Manganese in PDB 2a8s: 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp

The structure of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp, PDB code: 2a8s 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)	38.74 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.998, 82.553, 112.160, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.5

The binding sites of Manganese atom in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp (pdb code 2a8s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp, PDB code: 2a8s:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and 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, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:53.8 occ:1.00 O2B A:GTP250 2.0 60.7 1.0 O1A A:GTP250 2.1 51.1 1.0 O A:GLY72 2.1 53.1 1.0 OE2 A:GLU93 2.1 53.5 1.0 CD A:GLU93 2.9 49.4 1.0 OE1 A:GLU93 2.9 51.2 1.0 PB A:GTP250 3.1 58.4 1.0 C A:GLY72 3.3 52.0 1.0 PA A:GTP250 3.3 57.9 1.0 MN A:MN301 3.7 58.9 1.0 O1B A:GTP250 3.7 66.8 1.0 O3A A:GTP250 3.7 56.6 1.0 CA A:GLY73 4.0 53.7 1.0 N A:GLY73 4.0 52.3 1.0 O2A A:GTP250 4.1 59.4 1.0 OE1 A:GLU150 4.1 59.1 1.0 N A:GLY72 4.2 50.1 1.0 OE2 A:GLU89 4.2 56.2 1.0 NH1 A:ARG63 4.3 41.5 1.0 NE2 A:HIS37 4.3 45.0 1.0 CG A:GLU93 4.3 47.8 1.0 CA A:GLY72 4.3 51.0 1.0 CE A:MET61 4.3 58.0 1.0 O3B A:GTP250 4.5 58.4 1.0 O5' A:GTP250 4.5 62.5 1.0 CD2 A:HIS37 4.8 42.0 1.0

Manganese binding site 2 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and 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, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:58.9 occ:1.00 OE2 A:GLU93 2.2 53.5 1.0 OE2 A:GLU89 2.3 56.2 1.0 OE1 A:GLU150 2.4 59.1 1.0 O3G A:GTP250 2.5 55.8 1.0 O2B A:GTP250 2.5 60.7 1.0 CD A:GLU93 3.1 49.4 1.0 PB A:GTP250 3.2 58.4 1.0 O3B A:GTP250 3.3 58.4 1.0 CD A:GLU89 3.3 53.7 1.0 CD A:GLU150 3.4 52.4 1.0 PG A:GTP250 3.4 61.6 1.0 CG A:GLU93 3.4 47.8 1.0 O1B A:GTP250 3.5 66.8 1.0 MN A:MN300 3.7 53.8 1.0 OE1 A:GLU89 3.7 52.4 1.0 OE2 A:GLU150 3.7 47.1 1.0 O1G A:GTP250 3.9 51.6 1.0 OE2 A:GLU92 3.9 53.6 1.0 MN A:MN302 3.9 59.4 0.5 O A:GLY72 4.0 53.1 1.0 MN A:MN303 4.0 46.5 0.5 OD2 A:ASP146 4.0 54.2 1.0 OE1 A:GLU93 4.3 51.2 1.0 O A:HOH583 4.4 56.4 1.0 CG A:GLU89 4.7 48.5 1.0 CG A:GLU150 4.7 52.2 1.0 CD A:GLU92 4.7 55.1 1.0 O3A A:GTP250 4.8 56.6 1.0 CG A:ASP146 4.8 50.5 1.0 O2G A:GTP250 4.8 60.4 1.0 CB A:GLU93 4.9 49.5 1.0 CB A:GLU89 5.0 48.8 1.0 CB A:GLU150 5.0 50.0 1.0 CG A:GLU92 5.0 57.0 1.0

Manganese binding site 3 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and 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, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:59.4 occ:0.50 O1G A:GTP250 1.9 51.6 1.0 OE1 A:GLU89 2.1 52.4 1.0 O3G A:GTP250 2.1 55.8 1.0 PG A:GTP250 2.2 61.6 1.0 O2G A:GTP250 2.8 60.4 1.0 CD A:GLU89 3.1 53.7 1.0 OE2 A:GLU92 3.4 53.6 1.0 NH1 A:ARG88 3.5 57.8 1.0 OE2 A:GLU89 3.6 56.2 1.0 O3B A:GTP250 3.7 58.4 1.0 MN A:MN301 3.9 58.9 1.0 O1B A:GTP250 3.9 66.8 1.0 MN A:MN303 4.1 46.5 0.5 CD A:GLU92 4.3 55.1 1.0 CG A:GLU89 4.4 48.5 1.0 PB A:GTP250 4.4 58.4 1.0 OE1 A:GLU92 4.6 57.4 1.0 CZ A:ARG88 4.7 61.4 1.0 O A:PHE74 4.8 60.1 1.0 O A:HOH583 5.0 56.4 1.0

Manganese binding site 4 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and 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, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:46.5 occ:0.50 OE2 A:GLU150 2.1 47.1 1.0 O2G A:GTP250 2.4 60.4 1.0 O3B A:GTP250 2.4 58.4 1.0 O3G A:GTP250 2.5 55.8 1.0 PG A:GTP250 2.5 61.6 1.0 CD A:GLU150 3.2 52.4 1.0 OE1 A:GLU150 3.6 59.1 1.0 PB A:GTP250 3.9 58.4 1.0 O1G A:GTP250 4.0 51.6 1.0 MN A:MN301 4.0 58.9 1.0 MN A:MN302 4.1 59.4 0.5 O2B A:GTP250 4.2 60.7 1.0 O A:HOH583 4.4 56.4 1.0 CG A:GLU150 4.4 52.2 1.0 CE2 B:PHE49 4.6 50.3 1.0 O3A A:GTP250 4.7 56.6 1.0 O1B A:GTP250 4.8 66.8 1.0

