Magnesium in PDB 1su2: Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp

The structure of Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp, PDB code: 1su2 was solved by W.Ranatunga, E.E.Hill, J.L.Mooster, E.L.Holbrook, U.Schulze-Gahmen, W.Xu, M.J.Bessman, S.E.Brenner, S.R.Holbrook, Berkeleystructural Genomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	53.232, 53.232, 122.362, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp (pdb code 1su2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp, PDB code: 1su2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:32.4 occ:1.00 O2A A:ATP357 1.9 57.2 0.6 PA A:ATP357 3.0 57.8 0.6 O1A A:ATP357 3.2 57.5 0.6 O A:ARG14 3.3 17.4 1.0 CB A:ALA51 3.3 11.7 1.0 CD2 A:LEU13 3.6 12.6 1.0 CB A:LEU13 3.7 9.1 1.0 CA A:ALA51 3.8 11.9 1.0 N A:ARG14 3.8 14.3 0.5 N A:ARG14 3.9 14.3 0.5 O5' A:ATP357 4.0 57.2 0.6 C A:ARG14 4.0 15.8 1.0 CG A:LEU13 4.1 10.9 1.0 CA A:LEU13 4.2 8.9 1.0 O3A A:ATP357 4.3 57.5 0.6 C A:LEU13 4.4 7.9 1.0 N A:VAL52 4.5 11.5 1.0 CD1 A:LEU13 4.5 11.4 1.0 CA A:ARG14 4.6 15.7 0.5 C A:ALA51 4.6 13.1 1.0 CA A:ARG14 4.6 15.7 0.5 C5' A:ATP357 4.7 56.5 0.6 CD1 A:ILE93 4.8 11.9 1.0 N A:ALA15 4.8 9.1 1.0 N A:ALA51 4.8 12.3 1.0 O A:VAL52 4.9 14.6 1.0 O1B A:ATP357 5.0 58.4 0.6

