Manganese in PDB 6eiy: Crystal Structure of KDM5B in Complex with KDOPZ000034A.

The structure of Crystal Structure of KDM5B in Complex with KDOPZ000034A., PDB code: 6eiy was solved by V.Srikannathasan, J.A.Newman, A.Szykowska, M.Wright, G.F.Ruda, S.A.Vazquez-Rodriguez, K.Kupinska, C.Strain-Damerell, N.A.Burgess-Brown, C.H.Arrowsmith, A.Edwards, C.Bountra, U.Oppermann, K.Huber, F.Vondelft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.98 / 2.15
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.380, 142.380, 152.170, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 21.5

The structure of Crystal Structure of KDM5B in Complex with KDOPZ000034A. also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Manganese atom in the Crystal Structure of KDM5B in Complex with KDOPZ000034A. (pdb code 6eiy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of KDM5B in Complex with KDOPZ000034A., PDB code: 6eiy:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of KDM5B in Complex with KDOPZ000034A.


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 KDM5B in Complex with KDOPZ000034A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:84.3 occ:0.65 OD1 A:ASN91 2.6 52.3 1.0 O A:LEU413 2.7 47.1 1.0 O A:THR416 2.8 77.5 1.0 O A:GLU419 3.0 81.5 1.0 O A:LEU90 3.0 46.8 1.0 CG A:ASN91 3.8 54.6 1.0 C A:THR416 3.9 76.8 1.0 C A:LEU413 3.9 45.0 1.0 O A:VAL414 3.9 52.1 1.0 C A:GLU419 4.0 70.9 1.0 C A:VAL414 4.0 51.1 1.0 CA A:VAL414 4.1 43.8 1.0 C A:LEU90 4.1 47.6 1.0 CA A:ASN91 4.2 53.2 1.0 CB A:GLU419 4.2 62.5 1.0 N A:THR416 4.4 69.5 1.0 CB A:ASN91 4.5 54.9 1.0 N A:VAL414 4.5 44.2 1.0 CA A:GLU419 4.6 69.5 1.0 N A:ASN91 4.6 50.5 1.0 CA A:ILE417 4.7 85.6 1.0 CA A:THR416 4.7 71.1 1.0 N A:ILE417 4.7 81.7 1.0 N A:SER415 4.8 52.9 1.0 ND2 A:ASN91 4.8 58.9 1.0 N A:GLU419 4.9 69.6 1.0 N A:ASP420 4.9 65.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of KDM5B in Complex with KDOPZ000034A.


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 KDM5B in Complex with KDOPZ000034A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn809 b:37.0 occ:1.00 OE1 A:GLU501 2.0 46.3 1.0 NE2 A:HIS499 2.1 41.0 1.0 N4 A:B6W810 2.1 38.1 1.0 O A:HOH965 2.1 41.4 1.0 O A:HOH995 2.2 38.0 1.0 NE2 A:HIS587 2.2 37.7 1.0 CE1 A:HIS499 3.0 43.1 1.0 CD A:GLU501 3.0 44.2 1.0 CE1 A:HIS587 3.1 35.4 1.0 CD2 A:HIS499 3.2 41.1 1.0 C15 A:B6W810 3.2 35.4 1.0 CD2 A:HIS587 3.2 37.5 1.0 OE2 A:GLU501 3.4 51.1 1.0 O A:HOH1061 4.1 47.9 1.0 ND1 A:HIS499 4.1 41.1 1.0 ND1 A:HIS587 4.2 40.3 1.0 CG A:HIS499 4.2 37.0 1.0 CG A:GLU501 4.3 41.9 1.0 CG A:HIS587 4.3 41.1 1.0 O A:DMS807 4.3 68.3 1.0 O A:HOH991 4.4 38.4 1.0 C2 A:DMS807 4.5 63.6 1.0 OG A:SER507 4.5 43.1 1.0 C14 A:B6W810 4.7 42.2 1.0 O A:HOH1037 4.7 45.9 1.0 S A:DMS807 4.7 85.8 1.0

V.Srikannathasan, V.Srikannathasan, J.A.Newman, A.Szykowska, M.Wright, G.F.Ruda, S.A.Vazquez-Rodriguez, K.Kupinska, C.Strain-Damerell, N.A.Burgess-Brown, C.H.Arrowsmith, A.Edwards, C.Bountra, U.Oppermann, K.Huber, F.Vondelft. N/A N/A.