Manganese in PDB 4nhy: Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca)

The structure of Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca), PDB code: 4nhy was solved by S.Horita, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.680, 130.473, 175.784, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.6

The binding sites of Manganese atom in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca) (pdb code 4nhy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca), PDB code: 4nhy:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:36.1 occ:1.00 O21 A:PD2603 2.1 52.4 1.0 OD1 A:ASP157 2.2 42.3 1.0 NE2 A:HIS218 2.2 28.8 1.0 O A:HOH715 2.3 37.2 1.0 N1 A:PD2603 2.4 39.1 1.0 NE2 A:HIS155 2.4 40.6 1.0 C21 A:PD2603 2.9 49.1 1.0 CE1 A:HIS218 3.0 31.6 1.0 C2 A:PD2603 3.1 39.2 1.0 CG A:ASP157 3.1 34.6 1.0 CD2 A:HIS155 3.3 36.7 1.0 CE1 A:HIS155 3.3 39.9 1.0 OD2 A:ASP157 3.3 37.7 1.0 CD2 A:HIS218 3.4 32.5 1.0 C6 A:PD2603 3.4 44.4 1.0 O2 A:GOL602 3.9 77.2 1.0 O22 A:PD2603 4.2 55.2 1.0 ND1 A:HIS218 4.2 33.9 1.0 CZ2 A:TRP236 4.4 30.0 1.0 ND1 A:HIS155 4.4 38.7 1.0 CG A:HIS155 4.4 32.9 1.0 CG A:HIS218 4.4 28.9 1.0 C3 A:PD2603 4.4 40.7 1.0 CB A:ASP157 4.4 35.7 1.0 CD2 A:LEU152 4.7 32.6 1.0 C5 A:PD2603 4.7 50.4 1.0 CZ A:PHE210 4.8 39.8 1.0 CA A:ASP157 4.9 39.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:46.8 occ:1.00 O22 B:PD2603 2.1 42.2 1.0 OD1 B:ASP157 2.2 59.6 1.0 NE2 B:HIS218 2.2 35.8 1.0 N1 B:PD2603 2.2 51.2 1.0 OD2 B:ASP157 2.3 51.3 1.0 NE2 B:HIS155 2.4 40.2 1.0 CG B:ASP157 2.5 51.1 1.0 C21 B:PD2603 2.9 46.5 1.0 C2 B:PD2603 2.9 46.0 1.0 CE1 B:HIS218 3.1 37.2 1.0 CD2 B:HIS218 3.3 38.1 1.0 CE1 B:HIS155 3.3 43.0 1.0 C6 B:PD2603 3.3 57.1 1.0 CD2 B:HIS155 3.3 35.6 1.0 O2 B:GOL602 4.0 79.4 1.0 CB B:ASP157 4.0 41.5 1.0 O21 B:PD2603 4.1 48.5 1.0 ND1 B:HIS218 4.2 41.0 1.0 C3 B:PD2603 4.3 49.5 1.0 CZ2 B:TRP236 4.4 41.3 1.0 CG B:HIS218 4.4 37.4 1.0 ND1 B:HIS155 4.4 38.8 1.0 CG B:HIS155 4.4 33.9 1.0 C5 B:PD2603 4.5 57.5 1.0 CD2 B:LEU152 4.7 29.0 1.0 CA B:ASP157 4.8 44.2 1.0 C4 B:PD2603 4.9 58.5 1.0 CZ B:PHE210 5.0 45.6 1.0 N B:ASP157 5.0 49.5 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:45.6 occ:1.00 O22 C:PD2602 2.0 27.4 1.0 OD1 C:ASP157 2.1 69.1 1.0 NE2 C:HIS218 2.2 36.4 1.0 OD2 C:ASP157 2.3 66.1 1.0 NE2 C:HIS155 2.3 48.6 1.0 N1 C:PD2602 2.5 44.3 1.0 CG C:ASP157 2.5 57.8 1.0 C21 C:PD2602 2.9 36.2 1.0 C2 C:PD2602 3.1 30.8 1.0 CE1 C:HIS218 3.1 46.2 1.0 CE1 C:HIS155 3.2 43.6 1.0 CD2 C:HIS155 3.3 44.4 1.0 CD2 C:HIS218 3.3 37.0 1.0 C6 C:PD2602 3.6 49.6 1.0 CB C:ASP157 4.0 48.3 1.0 O21 C:PD2602 4.1 50.7 1.0 ND1 C:HIS155 4.3 39.3 1.0 ND1 C:HIS218 4.3 34.5 1.0 CG C:HIS155 4.3 38.7 1.0 CZ2 C:TRP236 4.4 37.7 1.0 CG C:HIS218 4.4 35.9 1.0 C3 C:PD2602 4.4 29.9 1.0 CD2 C:LEU152 4.8 33.6 1.0 CA C:ASP157 4.8 50.2 1.0 CZ C:PHE210 4.8 46.2 1.0 C5 C:PD2602 4.8 46.4 1.0 N C:ASP157 5.0 41.3 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with Pyridine-2,4- Dicarboxylic Acid (2,4-Pdca) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:61.2 occ:1.00 OD1 D:ASP157 2.2 85.9 1.0 NE2 D:HIS218 2.2 52.9 1.0 OD2 D:ASP157 2.2 92.5 1.0 O22 D:PD2603 2.3 55.1 1.0 NE2 D:HIS155 2.4 69.9 1.0 N1 D:PD2603 2.5 60.4 1.0 CG D:ASP157 2.5 82.6 1.0 CE1 D:HIS218 2.9 58.4 1.0 C21 D:PD2603 3.1 57.6 1.0 C2 D:PD2603 3.1 57.4 1.0 CE1 D:HIS155 3.3 65.4 1.0 CD2 D:HIS155 3.3 63.2 1.0 CD2 D:HIS218 3.5 53.4 1.0 C6 D:PD2603 3.5 57.9 1.0 CB D:ASP157 4.1 71.8 1.0 CZ2 D:TRP236 4.1 63.5 1.0 ND1 D:HIS218 4.1 55.5 1.0 O2 D:GOL602 4.2 85.5 1.0 O21 D:PD2603 4.2 63.0 1.0 ND1 D:HIS155 4.4 56.5 1.0 CG D:HIS155 4.4 59.0 1.0 CG D:HIS218 4.4 54.2 1.0 C3 D:PD2603 4.5 61.3 1.0 CD2 D:LEU152 4.6 44.0 1.0 C2 D:GOL602 4.7 89.4 1.0 CZ D:PHE210 4.7 76.1 1.0 C5 D:PD2603 4.8 54.5 1.0 CA D:ASP157 4.8 68.9 1.0 N D:ASP157 4.9 71.5 1.0 CH2 D:TRP236 4.9 57.6 1.0 CE2 D:TRP236 5.0 67.6 1.0

S.Horita, S.Horita, M.A.Mcdonough, C.J.Schofield. N/A N/A.