Manganese in PDB 4xbw: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor, PDB code: 4xbw was solved by J.J.Griese, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 1.99
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.374, 97.153, 128.067, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.4

The binding sites of Manganese atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor (pdb code 4xbw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor, PDB code: 4xbw:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:33.7 occ:1.00 O1 A:PLM404 1.5 61.4 1.0 OE2 A:GLU69 2.1 42.6 1.0 OE2 A:GLU102 2.1 36.3 1.0 ND1 A:HIS105 2.2 31.1 1.0 OE1 A:GLU202 2.4 41.1 1.0 C1 A:PLM404 2.6 49.4 1.0 CE1 A:HIS105 3.0 34.5 1.0 CD A:GLU69 3.0 49.6 1.0 HE1 A:HIS105 3.0 41.4 1.0 CD A:GLU102 3.2 39.9 1.0 O2 A:PLM404 3.2 48.7 1.0 OE1 A:GLU69 3.2 56.9 1.0 CG A:HIS105 3.3 37.1 1.0 OE1 A:GLU102 3.5 41.9 1.0 MN A:MN402 3.5 41.9 1.0 CD A:GLU202 3.6 47.5 1.0 HB2 A:HIS105 3.6 38.8 1.0 HB3 A:HIS105 3.6 38.8 1.0 HG21 A:VAL72 3.7 54.9 1.0 HA A:GLU102 3.7 33.1 1.0 H31 A:PLM404 3.7 52.3 1.0 CB A:HIS105 3.7 32.3 1.0 C2 A:PLM404 3.9 49.5 1.0 H22 A:PLM404 4.1 59.4 1.0 NE2 A:HIS105 4.2 34.1 1.0 HG A:LEU198 4.2 46.4 1.0 HE1 A:HIS205 4.2 46.5 1.0 HH A:TYR175 4.3 73.5 1.0 HA A:GLU69 4.3 53.9 1.0 C3 A:PLM404 4.3 43.6 1.0 CD2 A:HIS105 4.3 31.1 1.0 HG2 A:GLU202 4.4 57.4 1.0 OE2 A:GLU202 4.4 45.8 1.0 HG23 A:VAL72 4.4 54.9 1.0 CG A:GLU69 4.4 46.1 1.0 CG2 A:VAL72 4.4 45.7 1.0 HD21 A:LEU198 4.5 50.1 1.0 CG A:GLU202 4.5 47.8 1.0 CG A:GLU102 4.5 32.6 1.0 CA A:GLU102 4.6 27.6 1.0 HB3 A:GLU69 4.6 48.2 1.0 OH A:TYR175 4.6 61.2 1.0 HG3 A:GLU202 4.6 57.4 1.0 HB3 A:GLU102 4.7 39.4 1.0 H32 A:PLM404 4.7 52.3 1.0 HD22 A:LEU198 4.7 50.1 1.0 H21 A:PLM404 4.7 59.4 1.0 HG3 A:GLU69 4.8 55.3 1.0 HG22 A:VAL72 4.8 54.9 1.0 CB A:GLU102 4.8 32.8 1.0 CE1 A:HIS205 4.8 38.8 1.0 CD2 A:LEU198 4.9 41.8 1.0 HE2 A:HIS105 4.9 41.0 1.0 ND1 A:HIS205 4.9 35.7 1.0 CB A:GLU69 4.9 40.2 1.0 CG A:LEU198 5.0 38.7 1.0 HG2 A:GLU167 5.0 39.2 1.0

Manganese binding site 2 out of 3 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:41.9 occ:1.00 OE2 A:GLU167 2.0 39.4 1.0 O2 A:PLM404 2.0 48.7 1.0 OE1 A:GLU102 2.2 41.9 1.0 OE2 A:GLU202 2.2 45.8 1.0 ND1 A:HIS205 2.3 35.7 1.0 OE1 A:GLU202 2.4 41.1 1.0 CD A:GLU202 2.6 47.5 1.0 HG2 A:GLU167 2.8 39.2 1.0 C1 A:PLM404 2.9 49.4 1.0 CD A:GLU167 2.9 37.8 1.0 CE1 A:HIS205 3.1 38.8 1.0 CD A:GLU102 3.2 39.9 1.0 O1 A:PLM404 3.2 61.4 1.0 HE1 A:HIS205 3.2 46.5 1.0 CG A:GLU167 3.3 32.7 1.0 CG A:HIS205 3.3 31.6 1.0 HB3 A:HIS205 3.5 35.0 1.0 OE2 A:GLU102 3.5 36.3 1.0 MN A:MN401 3.5 33.7 1.0 HB2 A:HIS205 3.6 35.0 1.0 HE2 A:TYR162 3.6 52.7 1.0 CB A:HIS205 3.7 29.1 1.0 HE2 A:PHE98 3.8 47.6 1.0 HG3 A:GLU167 3.9 39.2 1.0 HA A:GLU202 3.9 46.2 1.0 OE1 A:GLU167 3.9 38.9 1.0 CG A:GLU202 4.0 47.8 1.0 HE1 A:HIS105 4.1 41.4 1.0 CE2 A:PHE98 4.1 39.7 1.0 HZ A:PHE98 4.2 43.9 1.0 NE2 A:HIS205 4.3 32.4 1.0 HB3 A:GLU167 4.3 36.8 1.0 C2 A:PLM404 4.3 49.5 1.0 CZ A:PHE98 4.4 36.5 1.0 H21 A:PLM404 4.4 59.4 1.0 CD2 A:HIS205 4.4 29.7 1.0 HG3 A:GLU202 4.5 57.4 1.0 HG21 A:VAL72 4.5 54.9 1.0 CB A:GLU167 4.5 30.7 1.0 HG2 A:GLU202 4.5 57.4 1.0 CE2 A:TYR162 4.5 44.0 1.0 CG A:GLU102 4.5 32.6 1.0 HG2 A:GLU102 4.7 39.1 1.0 HB3 A:GLU202 4.7 49.2 1.0 CA A:GLU202 4.7 38.5 1.0 CB A:GLU202 4.8 41.0 1.0 OH A:TYR162 4.8 45.8 1.0 CE1 A:HIS105 4.8 34.5 1.0 HG3 A:GLU102 4.8 39.1 1.0 ND1 A:HIS105 4.9 31.1 1.0 H22 A:PLM404 4.9 59.4 1.0 CD2 A:PHE98 5.0 34.0 1.0

Manganese binding site 3 out of 3 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Dimanganese Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:89.4 occ:0.92 NE2 A:HIS130 2.3 67.0 1.0 CE1 A:HIS130 3.2 61.6 1.0 CD2 A:HIS130 3.3 59.6 1.0 HE1 A:HIS130 3.3 73.9 1.0 HD2 A:HIS130 3.5 71.6 1.0 OD2 A:ASP129 4.2 80.1 1.0 ND1 A:HIS130 4.3 60.0 1.0 CG A:HIS130 4.4 58.6 1.0 OD1 A:ASP129 4.8 73.7 1.0 HA3 A:GLY240 4.8 57.5 1.0 CG A:ASP129 4.9 74.5 1.0 O A:HOH553 5.0 52.9 1.0

J.J.Griese, R.Kositzki, P.Schrapers, R.M.Branca, A.Nordstrom, J.Lehtio, M.Haumann, M.Hogbom. Structural Basis For Oxygen Activation at A Heterodinuclear Manganese/Iron Cofactor. J.Biol.Chem. V. 290 25254 2015.
ISSN: ESSN 1083-351X
PubMed: 26324712
DOI: 10.1074/JBC.M115.675223