Manganese in PDB 6imc: Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine

All present enzymatic activity of Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine:
1.14.11.33; 1.14.11.51; 4.2.99.18;

The structure of Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 6imc was solved by M.Zhang, S.Yang, W.Zhao, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.16 / 2.51
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	147.898, 147.898, 178.044, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.3

The binding sites of Manganese atom in the Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine (pdb code 6imc). 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 ALKBH1 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 6imc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine


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 ALKBH1 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:30.0 occ:1.00 O2 A:OGA502 2.0 32.4 1.0 OD1 A:ASP233 2.0 32.7 1.0 O2' A:OGA502 2.2 34.8 1.0 NE2 A:HIS231 2.2 32.5 1.0 O A:HOH661 2.3 34.5 1.0 NE2 A:HIS287 2.3 29.2 1.0 C1 A:OGA502 2.8 32.6 1.0 C2 A:OGA502 2.9 32.6 1.0 CG A:ASP233 3.0 37.5 1.0 CE1 A:HIS231 3.1 29.6 1.0 CD2 A:HIS231 3.2 34.8 1.0 CD2 A:HIS287 3.3 34.1 1.0 OD2 A:ASP233 3.3 33.8 1.0 CE1 A:HIS287 3.3 34.2 1.0 O1 A:OGA502 4.0 31.8 1.0 N1 A:OGA502 4.2 32.9 1.0 O A:HOH697 4.2 37.4 1.0 ND1 A:HIS231 4.2 34.7 1.0 CG A:HIS231 4.3 33.8 1.0 CB A:ASP233 4.4 37.8 1.0 ND1 A:HIS287 4.4 33.8 1.0 CG A:HIS287 4.4 33.7 1.0 NH2 A:ARG344 4.6 24.6 1.0 C4 A:OGA502 4.9 30.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine


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 ALKBH1 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:35.3 occ:1.00 O2 B:OGA502 2.1 34.2 1.0 OD1 B:ASP233 2.2 35.1 1.0 O2' B:OGA502 2.2 33.4 1.0 NE2 B:HIS231 2.2 37.7 1.0 NE2 B:HIS287 2.3 35.6 1.0 C1 B:OGA502 2.9 35.8 1.0 C2 B:OGA502 2.9 34.3 1.0 CG B:ASP233 3.1 37.5 1.0 CE1 B:HIS231 3.1 36.1 1.0 CD2 B:HIS287 3.2 33.8 1.0 CD2 B:HIS231 3.3 37.7 1.0 CE1 B:HIS287 3.3 38.0 1.0 OD2 B:ASP233 3.3 38.9 1.0 O1 B:OGA502 4.1 33.0 1.0 N1 B:OGA502 4.2 33.2 1.0 ND1 B:HIS231 4.3 35.5 1.0 CG B:HIS287 4.3 38.9 1.0 ND1 B:HIS287 4.3 35.3 1.0 CG B:HIS231 4.4 40.2 1.0 CB B:ASP233 4.5 39.0 1.0 NH2 B:ARG344 4.5 26.9 1.0 C4 B:OGA502 4.9 30.0 1.0 CD2 B:LEU228 5.0 30.9 1.0 CD1 B:LEU243 5.0 29.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine


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 ALKBH1 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn501 b:31.3 occ:1.00 O2 C:OGA502 1.9 41.5 1.0 OD2 C:ASP233 2.1 38.9 1.0 NE2 C:HIS231 2.2 37.8 1.0 O2' C:OGA502 2.2 41.4 1.0 NE2 C:HIS287 2.3 38.7 1.0 O C:HOH638 2.4 33.0 1.0 C1 C:OGA502 2.8 38.5 1.0 C2 C:OGA502 2.9 37.4 1.0 CG C:ASP233 3.0 44.7 1.0 CE1 C:HIS231 3.0 39.9 1.0 OD1 C:ASP233 3.1 38.2 1.0 CD2 C:HIS287 3.2 37.5 1.0 CD2 C:HIS231 3.2 41.7 1.0 CE1 C:HIS287 3.3 41.2 1.0 O1 C:OGA502 4.0 40.0 1.0 N1 C:OGA502 4.1 33.9 1.0 ND1 C:HIS231 4.2 37.3 1.0 CG C:HIS231 4.3 40.6 1.0 CG C:HIS287 4.4 42.1 1.0 CB C:ASP233 4.4 44.0 1.0 ND1 C:HIS287 4.4 40.9 1.0 O C:HOH666 4.4 36.1 1.0 NH2 C:ARG344 4.8 36.1 1.0 C4 C:OGA502 4.8 35.4 1.0 CD2 C:LEU228 4.9 31.2 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of ALKBH1 in Complex with Mn(II) and N-Oxalylglycine


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 ALKBH1 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:33.7 occ:1.00 O2 D:OGA502 1.9 38.5 1.0 NE2 D:HIS231 2.1 37.1 1.0 OD2 D:ASP233 2.2 38.4 1.0 O2' D:OGA502 2.3 44.0 1.0 NE2 D:HIS287 2.3 38.2 1.0 O D:HOH656 2.3 38.9 1.0 C1 D:OGA502 2.7 34.8 1.0 C2 D:OGA502 2.8 38.9 1.0 CG D:ASP233 2.9 45.3 1.0 CE1 D:HIS231 3.0 36.8 1.0 OD1 D:ASP233 3.1 41.9 1.0 CD2 D:HIS231 3.1 39.1 1.0 CD2 D:HIS287 3.2 35.3 1.0 CE1 D:HIS287 3.3 40.4 1.0 O1 D:OGA502 3.9 30.6 1.0 N1 D:OGA502 4.2 34.7 1.0 ND1 D:HIS231 4.2 39.7 1.0 CG D:HIS231 4.3 42.9 1.0 CG D:HIS287 4.4 36.2 1.0 NH2 D:ARG344 4.4 36.4 1.0 CB D:ASP233 4.4 44.0 1.0 ND1 D:HIS287 4.4 36.0 1.0 O D:HOH687 4.6 34.3 1.0 C4 D:OGA502 4.9 37.7 1.0 CD2 D:LEU228 4.9 29.2 1.0 CD1 D:LEU243 5.0 32.2 1.0

M.Zhang, S.Yang, W.Zhao, H.Li. Crystal Structure of Protein Zm To Be Published.