Manganese in PDB 4qkb: Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II)

The structure of Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II), PDB code: 4qkb was solved by G.Wang, Q.He, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.737, 82.759, 66.724, 90.00, 119.95, 90.00
R / Rfree (%)	15.8 / 18.1

The binding sites of Manganese atom in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) (pdb code 4qkb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II), PDB code: 4qkb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate 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 Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:13.4 occ:1.00 NE2 A:HIS177 2.0 19.2 1.0 OD1 A:ASP123 2.0 18.5 1.0 NE2 A:HIS121 2.1 16.0 1.0 O5 A:AKG302 2.2 20.1 1.0 O2 A:AKG302 2.2 20.7 1.0 C2 A:AKG302 2.8 20.6 1.0 CG A:ASP123 2.8 19.2 1.0 C1 A:AKG302 2.8 20.8 1.0 CE1 A:HIS177 2.9 19.4 1.0 CE1 A:HIS121 2.9 15.9 1.0 CD2 A:HIS177 3.0 19.1 1.0 OD2 A:ASP123 3.0 19.8 1.0 CD2 A:HIS121 3.2 16.3 1.0 ND1 A:HIS177 4.1 19.7 1.0 O1 A:AKG302 4.1 21.1 1.0 CG A:HIS177 4.1 19.4 1.0 ND1 A:HIS121 4.1 16.1 1.0 C3 A:AKG302 4.1 20.8 1.0 NH2 A:ARG203 4.2 19.5 1.0 CB A:ASP123 4.2 19.8 1.0 CG A:HIS121 4.3 16.5 1.0 CA A:ASP123 4.7 20.5 1.0 N A:ASP123 4.7 19.5 1.0 C4 A:AKG302 4.7 21.2 1.0

Manganese binding site 2 out of 7 in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate 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 Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:36.7 occ:1.00 NE2 B:HIS65 2.4 25.4 1.0 OE2 A:GLU75 2.4 18.6 1.0 OE2 A:GLU62 2.5 29.3 1.0 CD A:GLU62 3.2 28.4 1.0 CD2 B:HIS65 3.2 25.6 1.0 OE1 A:GLU62 3.3 27.9 1.0 CD A:GLU75 3.4 18.9 1.0 CE1 B:HIS65 3.5 25.4 1.0 CG A:GLU75 3.6 18.6 1.0 CG B:HIS65 4.5 26.2 1.0 CG A:GLU62 4.5 28.7 1.0 ND1 B:HIS65 4.5 25.9 1.0 CE2 A:PHE73 4.5 19.6 1.0 OE1 A:GLU75 4.6 18.6 1.0

Manganese binding site 3 out of 7 in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate 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 Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:34.2 occ:1.00 OE1 A:GLU189 2.1 27.1 1.0 CD A:GLU189 3.4 27.3 1.0 OE2 A:GLU189 4.2 27.4 1.0 CG A:GLU189 4.3 26.1 1.0 CB A:GLU189 5.0 25.6 1.0

Manganese binding site 4 out of 7 in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate 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 Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:15.9 occ:1.00 O5 B:AKG302 1.9 22.5 1.0 OD1 B:ASP123 2.0 21.1 1.0 NE2 B:HIS177 2.1 20.8 1.0 O2 B:AKG302 2.2 23.0 1.0 NE2 B:HIS121 2.3 19.3 1.0 C2 B:AKG302 2.6 22.5 1.0 CG B:ASP123 2.8 22.5 1.0 C1 B:AKG302 2.8 22.9 1.0 OD2 B:ASP123 2.9 22.6 1.0 CD2 B:HIS177 3.0 20.5 1.0 CE1 B:HIS177 3.1 20.6 1.0 CE1 B:HIS121 3.1 19.4 1.0 CD2 B:HIS121 3.3 19.2 1.0 C3 B:AKG302 4.0 21.6 1.0 O1 B:AKG302 4.0 23.3 1.0 CB B:ASP123 4.2 22.6 1.0 ND1 B:HIS177 4.2 20.5 1.0 CG B:HIS177 4.2 20.2 1.0 NH2 B:ARG203 4.2 19.0 1.0 ND1 B:HIS121 4.3 19.0 1.0 C4 B:AKG302 4.4 21.5 1.0 CG B:HIS121 4.4 19.2 1.0 CA B:ASP123 4.7 23.4 1.0 N B:ASP123 4.7 23.2 1.0

