Manganese in PDB 6h4z: Crystal Structure of Human KDM5B in Complex with Compound 16A

The structure of Crystal Structure of Human KDM5B in Complex with Compound 16A, PDB code: 6h4z was solved by Y.V.Le Bihan, S.Velupillai, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.69 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	144.480, 144.480, 154.350, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 21.1

The structure of Crystal Structure of Human KDM5B in Complex with Compound 16A also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Manganese atom in the Crystal Structure of Human KDM5B in Complex with Compound 16A (pdb code 6h4z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human KDM5B in Complex with Compound 16A, PDB code: 6h4z:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Human KDM5B in Complex with Compound 16A


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 KDM5B in Complex with Compound 16A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn803 b:40.4 occ:1.00 N2 A:FQ5805 1.9 29.7 0.8 N3 A:FQ5805 2.1 31.7 0.8 OE2 A:GLU501 2.2 48.7 1.0 NE2 A:HIS499 2.2 38.6 1.0 O A:HOH920 2.3 55.8 1.0 NE2 A:HIS587 2.4 39.5 1.0 N1 A:FQ5805 2.7 34.0 0.8 C14 A:FQ5805 2.9 31.6 0.8 C13 A:FQ5805 3.0 33.4 0.8 CD A:GLU501 3.2 50.5 1.0 CE1 A:HIS499 3.2 37.8 1.0 C15 A:FQ5805 3.2 27.9 0.8 CD2 A:HIS499 3.2 39.1 1.0 CD2 A:HIS587 3.3 39.2 1.0 CE1 A:HIS587 3.4 39.3 1.0 OE1 A:GLU501 3.6 40.1 1.0 C12 A:FQ5805 4.0 35.7 0.8 C11 A:FQ5805 4.1 38.6 0.8 C18 A:FQ5805 4.3 29.9 0.8 ND1 A:HIS499 4.3 39.0 1.0 CG A:HIS499 4.3 37.9 1.0 CG A:GLU501 4.5 43.1 1.0 C16 A:FQ5805 4.5 29.4 0.8 CG A:HIS587 4.5 37.8 1.0 ND1 A:HIS587 4.5 39.9 1.0 OG A:SER507 4.6 44.9 1.0 C1 A:DMS807 4.8 63.6 0.8 C17 A:FQ5805 4.9 30.3 0.8

Manganese binding site 2 out of 3 in the Crystal Structure of Human KDM5B in Complex with Compound 16A


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 KDM5B in Complex with Compound 16A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn804 b:82.7 occ:0.52 O A:THR416 2.6 76.5 1.0 O A:LEU413 2.7 59.4 1.0 O A:HOH936 2.8 80.0 1.0 OD1 A:ASN91 2.9 69.0 1.0 O A:GLU419 3.0 83.3 1.0 O A:LEU90 3.0 68.1 0.3 O A:LEU90 3.1 68.3 0.7 C A:THR416 3.7 77.9 1.0 C A:LEU413 3.9 58.9 1.0 C A:GLU419 4.0 84.3 1.0 O A:VAL414 4.1 59.1 1.0 CG A:ASN91 4.1 79.0 1.0 O A:HOH1043 4.1 70.5 1.0 C A:VAL414 4.1 59.2 1.0 C A:LEU90 4.2 67.7 0.3 CA A:VAL414 4.2 52.7 1.0 CB A:GLU419 4.3 81.4 1.0 C A:LEU90 4.3 67.7 0.7 N A:THR416 4.3 67.8 1.0 CA A:THR416 4.5 70.3 1.0 N A:VAL414 4.5 53.6 1.0 CA A:GLU419 4.6 82.2 1.0 CA A:ASN91 4.6 64.8 1.0 N A:ILE417 4.7 79.3 1.0 N A:GLU419 4.8 83.9 1.0 N A:SER415 4.8 57.8 1.0 CB A:ASN91 4.8 65.1 1.0 N A:ASN91 4.9 64.2 1.0 CA A:ILE417 4.9 82.0 1.0 O A:ILE417 4.9 88.8 1.0 CB A:THR416 5.0 76.2 1.0 C A:SER415 5.0 66.5 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Human KDM5B in Complex with Compound 16A


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 KDM5B in Complex with Compound 16A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn822 b:0.5 occ:1.00 OD2 A:ASP630 3.4 45.4 1.0 O A:HOH1178 3.6 58.7 1.0 O A:HOH1016 3.7 65.8 1.0 NH1 A:ARG612 4.2 42.5 1.0 OE1 A:GLU662 4.3 47.4 1.0 C2 A:EDO816 4.3 36.9 0.8 CG A:ASP630 4.3 41.4 1.0 O A:MET658 4.5 45.7 1.0 OD1 A:ASP630 4.5 41.7 1.0 CG A:MET658 4.5 41.1 1.0 CB A:ASP661 4.6 45.1 1.0 CD1 A:LEU665 4.9 45.9 1.0 O A:HOH906 4.9 54.6 1.0 O A:HOH1113 4.9 57.6 1.0 N A:GLU662 4.9 42.2 1.0 CA A:MET658 5.0 40.0 1.0

Y.V.Le Bihan, R.M.Lanigan, B.Atrash, M.G.Mclaughlin, S.Velupillai, A.G.Malcolm, K.S.England, G.F.Ruda, N.Y.Mok, A.Tumber, K.Tomlin, H.Saville, E.Shehu, C.Mcandrew, L.Carmichael, J.M.Bennett, F.Jeganathan, P.Eve, A.Donovan, A.Hayes, F.Wood, F.I.Raynaud, O.Fedorov, P.E.Brennan, R.Burke, R.L.M.Van Montfort, O.W.Rossanese, J.Blagg, V.Bavetsias. C8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-Ones: Studies Towards the Identification of Potent, Cell Penetrant Jumonji C Domain Containing Histone Lysine Demethylase 4 Subfamily (KDM4) Inhibitors, Compound Profiling in Cell-Based Target Engagement Assays. Eur.J.Med.Chem. V. 177 316 2019.
ISSN: ISSN 0223-5234
PubMed: 31158747
DOI: 10.1016/J.EJMECH.2019.05.041