Manganese in PDB 5dcs: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak)

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak):
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak), PDB code: 5dcs 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)	38.91 / 2.01
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.058, 97.419, 129.320, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 21.7

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak) also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Manganese atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak) (pdb code 5dcs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak), PDB code: 5dcs:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak)


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 Mn/Fe Cofactor (Long Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:29.2 occ:1.00 O1 A:PLM403 1.8 47.2 1.0 OE2 A:GLU69 2.1 31.6 1.0 OE2 A:GLU102 2.1 30.0 1.0 ND1 A:HIS105 2.2 24.1 1.0 O A:HOH521 2.2 33.5 1.0 O A:HOH501 2.4 39.9 1.0 C1 A:PLM403 2.6 48.2 1.0 CE1 A:HIS105 3.0 25.6 1.0 O2 A:PLM403 3.1 42.2 1.0 HE1 A:HIS105 3.1 30.7 1.0 CD A:GLU69 3.1 37.5 1.0 CD A:GLU102 3.1 33.1 1.0 CG A:HIS105 3.3 26.6 1.0 OE1 A:GLU69 3.4 43.5 1.0 OE1 A:GLU102 3.4 29.4 1.0 FE A:FE402 3.5 32.0 1.0 HB2 A:HIS105 3.5 36.1 1.0 HB3 A:HIS105 3.6 36.1 1.0 CB A:HIS105 3.7 30.1 1.0 HA A:GLU102 3.7 28.5 1.0 HG21 A:VAL72 3.8 37.6 1.0 C2 A:PLM403 4.0 41.6 1.0 HG A:LEU198 4.1 34.9 1.0 H31 A:PLM403 4.1 46.9 1.0 OE1 A:GLU202 4.1 42.9 1.0 HA A:GLU69 4.1 34.5 1.0 HE1 A:HIS205 4.2 36.0 1.0 NE2 A:HIS105 4.2 28.8 1.0 H32 A:PLM403 4.4 46.9 1.0 CD2 A:HIS105 4.4 27.0 1.0 HH A:TYR175 4.4 47.0 1.0 C3 A:PLM403 4.4 39.1 1.0 OH A:TYR175 4.5 39.2 1.0 CG A:GLU69 4.5 30.0 1.0 CG A:GLU102 4.5 29.9 1.0 H21 A:PLM403 4.5 50.0 1.0 CG2 A:VAL72 4.6 31.3 1.0 HB3 A:GLU69 4.6 35.1 1.0 CA A:GLU102 4.6 23.7 1.0 HG23 A:VAL72 4.6 37.6 1.0 HB3 A:GLU102 4.7 31.4 1.0 HD23 A:LEU198 4.7 44.7 1.0 OE2 A:GLU202 4.7 37.5 1.0 H22 A:PLM403 4.7 50.0 1.0 HG22 A:VAL72 4.7 37.6 1.0 CE1 A:HIS205 4.8 30.0 1.0 CD A:GLU202 4.8 47.7 1.0 ND1 A:HIS205 4.8 28.9 1.0 CB A:GLU102 4.9 26.1 1.0 CB A:GLU69 4.9 29.3 1.0 HG3 A:GLU69 4.9 36.0 1.0 CA A:GLU69 4.9 28.8 1.0 CG A:LEU198 4.9 29.1 1.0 HE2 A:HIS105 4.9 34.5 1.0 HD21 A:LEU198 5.0 44.7 1.0 HG2 A:GLU102 5.0 35.8 1.0

Manganese binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak)


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 Mn/Fe Cofactor (Long Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:67.5 occ:0.76 O A:HOH552 2.2 60.7 1.0 O A:HOH561 2.2 68.6 1.0 NE2 A:HIS130 2.4 48.2 1.0 CD2 A:HIS130 3.3 50.7 1.0 HD2 A:HIS130 3.4 60.9 1.0 CE1 A:HIS130 3.4 49.2 1.0 HE1 A:HIS130 3.6 59.0 1.0 OD2 A:ASP129 4.3 69.1 1.0 O A:HOH531 4.3 49.1 1.0 CG A:HIS130 4.4 47.9 1.0 ND1 A:HIS130 4.5 50.5 1.0 OD1 A:ASP129 4.6 50.7 1.0 CG A:ASP129 4.9 58.4 1.0 HA3 A:GLY240 4.9 49.8 1.0 O A:HOH545 5.0 43.3 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