Manganese binding site 5 out of 7 in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:35.0 occ:1.00 OE2 B:GLU62 2.2 31.6 1.0 OE2 B:GLU75 2.4 20.6 1.0 NE2 C:HIS65 2.5 33.8 1.0 CD2 C:HIS65 3.1 33.5 1.0 CD B:GLU62 3.2 30.2 1.0 CD B:GLU75 3.3 20.2 1.0 CG B:GLU75 3.4 20.1 1.0 OE1 B:GLU62 3.5 30.7 1.0 CE1 C:HIS65 3.7 34.2 1.0 CG C:HIS65 4.4 32.8 1.0 OE1 B:GLU75 4.5 20.0 1.0 CG B:GLU62 4.6 29.5 1.0 CE2 B:PHE73 4.6 19.6 1.0 ND1 C:HIS65 4.6 34.1 1.0 CB B:GLU75 4.9 20.0 1.0

Manganese binding site 6 out of 7 in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:19.8 occ:1.00 OD1 C:ASP123 2.0 24.1 1.0 NE2 C:HIS177 2.0 26.1 1.0 O5 C:AKG302 2.1 26.3 1.0 NE2 C:HIS121 2.2 23.4 1.0 O2 C:AKG302 2.2 26.3 1.0 C2 C:AKG302 2.8 26.6 1.0 C1 C:AKG302 2.9 26.6 1.0 CG C:ASP123 2.9 24.6 1.0 CD2 C:HIS177 3.0 25.6 1.0 CE1 C:HIS177 3.0 26.1 1.0 CD2 C:HIS121 3.1 23.5 1.0 CE1 C:HIS121 3.1 23.7 1.0 OD2 C:ASP123 3.2 25.4 1.0 NH2 C:ARG203 3.9 21.2 1.0 O1 C:AKG302 4.1 26.7 1.0 ND1 C:HIS177 4.1 26.6 1.0 CG C:HIS177 4.2 26.2 1.0 C3 C:AKG302 4.2 26.4 1.0 ND1 C:HIS121 4.2 23.6 1.0 CG C:HIS121 4.3 24.0 1.0 CB C:ASP123 4.3 25.1 1.0 C4 C:AKG302 4.6 26.6 1.0 CA C:ASP123 4.7 26.2 1.0 N C:ASP123 4.7 25.4 1.0

Manganese binding site 7 out of 7 in the Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Seleno-Methionine Labelled Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn303 b:40.6 occ:1.00 OE2 C:GLU75 2.3 32.5 1.0 OE2 C:GLU62 2.5 33.5 1.0 NE2 A:HIS65 2.6 29.0 1.0 OE1 C:GLU62 3.0 33.4 1.0 CD C:GLU62 3.0 33.6 1.0 CD C:GLU75 3.2 31.2 1.0 CD2 A:HIS65 3.4 28.3 1.0 CG C:GLU75 3.5 29.7 1.0 CE1 A:HIS65 3.7 29.1 1.0 CE2 C:PHE73 4.2 26.5 1.0 CG C:GLU62 4.4 33.5 1.0 OE1 C:GLU75 4.4 31.2 1.0 CG A:HIS65 4.7 28.1 1.0 CZ C:PHE73 4.7 26.5 1.0 ND1 A:HIS65 4.8 29.0 1.0 CD2 A:TYR63 4.8 36.3 1.0 CB C:GLU75 4.9 27.5 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