Manganese in PDB 5fy4: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate, PDB code: 5fy4 was solved by R.Nowak, V.Srikannathasan, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.07 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.140, 142.140, 152.100, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 19.3

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate (pdb code 5fy4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate, PDB code: 5fy4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate


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 the Catalytic Domain of Human JARID1B in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1755 b:64.1 occ:0.53 O A:HOH2038 2.5 61.6 1.0 O A:LEU413 2.6 50.3 1.0 O A:THR416 2.7 60.8 1.0 O A:LEU90 2.9 52.7 1.0 O A:HOH2040 2.9 70.0 1.0 O A:GLU419 2.9 69.9 1.0 C A:THR416 3.7 64.5 1.0 C A:LEU413 3.7 44.5 1.0 O A:VAL414 3.9 42.6 1.0 C A:GLU419 3.9 64.3 1.0 C A:LEU90 4.0 46.1 1.0 CA A:VAL414 4.0 41.9 1.0 C A:VAL414 4.0 45.5 1.0 ND2 A:ASN91 4.1 85.2 1.0 CG A:ASN91 4.1 61.5 1.0 N A:THR416 4.3 54.0 1.0 CB A:GLU419 4.3 66.2 1.0 OD1 A:ASN91 4.3 80.8 1.0 N A:VAL414 4.4 40.1 1.0 CA A:ASN91 4.5 53.5 1.0 CA A:THR416 4.5 61.5 1.0 N A:ILE417 4.6 59.7 1.0 CA A:GLU419 4.6 65.8 1.0 N A:ASN91 4.6 49.6 1.0 CA A:ILE417 4.7 66.5 1.0 N A:SER415 4.7 46.1 1.0 N A:GLU419 4.8 67.4 1.0 CA A:LEU413 4.9 40.8 1.0 N A:ASP420 4.9 66.8 1.0 C A:ILE417 4.9 65.4 1.0 CB A:ASN91 5.0 54.9 1.0 O A:ILE417 5.0 66.1 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate


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 the Catalytic Domain of Human JARID1B in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1756 b:0.5 occ:0.95 O A:HOH2157 3.4 51.3 1.0 NE2 A:HIS718 3.7 62.1 1.0 NE2 A:HIS622 3.9 69.1 1.0 CE A:LYS694 4.1 59.8 1.0 CE1 A:HIS622 4.2 68.7 1.0 CD2 A:HIS718 4.4 50.9 1.0 CE1 A:HIS718 4.7 56.6 1.0 CG A:LYS694 4.9 55.9 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate


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 the Catalytic Domain of Human JARID1B in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1764 b:81.7 occ:0.50 CE1 A:HIS399 2.6 83.8 1.0 ND1 A:HIS399 3.2 75.7 1.0 CG2 A:VAL398 3.5 64.9 1.0 NE2 A:HIS399 3.7 83.3 1.0 O A:HOH2059 3.7 47.9 1.0 CG A:HIS399 4.4 73.2 1.0 CD2 A:HIS399 4.6 71.2 1.0 O A:HOH2071 4.7 47.6 1.0 OD2 A:ASP387 4.9 47.5 1.0 CB A:VAL398 4.9 54.7 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate


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 the Catalytic Domain of Human JARID1B in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1765 b:33.0 occ:1.00 O A:HOH2047 2.1 34.7 1.0 OE2 A:GLU501 2.1 43.9 1.0 NE2 A:HIS499 2.1 41.6 1.0 O3 A:FUM1767 2.2 34.4 1.0 O A:HOH2107 2.2 35.2 1.0 NE2 A:HIS587 2.2 37.4 1.0 CE1 A:HIS499 3.0 43.4 1.0 CD A:GLU501 3.1 36.6 1.0 CE1 A:HIS587 3.2 36.7 1.0 C2 A:FUM1767 3.2 39.0 1.0 CD2 A:HIS499 3.2 38.7 1.0 CD2 A:HIS587 3.3 32.2 1.0 OE1 A:GLU501 3.4 38.2 1.0 O1 A:FUM1767 3.5 38.2 1.0 ND1 A:HIS499 4.2 40.5 1.0 NH2 A:ARG98 4.2 49.5 0.5 O A:HOH2097 4.3 47.0 1.0 OG A:SER507 4.3 36.1 1.0 O A:HOH2045 4.3 43.9 1.0 CG A:HIS499 4.3 42.0 1.0 ND1 A:HIS587 4.3 35.2 1.0 CG A:HIS587 4.4 35.1 1.0 CG A:GLU501 4.4 35.7 1.0 C4 A:FUM1767 4.5 37.7 1.0 CB A:SER507 4.8 37.7 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate


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 the Catalytic Domain of Human JARID1B in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1766 b:72.0 occ:1.00 O A:HOH2106 3.7 48.8 1.0 O A:HOH2135 3.7 44.2 1.0 NE1 A:TRP504 3.7 33.9 1.0 O A:HOH2162 3.7 59.9 1.0 CE1 A:TYR618 3.8 53.9 1.0 NH1 A:ARG623 3.8 80.7 1.0 ND1 A:HIS617 3.9 56.7 1.0 CD1 A:ILE500 4.0 34.6 1.0 O A:HOH2163 4.0 62.2 1.0 CE1 A:HIS617 4.2 62.1 1.0 CD1 A:TYR618 4.3 52.5 1.0 O A:HOH2133 4.3 60.4 1.0 CD2 A:LEU621 4.3 64.5 1.0 CE2 A:TRP504 4.6 36.7 1.0 CD1 A:TRP504 4.7 36.3 1.0 CZ2 A:TRP504 4.7 36.0 1.0 CZ A:ARG623 4.8 76.4 1.0 OE2 A:GLU531 4.8 47.7 1.0 CD A:ARG623 4.8 75.6 1.0 CG1 A:ILE500 4.9 37.2 1.0 CZ A:TYR618 4.9 56.7 1.0 O A:HOH2091 5.0 60.5 1.0

R.Nowak, V.Srikannathasan, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Succinate To Be Published.