Manganese in PDB 6ej0: Crystal Structure of KDM5B in Complex with KDOPZ000049A.

The structure of Crystal Structure of KDM5B in Complex with KDOPZ000049A., PDB code: 6ej0 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)	51.81 / 2.06
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.820, 141.820, 151.750, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 21

The structure of Crystal Structure of KDM5B in Complex with KDOPZ000049A. also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Crystal Structure of KDM5B in Complex with KDOPZ000049A. (pdb code 6ej0). 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 KDOPZ000049A., PDB code: 6ej0:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of KDM5B in Complex with KDOPZ000049A.


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 KDOPZ000049A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:81.9 occ:0.60 O A:HOH909 2.4 63.7 1.0 O A:THR416 2.6 71.1 1.0 OD1 A:ASN91 2.6 56.8 1.0 O A:LEU413 2.7 55.0 1.0 O A:LEU90 3.0 57.9 1.0 O A:GLU419 3.1 78.2 1.0 C A:THR416 3.6 74.4 1.0 CG A:ASN91 3.8 62.8 1.0 C A:LEU413 3.9 52.9 1.0 O A:VAL414 3.9 49.9 1.0 C A:VAL414 4.0 51.8 1.0 CA A:VAL414 4.0 46.4 1.0 C A:LEU90 4.1 51.5 1.0 C A:GLU419 4.2 76.0 1.0 N A:THR416 4.2 67.0 1.0 CA A:ASN91 4.2 59.4 1.0 CA A:ILE417 4.3 85.1 1.0 N A:ILE417 4.4 78.8 1.0 N A:VAL414 4.4 49.0 1.0 CA A:THR416 4.5 70.2 1.0 CB A:ASN91 4.5 60.0 1.0 CB A:GLU419 4.5 74.4 1.0 N A:ASN91 4.6 53.5 1.0 N A:GLU419 4.7 78.4 1.0 N A:SER415 4.7 57.0 1.0 CA A:GLU419 4.7 77.5 1.0 C A:ILE417 4.8 85.8 1.0 ND2 A:ASN91 4.8 67.8 1.0 C A:SER415 4.9 69.7 1.0 CB A:THR416 5.0 73.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of KDM5B in Complex with KDOPZ000049A.


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 KDOPZ000049A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn810 b:36.0 occ:1.00 O A:HOH926 1.9 43.3 1.0 NE2 A:HIS499 2.0 37.3 1.0 OE2 A:GLU501 2.0 45.5 1.0 N2 A:B7K811 2.1 41.0 1.0 O A:HOH975 2.1 38.3 1.0 NE2 A:HIS587 2.2 41.2 1.0 CE1 A:HIS499 2.9 41.1 1.0 CE1 A:HIS587 3.1 42.2 1.0 CD A:GLU501 3.1 39.8 1.0 CD2 A:HIS499 3.1 39.5 1.0 CD2 A:HIS587 3.2 40.3 1.0 C3 A:B7K811 3.2 43.2 1.0 OE1 A:GLU501 3.4 47.1 1.0 ND1 A:HIS499 4.1 40.0 1.0 O A:HOH1063 4.1 59.2 1.0 CG A:HIS499 4.2 35.6 1.0 ND1 A:HIS587 4.2 40.5 1.0 CG A:HIS587 4.3 38.2 1.0 CG A:GLU501 4.4 41.1 1.0 O A:DMS806 4.4 66.5 1.0 OG A:SER507 4.4 44.3 1.0 O A:HOH999 4.5 47.0 1.0 O A:HOH1009 4.5 48.8 1.0 C2 A:DMS806 4.6 67.3 1.0 C2 A:B7K811 4.6 41.8 1.0 S A:DMS806 4.8 86.9 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.