Manganese in PDB 2a8r: 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp

The structure of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp, PDB code: 2a8r 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)	23.00 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.200, 82.150, 112.240, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26.3

The binding sites of Manganese atom in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp (pdb code 2a8r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp, PDB code: 2a8r:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:70.0 occ:1.00 O3 A:POP1307 2.2 53.6 0.5 OE2 A:GLU93 2.3 67.2 1.0 O A:GLY72 2.3 65.8 1.0 O6 A:POP1307 2.7 50.8 0.5 CD A:GLU93 3.1 63.0 1.0 OE1 A:GLU93 3.2 63.2 1.0 MN A:MN301 3.3 72.6 1.0 OE1 A:GLU150 3.3 69.3 1.0 P1 A:POP1307 3.4 45.5 0.5 C A:GLY72 3.5 63.4 1.0 P2 A:POP1307 3.5 53.7 0.5 O A:POP1307 3.8 50.9 0.5 O4 A:POP1307 3.8 52.6 0.5 O2 A:POP1307 4.0 45.7 0.5 CA A:GLY73 4.0 64.2 1.0 NH1 A:ARG63 4.1 61.1 1.0 N A:GLY73 4.2 63.0 1.0 N A:GLY72 4.4 61.2 1.0 CG A:GLU93 4.4 61.2 1.0 OE2 A:GLU89 4.4 70.7 1.0 NE2 A:HIS37 4.5 70.2 1.0 CD A:GLU150 4.5 64.0 1.0 CA A:GLY72 4.6 61.6 1.0 O1 A:POP1307 4.6 41.2 0.5 CD2 A:HIS37 4.9 61.7 1.0 O5 A:POP1307 4.9 59.4 0.5 CE A:MET61 5.0 59.8 1.0

Manganese binding site 2 out of 5 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:72.6 occ:1.00 OE2 A:GLU93 2.2 67.2 1.0 OE2 A:GLU89 2.2 70.7 1.0 O3 A:POP1307 2.3 53.6 0.5 OE1 A:GLU150 2.6 69.3 1.0 MN A:MN300 3.3 70.0 1.0 CD A:GLU150 3.3 64.0 1.0 CD A:GLU93 3.3 63.0 1.0 OE2 A:GLU150 3.4 67.6 1.0 P1 A:POP1307 3.4 45.5 0.5 CD A:GLU89 3.4 64.5 1.0 MN A:MN302 3.5 75.2 0.5 O1 A:POP1307 3.6 41.2 0.5 O A:GLY72 3.7 65.8 1.0 CG A:GLU93 3.7 61.2 1.0 O2 A:POP1307 3.9 45.7 0.5 OE1 A:GLU89 4.0 64.7 1.0 OE1 A:GLU93 4.4 63.2 1.0 CG A:GLU89 4.6 62.0 1.0 CG A:GLU150 4.6 65.4 1.0 OD2 A:ASP146 4.6 61.8 1.0 C A:GLY72 4.7 63.4 1.0 CA A:GLY73 4.7 64.2 1.0 O A:POP1307 4.7 50.9 0.5 CB A:GLU89 4.8 62.0 1.0 OE2 A:GLU92 4.8 77.5 1.0

Manganese binding site 3 out of 5 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:75.2 occ:0.50 O1 A:POP1307 1.9 41.2 0.5 OE1 A:GLU89 2.8 64.7 1.0 OE2 A:GLU89 2.9 70.7 1.0 CD A:GLU89 3.0 64.5 1.0 P1 A:POP1307 3.2 45.5 0.5 O3 A:POP1307 3.5 53.6 0.5 MN A:MN301 3.5 72.6 1.0 N A:PHE74 3.8 67.3 1.0 O2 A:POP1307 4.0 45.7 0.5 O A:PHE74 4.1 70.3 1.0 CG A:GLU89 4.3 62.0 1.0 O A:POP1307 4.3 50.9 0.5 CB A:PHE74 4.4 70.7 1.0 CA A:GLY73 4.4 64.2 1.0 CA A:PHE74 4.5 70.3 1.0 C A:GLY73 4.5 65.2 1.0 CD2 A:PHE74 4.6 70.6 1.0 C A:PHE74 4.7 71.8 1.0 OE2 A:GLU150 4.8 67.6 1.0

Manganese binding site 4 out of 5 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:80.7 occ:1.00 O3 B:POP2308 2.1 55.1 0.5 O B:GLY72 2.3 65.7 1.0 OE2 B:GLU93 2.3 71.9 1.0 O6 B:POP2308 2.6 57.6 0.5 CD B:GLU93 3.0 54.0 1.0 O B:HOH2344 3.1 64.2 1.0 O4 B:POP2308 3.2 58.2 0.5 OE1 B:GLU93 3.2 63.4 1.0 MN B:MN305 3.2 74.8 1.0 P2 B:POP2308 3.3 55.2 0.5 C B:GLY72 3.5 62.0 1.0 P1 B:POP2308 3.5 58.6 0.5 OE1 B:GLU150 3.8 76.0 1.0 O B:POP2308 3.9 57.6 0.5 CA B:GLY73 4.1 56.4 1.0 N B:GLY73 4.2 58.1 1.0 O2 B:POP2308 4.3 60.2 0.5 NE2 B:HIS37 4.3 68.0 1.0 N B:GLY72 4.3 59.6 1.0 CG B:GLU93 4.4 59.4 1.0 NH1 B:ARG63 4.4 53.3 1.0 CA B:GLY72 4.5 60.0 1.0 O1 B:POP2308 4.6 50.5 0.5 O5 B:POP2308 4.7 63.5 0.5 CG B:GLU89 4.7 73.3 1.0 CD2 B:HIS37 4.8 66.0 1.0 CD B:GLU150 5.0 70.2 1.0

Manganese binding site 5 out of 5 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-Methyl-Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn305 b:74.8 occ:1.00 OE2 B:GLU93 2.2 71.9 1.0 OE2 B:GLU89 2.4 88.3 1.0 OE1 B:GLU150 2.5 76.0 1.0 O3 B:POP2308 2.5 55.1 0.5 CD B:GLU89 3.0 69.8 1.0 CD B:GLU93 3.2 54.0 1.0 MN B:MN304 3.2 80.7 1.0 CG B:GLU89 3.4 73.3 1.0 CD B:GLU150 3.5 70.2 1.0 P1 B:POP2308 3.6 58.6 0.5 CG B:GLU93 3.6 59.4 1.0 OE2 B:GLU150 3.8 79.1 1.0 O B:HOH2346 3.8 69.2 1.0 OE1 B:GLU89 3.8 75.4 1.0 O2 B:POP2308 3.9 60.2 0.5 O B:GLY72 3.9 65.7 1.0 O1 B:POP2308 4.0 50.5 0.5 OE1 B:GLU93 4.3 63.4 1.0 OD2 B:ASP146 4.3 82.5 1.0 O B:HOH2322 4.4 63.9 1.0 O B:HOH2344 4.5 64.2 1.0 O B:HOH2347 4.7 79.0 1.0 C B:GLY72 4.8 62.0 1.0 CG B:GLU150 4.8 69.7 1.0 CA B:GLY73 4.8 56.4 1.0 OE2 B:GLU92 4.8 86.1 1.0 CB B:GLU89 4.9 60.5 1.0 O B:GLU89 5.0 64.9 1.0 O B:POP2308 5.0 57.6 0.5

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