHE74 4.1 68.4 1.0 O2 A:POP1307 4.3 56.1 0.5 O A:POP1307 4.6 55.0 0.5 CB A:PHE74 4.6 67.8 1.0 CA A:PHE74 4.7 66.5 1.0 CA A:GLY73 4.7 59.6 1.0 C A:GLY73 4.8 61.1 1.0 OE1 A:GLU92 4.8 74.0 1.0 C A:PHE74 4.8 67.4 1.0 CD2 A:PHE74 5.0 73.3 1.0

Manganese binding site 4 out of 5 in the 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:68.6 occ:0.25 O B:GLY72 2.0 62.8 1.0 OE2 B:GLU93 2.8 69.4 1.0 O B:HOH309 3.0 61.2 1.0 C B:GLY72 3.2 61.2 1.0 MN B:MN305 3.3 60.1 0.2 OE1 B:GLU93 3.4 64.4 1.0 CD B:GLU93 3.4 57.8 1.0 O B:HOH327 3.9 44.8 1.0 N B:GLY72 3.9 58.5 1.0 CA B:GLY73 4.1 58.4 1.0 N B:GLY73 4.1 60.5 1.0 CE1 B:HIS37 4.1 65.0 1.0 CA B:GLY72 4.2 59.4 1.0 NH1 B:ARG63 4.2 49.4 1.0 O B:HOH313 4.2 68.0 1.0 CE B:MET61 4.3 62.9 1.0 ND1 B:HIS37 4.5 66.9 1.0 O B:PHE70 4.7 56.2 1.0 CG B:GLU93 4.7 63.8 1.0 C B:PRO71 4.8 56.9 1.0

Manganese binding site 5 out of 5 in the 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn305 b:60.1 occ:0.25 OE2 B:GLU93 2.5 69.4 1.0 OE2 B:GLU89 2.9 81.6 1.0 O B:HOH313 3.1 68.0 1.0 MN B:MN304 3.3 68.6 0.2 CD B:GLU93 3.6 57.8 1.0 O B:GLY72 3.6 62.8 1.0 CD B:GLU89 3.6 79.8 1.0 CG B:GLU89 3.7 74.8 1.0 CG B:GLU93 4.1 63.8 1.0 C B:GLY72 4.5 61.2 1.0 CA B:GLY73 4.5 58.4 1.0 OE1 B:GLU93 4.5 64.4 1.0 OD2 B:ASP146 4.6 64.8 1.0 OE1 B:GLU89 4.7 82.4 1.0 O B:HOH309 4.8 61.2 1.0 N B:GLY73 4.9 60.5 1.0

J.N.Scarsdale, B.A.Peculis, H.T.Wright. Crystal Structures of U8 Snorna Decapping Nudix Hydrolase, X29, and Its Metal and Cap Complexes Structure V. 14 331 2006.
ISSN: ISSN 0969-2126
PubMed: 16472752
DOI: 10.1016/J.STR.2005.11.010