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

The structure of Crystal Structure of Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II), PDB code: 4qkd 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)	33.40 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.426, 82.048, 66.414, 90.00, 120.03, 90.00
R / Rfree (%)	14.6 / 16.3

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) (pdb code 4qkd). 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II), PDB code: 4qkd:
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 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:9.0 occ:1.00 O2 A:AKG302 2.1 10.1 1.0 NE2 A:HIS121 2.1 11.5 1.0 O5 A:AKG302 2.1 9.7 1.0 OD1 A:ASP123 2.1 9.6 1.0 NE2 A:HIS177 2.1 8.9 1.0 O A:HOH437 2.2 10.9 1.0 C2 A:AKG302 2.8 10.3 1.0 C1 A:AKG302 2.8 10.8 1.0 CE1 A:HIS121 3.0 12.1 1.0 CG A:ASP123 3.0 12.1 1.0 CE1 A:HIS177 3.1 9.7 1.0 CD2 A:HIS121 3.1 10.7 1.0 CD2 A:HIS177 3.1 10.1 1.0 OD2 A:ASP123 3.3 11.1 1.0 O A:HOH404 4.0 17.7 1.0 O1 A:AKG302 4.0 13.4 1.0 O A:HOH488 4.0 14.7 1.0 ND1 A:HIS121 4.1 11.2 1.0 C3 A:AKG302 4.2 11.6 1.0 ND1 A:HIS177 4.2 13.3 1.0 CG A:HIS121 4.2 9.8 1.0 NH2 A:ARG203 4.3 11.8 1.0 CG A:HIS177 4.3 10.9 1.0 CB A:ASP123 4.4 12.2 1.0 C4 A:AKG302 4.6 12.8 1.0 CA A:ASP123 4.8 11.2 1.0 N A:ASP123 4.8 11.1 1.0

Manganese binding site 2 out of 7 in the Crystal Structure of 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:14.6 occ:1.00 O A:HOH446 2.2 17.1 1.0 OE2 A:GLU62 2.2 15.0 1.0 OE2 A:GLU75 2.2 11.5 1.0 O A:HOH422 2.3 17.7 1.0 NE2 C:HIS65 2.3 16.0 1.0 O A:HOH442 2.3 14.1 1.0 CD A:GLU62 3.1 15.2 1.0 CD2 C:HIS65 3.2 14.4 1.0 CD A:GLU75 3.2 12.3 1.0 CE1 C:HIS65 3.3 16.6 1.0 OE1 A:GLU62 3.4 14.1 1.0 CG A:GLU75 3.5 11.7 1.0 O A:HOH411 3.8 13.3 1.0 O A:HOH457 3.9 22.8 1.0 O C:HOH428 4.0 20.6 1.0 O A:HOH582 4.3 37.1 1.0 CE2 A:PHE73 4.4 14.2 1.0 ND1 C:HIS65 4.4 16.7 1.0 CG C:HIS65 4.4 14.9 1.0 OE1 A:GLU75 4.4 14.1 1.0 CG A:GLU62 4.5 13.8 1.0 O A:HOH491 4.7 30.3 1.0 O C:HOH463 4.7 18.1 1.0 CZ A:PHE73 4.9 12.6 1.0 CB A:GLU75 5.0 11.6 1.0

Manganese binding site 3 out of 7 in the Crystal Structure of 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:9.2 occ:1.00 O2 B:AKG302 2.1 10.1 1.0 NE2 B:HIS177 2.1 11.1 1.0 NE2 B:HIS121 2.1 11.4 1.0 OD1 B:ASP123 2.1 11.1 1.0 O5 B:AKG302 2.2 10.7 1.0 O B:HOH427 2.2 12.6 1.0 C2 B:AKG302 2.8 11.7 1.0 C1 B:AKG302 2.8 11.8 1.0 CE1 B:HIS121 2.9 10.4 1.0 CG B:ASP123 3.0 11.1 1.0 CE1 B:HIS177 3.0 12.5 1.0 CD2 B:HIS177 3.1 10.0 1.0 CD2 B:HIS121 3.2 10.4 1.0 OD2 B:ASP123 3.4 13.1 1.0 O B:HOH446 3.9 20.2 1.0 O B:HOH428 3.9 12.9 1.0 O1 B:AKG302 4.0 13.3 1.0 ND1 B:HIS121 4.1 10.4 1.0 ND1 B:HIS177 4.1 12.5 1.0 C3 B:AKG302 4.2 11.5 1.0 CG B:HIS177 4.2 11.2 1.0 CG B:HIS121 4.2 11.5 1.0 NH2 B:ARG203 4.2 11.8 1.0 CB B:ASP123 4.4 11.4 1.0 C4 B:AKG302 4.6 11.3 1.0 CA B:ASP123 4.8 12.4 1.0 N B:ASP123 4.8 11.6 1.0

