Manganese in PDB 4qkf: Crystal Structure of Human ALKBH7 in Complex with N-Oxalylglycine and Mn(II)

The structure of Crystal Structure of Human ALKBH7 in Complex with N-Oxalylglycine and Mn(II), PDB code: 4qkf was solved by G.Wang, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.37 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.364, 81.958, 66.082, 90.00, 119.94, 90.00
R / Rfree (%)	15.9 / 16.5

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH7 in Complex with N-Oxalylglycine and Mn(II) (pdb code 4qkf). 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 ALKBH7 in Complex with N-Oxalylglycine and Mn(II), PDB code: 4qkf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Human ALKBH7 in Complex with N-Oxalylglycine and Mn(II)


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 ALKBH7 in Complex with N-Oxalylglycine and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:21.3 occ:1.00 OD1 A:ASP123 2.3 14.5 1.0 NE2 A:HIS121 2.4 27.5 1.0 NE2 A:HIS177 2.4 19.7 1.0 O2' A:OGA301 2.4 23.1 1.0 C2 A:OGA301 2.7 25.3 1.0 O2 A:OGA301 2.7 25.1 1.0 C1 A:OGA301 2.9 24.4 1.0 CD2 A:HIS121 3.0 29.3 1.0 CE1 A:HIS177 3.1 22.1 1.0 CG A:ASP123 3.3 17.2 1.0 O A:HOH430 3.4 33.7 1.0 CE1 A:HIS121 3.5 23.2 1.0 CD2 A:HIS177 3.5 22.7 1.0 OD2 A:ASP123 3.7 15.3 1.0 N1 A:OGA301 3.7 26.7 1.0 O1 A:OGA301 3.8 30.5 1.0 NH2 A:ARG203 4.2 19.2 1.0 CG A:HIS121 4.2 28.5 1.0 ND1 A:HIS177 4.3 23.6 1.0 ND1 A:HIS121 4.4 27.5 1.0 CG A:HIS177 4.5 22.6 1.0 CB A:ASP123 4.6 19.4 1.0 C4 A:OGA301 4.8 28.6 1.0 N A:ASP123 4.8 22.7 1.0 CA A:ASP123 4.8 22.2 1.0 O A:HIS121 5.0 31.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human ALKBH7 in Complex with N-Oxalylglycine and Mn(II)


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 ALKBH7 in Complex with N-Oxalylglycine and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:27.5 occ:1.00 NE2 B:HIS121 2.0 32.2 1.0 NE2 B:HIS177 2.3 33.1 1.0 OD1 B:ASP123 2.3 28.2 1.0 CE1 B:HIS121 2.6 34.5 1.0 O B:HOH426 2.6 28.3 1.0 O A:HOH449 2.8 17.3 1.0 CE1 B:HIS177 3.1 34.3 1.0 CD2 B:HIS121 3.2 33.7 1.0 CG B:ASP123 3.3 29.4 1.0 CD2 B:HIS177 3.4 35.3 1.0 OD2 B:ASP123 3.6 26.4 1.0 ND1 B:HIS121 3.8 31.9 1.0 CG B:HIS121 4.1 30.5 1.0 ND1 B:HIS177 4.3 33.2 1.0 NH2 B:ARG203 4.4 31.4 1.0 CG B:HIS177 4.4 34.0 1.0 O B:HOH428 4.6 51.6 1.0 CB B:ASP123 4.6 29.9 1.0 N B:ASP123 4.7 29.0 1.0 O A:HOH418 4.8 21.1 1.0 CA B:ASP123 4.9 30.9 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human ALKBH7 in Complex with N-Oxalylglycine and Mn(II)


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 ALKBH7 in Complex with N-Oxalylglycine and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:25.4 occ:1.00 OD1 C:ASP123 2.0 26.7 1.0 O2 C:OGA302 2.3 32.6 1.0 O2' C:OGA302 2.4 32.1 1.0 NE2 C:HIS121 2.4 22.5 1.0 NE2 C:HIS177 2.4 21.8 1.0 CG C:ASP123 2.8 28.6 1.0 OD2 C:ASP123 3.0 29.6 1.0 C1 C:OGA302 3.1 31.6 1.0 C2 C:OGA302 3.1 31.4 1.0 CD2 C:HIS121 3.1 25.4 1.0 CE1 C:HIS121 3.4 26.4 1.0 CE1 C:HIS177 3.4 23.9 1.0 CD2 C:HIS177 3.4 22.1 1.0 O C:HOH408 3.7 21.7 1.0 O C:HOH457 3.9 24.7 1.0 CB C:ASP123 4.1 28.1 1.0 O1 C:OGA302 4.2 39.6 1.0 NH2 C:ARG203 4.2 29.9 1.0 CG C:HIS121 4.2 24.6 1.0 ND1 C:HIS121 4.3 26.4 1.0 N1 C:OGA302 4.4 29.2 1.0 ND1 C:HIS177 4.5 21.9 1.0 N C:ASP123 4.5 25.9 1.0 CA C:ASP123 4.5 28.1 1.0 CG C:HIS177 4.6 21.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human ALKBH7 in Complex with N-Oxalylglycine and Mn(II)


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 ALKBH7 in Complex with N-Oxalylglycine and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn303 b:37.5 occ:1.00 OE1 C:GLU189 2.5 32.4 1.0 CD C:GLU189 3.3 34.1 1.0 CG C:GLU189 3.7 35.0 1.0 OE2 C:GLU189 4.4 36.8 1.0 CB C:GLU189 4.5 35.8 1.0

G.Wang, Q.He, C.Feng, Y.Liu, Z.Deng, X.Qi, W.Wu, P.Mei, Z.Chen. The Atomic-Resolution Structure of Human Alkb Homolog 7 (ALKBH7), A Key Protein For Programmed Necrosis and Fat Metabolism J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.590505