Manganese in PDB 4ima: The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp

All present enzymatic activity of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp:
2.7.1.40;

The structure of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp, PDB code: 4ima was solved by B.Zhang, T.Holyoak, A.W.Fenton, Q.L.Tang, C.B.Prasannan, J.P.Deng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.89 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.751, 204.727, 86.532, 90.00, 96.75, 90.00
R / Rfree (%)	19.8 / 23.3

The binding sites of Manganese atom in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp (pdb code 4ima). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp, PDB code: 4ima:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:37.9 occ:1.00 OE1 A:GLU284 2.1 32.9 1.0 OD2 A:ASP308 2.1 34.5 1.0 OB1 A:FLC602 2.2 33.8 1.0 OHB A:FLC602 2.2 32.9 0.8 O A:HOH894 2.3 37.0 1.0 O A:HOH886 2.3 37.8 1.0 CBC A:FLC602 2.9 32.8 1.0 CB A:FLC602 3.0 37.1 1.0 CG A:ASP308 3.2 35.8 1.0 CD A:GLU284 3.2 33.8 1.0 CB A:ASP308 3.5 33.9 1.0 OE2 A:GLU284 3.5 34.3 1.0 CG A:FLC602 3.8 35.8 0.9 OG1 A:FLC602 4.0 37.3 0.8 OB2 A:FLC602 4.1 29.2 1.0 NZ A:LYS282 4.2 31.5 1.0 CA A:FLC602 4.3 30.8 0.9 OD1 A:ASP308 4.3 39.2 1.0 CE1 A:PHE256 4.3 40.5 1.0 N A:ASP308 4.4 28.5 1.0 CGC A:FLC602 4.4 36.0 0.0 O A:HOH872 4.4 44.9 1.0 CG A:GLU284 4.5 35.9 1.0 CE A:LYS282 4.5 33.6 1.0 CA A:ASP308 4.6 30.5 1.0 CB A:ALA305 4.7 32.3 1.0 CB A:GLU284 4.8 30.7 1.0 CZ A:PHE256 4.9 41.6 1.0 CD1 A:PHE256 5.0 36.4 1.0

Manganese binding site 2 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:34.4 occ:1.00 OD2 B:ASP308 2.1 32.0 1.0 OE2 B:GLU284 2.1 30.0 1.0 OHB B:FLC602 2.2 29.5 1.0 OB2 B:FLC602 2.2 33.1 1.0 O B:HOH893 2.3 30.6 1.0 O B:HOH898 2.3 34.9 1.0 CBC B:FLC602 3.0 32.2 1.0 CB B:FLC602 3.1 33.1 0.5 CG B:ASP308 3.1 35.0 1.0 CD B:GLU284 3.1 32.2 1.0 OE1 B:GLU284 3.5 31.6 1.0 CB B:ASP308 3.6 28.7 1.0 CG B:FLC602 3.9 36.4 0.7 OG2 B:FLC602 4.0 35.1 0.6 OB1 B:FLC602 4.2 35.5 1.0 OD1 B:ASP308 4.2 36.3 1.0 NZ B:LYS282 4.2 31.6 1.0 O B:HOH895 4.3 39.2 1.0 CA B:FLC602 4.3 32.7 1.0 N B:ASP308 4.3 30.0 1.0 CGC B:FLC602 4.4 35.1 0.1 CE1 B:PHE256 4.4 35.1 1.0 CG B:GLU284 4.4 25.6 1.0 CE B:LYS282 4.5 31.4 1.0 CA B:ASP308 4.6 33.4 1.0 CB B:ALA305 4.6 30.3 1.0 CB B:GLU284 4.8 31.9 1.0 O B:HOH852 4.8 49.9 1.0 CD1 B:PHE256 5.0 36.6 1.0

Manganese binding site 3 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:36.4 occ:1.00 OHB C:FLC602 2.1 32.8 1.0 OD2 C:ASP308 2.1 33.9 1.0 OB1 C:FLC602 2.1 33.5 1.0 OE2 C:GLU284 2.1 33.1 1.0 O C:HOH759 2.3 33.3 1.0 O C:HOH906 2.3 35.7 1.0 CBC C:FLC602 2.9 31.4 1.0 CB C:FLC602 2.9 36.8 1.0 CD C:GLU284 3.1 29.8 1.0 CG C:ASP308 3.2 30.8 1.0 OE1 C:GLU284 3.6 31.7 1.0 CB C:ASP308 3.6 30.7 1.0 CG C:FLC602 3.6 35.4 1.0 OG2 C:FLC602 3.9 37.8 0.6 OB2 C:FLC602 4.1 33.1 1.0 CA C:FLC602 4.2 33.1 1.0 CGC C:FLC602 4.2 36.6 0.2 NZ C:LYS282 4.2 33.9 1.0 OD1 C:ASP308 4.3 36.9 1.0 N C:ASP308 4.3 33.1 1.0 CG C:GLU284 4.4 29.5 1.0 CE C:LYS282 4.5 28.3 1.0 CA C:ASP308 4.6 32.6 1.0 CE1 C:PHE256 4.7 38.6 1.0 CB C:ALA305 4.7 27.8 1.0 O C:HOH765 4.9 49.5 1.0 CB C:GLU284 4.9 30.8 1.0 CAC C:FLC602 4.9 35.1 0.7

Manganese binding site 4 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:43.8 occ:1.00 OD2 D:ASP308 2.1 44.5 1.0 OE2 D:GLU284 2.1 33.2 1.0 OB1 D:FLC602 2.2 35.2 1.0 OHB D:FLC602 2.2 39.5 1.0 O D:HOH880 2.3 42.4 1.0 O D:HOH884 2.3 47.2 1.0 CBC D:FLC602 2.9 38.1 1.0 CB D:FLC602 3.0 42.7 1.0 CG D:ASP308 3.2 37.2 1.0 CD D:GLU284 3.2 37.6 1.0 OE1 D:GLU284 3.6 40.4 1.0 CB D:ASP308 3.6 35.6 1.0 CG D:FLC602 3.8 44.8 1.0 OG2 D:FLC602 4.0 44.0 1.0 OB2 D:FLC602 4.1 33.8 1.0 NZ D:LYS282 4.2 35.5 1.0 OD1 D:ASP308 4.2 40.4 1.0 CA D:FLC602 4.3 34.7 1.0 CGC D:FLC602 4.3 42.0 0.0 N D:ASP308 4.4 31.0 1.0 CG D:GLU284 4.4 36.8 1.0 CE D:LYS282 4.5 33.5 1.0 CE1 D:PHE256 4.5 46.0 1.0 CA D:ASP308 4.6 39.3 1.0 CB D:ALA305 4.6 27.6 1.0 CB D:GLU284 4.9 32.7 1.0 CAC D:FLC602 5.0 38.2 0.3 CD1 D:PHE256 5.0 39.3 1.0

T.Holyoak, B.Zhang, J.Deng, Q.Tang, C.B.Prasannan, A.W.Fenton. Energetic Coupling Between An Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase. Biochemistry V. 52 466 2013.
ISSN: ISSN 0006-2960
PubMed: 23270483
DOI: 10.1021/BI301341R