Manganese binding site 4 out of 7 in the Crystal Structure of 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:14.1 occ:1.00 O B:HOH409 2.2 15.6 1.0 OE2 B:GLU62 2.2 12.8 1.0 O B:HOH444 2.2 13.4 1.0 O B:HOH449 2.2 15.8 1.0 OE2 B:GLU75 2.2 12.4 1.0 NE2 A:HIS65 2.3 13.6 1.0 CD B:GLU62 3.1 14.9 1.0 CD B:GLU75 3.2 12.6 1.0 CD2 A:HIS65 3.2 13.7 1.0 CE1 A:HIS65 3.2 15.0 1.0 OE1 B:GLU62 3.4 15.3 1.0 CG B:GLU75 3.5 10.9 1.0 O B:HOH467 3.8 22.9 1.0 O B:HOH423 3.8 11.2 1.0 O A:HOH518 4.0 21.4 1.0 ND1 A:HIS65 4.4 17.3 1.0 OE1 B:GLU75 4.4 12.7 1.0 CG A:HIS65 4.4 15.4 1.0 CE2 B:PHE73 4.5 9.6 1.0 CG B:GLU62 4.5 14.8 1.0 O B:HOH541 4.5 28.1 1.0 O B:HOH498 4.6 21.7 1.0 CZ B:PHE73 5.0 9.4 1.0

Manganese binding site 5 out of 7 in the Crystal Structure of 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:25.3 occ:1.00 OE1 B:GLU189 2.1 20.8 1.0 O B:HOH554 2.1 32.4 1.0 O B:HOH528 2.3 29.0 1.0 O B:HOH502 2.4 33.9 1.0 CD B:GLU189 3.2 16.1 1.0 CG B:GLU189 3.7 14.5 1.0 O B:HOH515 3.9 24.7 1.0 O B:HOH546 4.0 32.9 1.0 OE2 B:GLU189 4.2 17.2 1.0 CB B:GLU189 4.7 13.8 1.0 NH2 B:ARG19 4.8 33.1 1.0

Manganese binding site 6 out of 7 in the Crystal Structure of 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:12.8 occ:1.00 O2 C:AKG302 2.0 13.6 1.0 NE2 C:HIS121 2.1 16.2 1.0 OD1 C:ASP123 2.1 15.4 1.0 O C:HOH421 2.1 15.1 1.0 O5 C:AKG302 2.1 15.4 1.0 NE2 C:HIS177 2.1 14.3 1.0 C1 C:AKG302 2.8 15.1 1.0 C2 C:AKG302 2.8 16.0 1.0 CE1 C:HIS121 3.0 13.8 1.0 CE1 C:HIS177 3.0 14.4 1.0 CG C:ASP123 3.0 15.2 1.0 CD2 C:HIS121 3.1 12.9 1.0 CD2 C:HIS177 3.1 15.6 1.0 OD2 C:ASP123 3.4 16.2 1.0 O C:HOH444 3.9 17.1 1.0 O C:HOH401 3.9 21.7 1.0 O1 C:AKG302 4.0 15.8 1.0 ND1 C:HIS121 4.1 12.8 1.0 ND1 C:HIS177 4.2 17.1 1.0 CG C:HIS121 4.2 12.9 1.0 C3 C:AKG302 4.2 16.3 1.0 CG C:HIS177 4.2 17.0 1.0 NH2 C:ARG203 4.3 13.6 1.0 CB C:ASP123 4.4 15.5 1.0 C4 C:AKG302 4.6 17.3 1.0 CA C:ASP123 4.8 15.0 1.0 N C:ASP123 4.8 16.3 1.0

Manganese binding site 7 out of 7 in the Crystal Structure of 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 Human ALKBH7 in Complex with Alpha-Ketoglutarate and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn303 b:15.3 occ:1.00 OE2 C:GLU62 2.1 15.0 1.0 OE2 C:GLU75 2.2 14.4 1.0 O C:HOH477 2.2 15.3 1.0 O C:HOH476 2.2 18.6 1.0 NE2 B:HIS65 2.3 14.3 1.0 O C:HOH479 2.3 14.9 1.0 CD C:GLU62 3.1 14.1 1.0 CD2 B:HIS65 3.2 14.1 1.0 CD C:GLU75 3.2 15.0 1.0 CE1 B:HIS65 3.3 15.6 1.0 OE1 C:GLU62 3.4 18.4 1.0 CG C:GLU75 3.5 15.4 1.0 O C:HOH408 3.8 15.9 1.0 O C:HOH488 3.9 23.1 1.0 O B:HOH403 4.1 20.2 1.0 CE2 C:PHE73 4.4 15.1 1.0 CG B:HIS65 4.4 15.6 1.0 ND1 B:HIS65 4.4 16.8 1.0 OE1 C:GLU75 4.4 16.1 1.0 CG C:GLU62 4.5 15.2 1.0 O C:HOH470 4.6 20.3 1.0 O C:HOH513 4.7 35.5 1.0 CZ C:PHE73 4.9 14.5 1.0 CB C:GLU75 5.0 14.8 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