Magnesium in PDB 4ohf: Crystal Structure of Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1

The structure of Crystal Structure of Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1, PDB code: 4ohf was solved by B.Srinivisan, F.Forouhar, A.Shukla, C.Sampangi, S.Kulkarni, M.Abashidze, J.Seetharaman, S.Lew, L.Mao, T.B.Acton, R.Xiao, J.K.Everett, G.M.Montelione, L.Tong, H.Balaram, Northeast Structural Genomicsconsortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.70 / 2.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.334, 92.720, 161.892, 90.00, 96.60, 90.00
R / Rfree (%)	23.1 / 27.2

The binding sites of Magnesium atom in the Crystal Structure of Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1 (pdb code 4ohf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1, PDB code: 4ohf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1


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 Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:44.8 occ:1.00 O B:HOH667 2.1 61.4 1.0 O B:ASP25 2.1 39.3 1.0 O2 B:PO4501 2.2 42.1 1.0 OD1 B:ASP23 2.2 46.9 1.0 OD1 B:ASP303 2.2 40.5 1.0 OD2 B:ASP23 2.5 47.0 1.0 CG B:ASP23 2.7 44.1 1.0 CG B:ASP303 3.0 37.5 1.0 OD2 B:ASP303 3.1 37.0 1.0 C B:ASP25 3.3 38.0 1.0 P B:PO4501 3.6 42.9 1.0 O B:HOH622 3.7 26.3 1.0 CB B:HIS26 4.1 34.9 1.0 CA B:ASP25 4.1 38.3 1.0 CB B:ASP23 4.1 42.4 1.0 N B:ASP25 4.2 36.8 1.0 O3 B:PO4501 4.2 38.2 1.0 O4 B:PO4501 4.2 45.6 1.0 N B:HIS26 4.3 37.1 1.0 ND1 B:HIS26 4.3 40.0 1.0 OG1 B:THR27 4.3 29.7 1.0 O B:HOH601 4.4 62.4 1.0 CB B:ASP25 4.4 41.3 1.0 CB B:ASP303 4.4 37.8 1.0 CA B:HIS26 4.5 36.1 1.0 O1 B:PO4501 4.6 41.5 1.0 N B:THR27 4.6 35.5 1.0 CG B:HIS26 4.7 38.1 1.0 C B:MET24 4.8 37.1 1.0 C B:HIS26 4.8 36.9 1.0 N B:ASP303 4.8 36.4 1.0 N B:MET24 4.9 37.6 1.0 C B:ASP23 5.0 37.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1


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 Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:69.5 occ:1.00 OD1 C:ASP23 2.1 47.2 1.0 O C:HOH648 2.1 79.2 1.0 O C:ASP25 2.1 41.0 1.0 O4 C:PO4502 2.2 50.2 1.0 OD1 C:ASP303 2.5 39.2 1.0 OD2 C:ASP23 2.6 45.0 1.0 CG C:ASP23 2.6 44.9 1.0 CG C:ASP303 3.2 37.5 1.0 OD2 C:ASP303 3.2 34.4 1.0 O C:HOH612 3.3 32.9 1.0 C C:ASP25 3.3 40.7 1.0 P C:PO4502 3.5 46.6 1.0 O1 C:PO4502 4.0 48.0 1.0 O2 C:PO4502 4.0 48.2 1.0 CB C:ASP23 4.0 43.2 1.0 CB C:HIS26 4.1 38.4 1.0 CA C:ASP25 4.2 40.8 1.0 OG1 C:THR27 4.3 33.6 1.0 CB C:ASP25 4.3 38.9 1.0 N C:ASP25 4.3 41.1 1.0 N C:HIS26 4.4 39.6 1.0 CD2 C:HIS26 4.5 41.0 1.0 CA C:HIS26 4.6 38.0 1.0 O3 C:PO4502 4.6 50.5 1.0 CB C:ASP303 4.7 38.7 1.0 CG C:HIS26 4.7 41.3 1.0 N C:THR27 4.7 37.7 1.0 C C:HIS26 4.8 38.3 1.0 N C:ASP303 4.8 37.4 1.0 C C:MET24 4.9 41.9 1.0 N C:MET24 4.9 42.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1


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 Cytosolic Nucleotidase II (LPG0095) in Complex with Gmp From Legionella Pneumophila, Northeast Structural Genomics Consortium Target LGR1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:62.4 occ:1.00 OD2 D:ASP23 2.1 46.7 1.0 OD1 D:ASP23 2.1 45.5 1.0 O D:HOH636 2.2 66.3 1.0 O1 D:PO4501 2.2 54.8 1.0 OD1 D:ASP303 2.2 37.1 1.0 CG D:ASP23 2.4 46.3 1.0 O D:ASP25 2.6 42.7 1.0 CG D:ASP303 3.0 37.8 1.0 OD2 D:ASP303 3.2 37.6 1.0 O D:HOH606 3.5 42.4 1.0 P D:PO4501 3.5 56.1 1.0 C D:ASP25 3.7 41.2 1.0 O4 D:PO4501 3.8 56.7 1.0 CB D:ASP23 3.8 43.1 1.0 O2 D:PO4501 4.2 52.5 1.0 OG1 D:THR27 4.2 31.7 1.0 N D:ASP25 4.4 38.8 1.0 CB D:HIS26 4.4 35.6 1.0 CA D:ASP25 4.5 40.9 1.0 CB D:ASP303 4.5 37.9 1.0 O3 D:PO4501 4.6 55.7 1.0 O D:HOH645 4.6 59.9 1.0 N D:ASP303 4.6 36.8 1.0 N D:HIS26 4.7 39.8 1.0 ND1 D:HIS26 4.7 38.7 1.0 NZ D:LYS247 4.7 42.1 1.0 CB D:ASP25 4.7 42.3 1.0 N D:THR27 4.8 36.1 1.0 N D:MET24 4.8 40.6 1.0 CA D:ASP23 4.8 40.8 1.0 C D:ASP23 4.9 40.9 1.0 CA D:HIS26 4.9 38.7 1.0 OH D:TYR306 4.9 81.4 1.0 C D:MET24 4.9 39.6 1.0 C D:HIS26 5.0 36.9 1.0

B.Srinivasan, F.Forouhar, A.Shukla, C.Sampangi, S.Kulkarni, M.Abashidze, J.Seetharaman, S.Lew, L.Mao, T.B.Acton, R.Xiao, J.K.Everett, G.T.Montelione, L.Tong, H.Balaram. Allosteric Regulation and Substrate Activation in Cytosolic Nucleotidase II From Legionella Pneumophila. Febs J. V. 281 1613 2014.
ISSN: ISSN 1742-464X
PubMed: 24456211
DOI: 10.1111/FEBS.12727