Magnesium binding site 2 out of 6 in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:27.9 occ:1.00 O2B A:ATP357 2.1 58.1 0.6 OG A:SER49 2.4 12.9 1.0 O1B A:ATP357 2.4 58.4 0.6 PB A:ATP357 2.6 58.2 0.6 CB B:MET1 2.7 51.0 1.0 SD B:MET1 2.9 53.9 1.0 NH1 A:ARG95 3.1 14.6 1.0 CG B:MET1 3.2 51.9 1.0 C A:SER49 3.4 13.3 1.0 N A:GLY50 3.5 10.6 1.0 O A:SER49 3.5 14.7 1.0 CB A:SER49 3.6 11.7 1.0 O3A A:ATP357 3.6 57.5 0.6 CA A:GLY50 3.7 12.8 1.0 CB A:ALA15 3.8 11.3 1.0 CA B:MET1 3.9 50.5 1.0 O3B A:ATP357 4.0 58.1 0.6 CA A:SER49 4.0 12.1 1.0 N B:MET1 4.1 51.0 1.0 C A:GLY50 4.2 12.2 1.0 CZ A:ARG95 4.3 15.1 1.0 O A:GLY50 4.3 10.3 1.0 O A:HOH866 4.3 24.0 1.0 C B:MET1 4.5 50.0 1.0 NH2 A:ARG95 4.6 17.0 1.0 N A:SER49 4.6 11.9 1.0 O1G A:ATP357 4.7 58.3 0.6 CE B:MET1 4.7 52.0 1.0 PG A:ATP357 4.7 57.4 0.6 O B:MET1 4.7 50.6 1.0 O A:HOH841 4.7 30.4 1.0 O2G A:ATP357 4.7 57.7 0.6 O A:HOH737 4.7 14.8 1.0 N A:ALA51 4.9 12.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:18.9 occ:1.00 O A:HOH816 2.4 30.5 1.0 O A:HOH771 2.5 17.9 1.0 O A:HOH889 2.5 34.9 1.0 OE2 A:GLU65 2.6 24.0 1.0 O A:HOH827 2.6 35.1 1.0 CD A:GLU65 3.5 19.9 1.0 OE1 A:GLU65 3.8 22.2 1.0 N A:ALA51 4.1 12.3 1.0 NH1 A:ARG64 4.3 27.6 1.0 OE1 A:GLU68 4.3 24.7 1.0 O A:HOH996 4.3 41.4 1.0 O A:HOH841 4.4 30.4 1.0 O A:ALA51 4.6 14.0 1.0 CB A:ALA51 4.6 11.7 1.0 CA A:GLY50 4.7 12.8 1.0 CG A:GLU65 4.8 17.3 1.0 C A:GLY50 4.9 12.2 1.0 CA A:ALA51 4.9 11.9 1.0 OE2 A:GLU53 4.9 33.6 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:20.5 occ:1.00 N A:MET1 2.1 48.5 1.0 O1B B:ATP257 2.2 57.9 0.6 OG B:SER49 2.7 14.3 1.0 PB B:ATP257 2.9 57.8 0.6 NH1 B:ARG95 3.1 15.2 1.0 O2B B:ATP257 3.2 58.0 0.6 O3B B:ATP257 3.2 58.0 0.6 CB B:SER49 3.3 11.4 1.0 C B:SER49 3.4 12.2 1.0 CA A:MET1 3.4 48.2 1.0 N B:GLY50 3.4 9.6 1.0 O B:SER49 3.6 14.1 1.0 CA B:GLY50 3.7 12.1 1.0 CB B:ALA15 3.8 11.0 1.0 CB A:MET1 3.8 49.2 1.0 O A:MET1 3.8 47.7 1.0 PG B:ATP257 3.9 57.9 0.6 CA B:SER49 3.9 11.2 1.0 C A:MET1 4.1 47.6 1.0 C B:GLY50 4.1 12.4 1.0 CZ B:ARG95 4.2 15.5 1.0 O1G B:ATP257 4.2 58.4 0.6 CG A:MET1 4.2 50.3 0.4 O3G B:ATP257 4.3 58.4 0.6 O B:GLY50 4.3 10.3 1.0 O3A B:ATP257 4.4 57.1 0.6 O B:HOH902 4.4 33.6 1.0 NH2 B:ARG95 4.4 17.0 1.0 O B:HOH743 4.7 14.8 1.0 O B:HOH835 4.7 28.8 1.0 SD A:MET1 4.8 51.8 1.0 N B:ALA51 4.9 12.5 1.0 N B:SER49 4.9 11.0 1.0 CA B:ALA15 5.0 9.2 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:36.8 occ:1.00 O2A B:ATP257 1.9 57.2 0.6 PA B:ATP257 2.7 57.0 0.6 O1A B:ATP257 2.8 57.3 0.6 O B:HOH713 2.8 15.4 1.0 O B:ARG14 3.3 10.4 1.0 O3A B:ATP257 3.4 57.1 0.6 CB B:ALA51 3.5 12.9 1.0 CB B:LEU13 3.5 8.7 1.0 CD2 B:LEU13 3.6 11.6 1.0 N B:ARG14 3.8 9.2 0.1 N B:ARG14 3.8 10.6 0.9 CA B:ALA51 3.9 11.9 1.0 CG B:LEU13 4.0 11.5 1.0 C B:ARG14 4.0 9.9 1.0 CA B:LEU13 4.1 8.5 1.0 O5' B:ATP257 4.2 56.5 0.6 CD1 B:LEU13 4.3 10.3 1.0 C B:LEU13 4.3 8.0 1.0 CA B:ARG14 4.6 10.9 0.9 CA B:ARG14 4.6 9.7 0.1 N B:VAL52 4.6 12.3 1.0 CD1 B:ILE93 4.6 12.7 1.0 PB B:ATP257 4.7 57.8 0.6 C B:ALA51 4.8 13.5 1.0 C5' B:ATP257 4.8 55.7 0.6 N B:ALA15 4.8 9.7 1.0 O3B B:ATP257 4.8 58.0 0.6 N B:ALA51 5.0 12.5 1.0 O B:VAL52 5.0 13.7 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Nudix Hydrolase DR1025 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:18.6 occ:1.00 O B:HOH853 2.5 33.6 1.0 O B:HOH764 2.6 17.5 1.0 OE2 B:GLU65 2.6 24.1 1.0 O B:HOH980 2.6 43.8 1.0 O B:HOH782 2.7 18.6 1.0 O B:HOH871 2.8 37.1 1.0 CD B:GLU65 3.5 20.4 1.0 OE1 B:GLU65 3.7 23.0 1.0 NH1 B:ARG64 3.9 29.0 1.0 O B:HOH997 3.9 41.1 1.0 N B:ALA51 4.1 12.5 1.0 O B:HOH995 4.2 47.3 1.0 OE1 B:GLU68 4.3 24.4 1.0 O B:HOH835 4.5 28.8 1.0 O B:ALA51 4.6 14.1 1.0 CB B:ALA51 4.6 12.9 1.0 CA B:GLY50 4.7 12.1 1.0 O B:HOH965 4.8 43.5 1.0 CG B:GLU65 4.8 17.9 1.0 CZ B:ARG64 4.8 28.8 1.0 C B:GLY50 4.8 12.4 1.0 CA B:ALA51 4.9 11.9 1.0 NH2 B:ARG64 4.9 29.1 1.0 OE2 B:GLU53 5.0 35.7 1.0

W.Ranatunga, E.E.Hill, J.L.Mooster, E.L.Holbrook, U.Schulze-Gahmen, W.Xu, M.J.Bessman, S.E.Brenner, S.R.Holbrook. Structural Studies of the Nudix Hydrolase DR1025 From Deinococcus Radiodurans and Its Ligand Complexes. J.Mol.Biol. V. 339 103 2004.
ISSN: ISSN 0022-2836
PubMed: 15123424
DOI: 10.1016/J.JMB.2004.01.065