Manganese binding site 5 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and 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, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:56.2 occ:1.00 O2B B:GTP251 1.9 51.6 0.8 OE2 B:GLU93 2.0 55.8 1.0 O1A B:GTP251 2.0 50.4 0.8 O B:GLY72 2.1 51.2 1.0 CD B:GLU93 2.9 43.0 1.0 MN B:MN305 3.0 52.8 0.5 OE1 B:GLU93 3.1 49.7 1.0 PB B:GTP251 3.3 59.7 0.8 PA B:GTP251 3.3 43.9 0.8 C B:GLY72 3.3 49.7 1.0 O3A B:GTP251 3.8 47.0 0.8 O B:HOH511 3.9 50.9 1.0 CA B:GLY73 3.9 49.2 1.0 O2A B:GTP251 4.0 40.5 0.8 N B:GLY73 4.1 49.3 1.0 O3B B:GTP251 4.2 62.0 0.8 N B:GLY72 4.2 47.8 1.0 CG B:GLU93 4.3 48.5 1.0 NE2 B:HIS37 4.3 57.1 1.0 O1B B:GTP251 4.4 49.8 0.8 CA B:GLY72 4.4 48.5 1.0 O5' B:GTP251 4.5 49.6 0.8 CG B:GLU89 4.6 55.7 1.0 CE B:MET61 4.6 54.7 1.0 O3G B:GTP251 4.7 63.6 0.8 NH1 B:ARG63 4.7 46.2 1.0 OE2 B:GLU89 4.7 60.4 1.0 O B:HOH506 4.8 38.1 1.0 CD2 B:HIS37 4.8 58.9 1.0

Manganese binding site 6 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn305 b:52.8 occ:0.50 OE2 B:GLU93 2.1 55.8 1.0 OE2 B:GLU89 2.2 60.4 1.0 O3G B:GTP251 2.3 63.6 0.8 O2B B:GTP251 2.4 51.6 0.8 MN B:MN304 3.0 56.2 1.0 CD B:GLU89 3.1 53.1 1.0 CD B:GLU93 3.2 43.0 1.0 PG B:GTP251 3.2 64.4 0.8 PB B:GTP251 3.3 59.7 0.8 O3B B:GTP251 3.4 62.0 0.8 CG B:GLU89 3.5 55.7 1.0 CG B:GLU93 3.6 48.5 1.0 O1G B:GTP251 3.6 58.9 0.8 O B:GLY72 3.8 51.2 1.0 O1B B:GTP251 3.9 49.8 0.8 MN B:MN307 4.1 56.3 0.5 OD2 B:ASP146 4.1 60.8 1.0 OE1 B:GLU89 4.2 50.6 1.0 OE1 B:GLU93 4.2 49.7 1.0 MN B:MN306 4.4 71.8 0.2 O1A B:GTP251 4.5 50.4 0.8 O2G B:GTP251 4.6 64.7 0.8 CA B:GLY73 4.7 49.2 1.0 C B:GLY72 4.7 49.7 1.0 O3A B:GTP251 4.8 47.0 0.8 CB B:GLU89 4.9 51.1 1.0 O B:GLU89 4.9 53.3 1.0

Manganese binding site 7 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn306 b:71.8 occ:0.25 OE2 B:GLU92 2.7 72.0 1.0 OD2 B:ASP146 3.0 60.8 1.0 OD1 B:ASP146 3.1 54.9 1.0 O3G B:GTP251 3.2 63.6 0.8 OE2 B:GLU150 3.4 69.6 1.0 CG B:ASP146 3.4 51.1 1.0 CD B:GLU92 3.4 70.3 1.0 OE1 B:GLU150 3.4 74.1 1.0 CG B:GLU92 3.6 63.0 1.0 CD B:GLU150 3.7 65.6 1.0 NZ B:LYS145 3.9 57.7 1.0 OE2 B:GLU89 4.2 60.4 1.0 PG B:GTP251 4.3 64.4 0.8 MN B:MN305 4.4 52.8 0.5 CE B:LYS145 4.4 54.8 1.0 OE1 B:GLU92 4.5 70.2 1.0 CB B:GLU92 4.5 53.4 1.0 O2G B:GTP251 4.6 64.7 0.8 O1G B:GTP251 4.6 58.9 0.8 CD B:LYS145 4.7 51.4 1.0 MN B:MN307 4.7 56.3 0.5 CB B:ASP146 4.9 47.2 1.0 CG B:GLU150 4.9 56.1 1.0

Manganese binding site 8 out of 8 in the 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear Snorna Decapping Nudix Hydrolase X29, Manganese and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn307 b:56.3 occ:0.50 OE1 B:GLU89 2.3 50.6 1.0 O1G B:GTP251 2.3 58.9 0.8 OE2 B:GLU89 2.6 60.4 1.0 CD B:GLU89 2.7 53.1 1.0 PG B:GTP251 3.6 64.4 0.8 O1B B:GTP251 3.8 49.8 0.8 O3G B:GTP251 3.9 63.6 0.8 MN B:MN305 4.1 52.8 0.5 CG B:GLU89 4.2 55.7 1.0 PB B:GTP251 4.6 59.7 0.8 O3B B:GTP251 4.6 62.0 0.8 OE2 B:GLU92 4.6 72.0 1.0 O2G B:GTP251 4.7 64.7 0.8 O B:PHE74 4.7 48.6 1.0 MN B:MN306 4.7 71.8 0.2 OE1 B:GLU92 4.9 70.2 1.0 O2B B:GTP251 5.0 51.6 0.8 CD B:GLU92 5.0 70.3 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