Manganese in PDB 5f13: Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae

The structure of Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae, PDB code: 5f13 was solved by B.Nocek, T.Skarina, A.Joachimiak, A.Savchenko, A.Yakunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.17 / 2.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	223.035, 95.550, 78.097, 90.00, 105.84, 90.00
R / Rfree (%)	19.9 / 23.7

The structure of Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Manganese atom in the Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae (pdb code 5f13). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae, PDB code: 5f13:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:33.0 occ:0.94 OD1 A:ASP292 2.3 21.1 1.0 O A:HOH632 2.3 29.5 1.0 O1 A:PO4502 2.3 42.4 1.0 OD1 A:ASP254 2.4 24.4 1.0 O A:HOH636 2.5 29.8 1.0 OD1 A:ASN255 2.6 28.1 1.0 HD21 A:ASN255 3.1 33.2 1.0 O3 A:PO4502 3.1 42.1 1.0 CG A:ASN255 3.2 27.5 1.0 P A:PO4502 3.3 42.4 1.0 CG A:ASP254 3.4 24.4 1.0 CG A:ASP292 3.4 19.9 1.0 ND2 A:ASN255 3.4 27.7 1.0 HG A:SER291 3.6 29.5 1.0 HB3 A:MET289 3.7 30.9 1.0 OD2 A:ASP254 3.8 25.6 1.0 OD2 A:ASP292 3.9 18.8 1.0 HB2 A:MET289 3.9 30.9 1.0 HD22 A:ASN255 4.1 33.2 1.0 HA A:ASN255 4.2 29.6 1.0 O2 A:PO4502 4.2 42.7 1.0 O A:HOH627 4.2 43.0 1.0 CB A:MET289 4.3 25.7 1.0 HA A:ASP292 4.3 25.6 1.0 N A:ASN255 4.3 23.4 1.0 OG A:SER291 4.3 24.6 1.0 O4 A:PO4502 4.4 40.3 1.0 CB A:ASN255 4.4 26.8 1.0 H A:ASN255 4.4 28.1 1.0 C A:ASP254 4.5 23.1 1.0 O A:MET289 4.5 31.1 1.0 CA A:ASN255 4.5 24.7 1.0 HG3 A:MET289 4.6 28.9 1.0 HA A:ASP254 4.6 27.1 1.0 CB A:ASP292 4.6 20.1 1.0 O2 A:PO4503 4.6 38.7 1.0 O A:HOH649 4.7 30.4 1.0 CB A:ASP254 4.7 23.4 1.0 N A:ASP292 4.7 23.8 1.0 CA A:ASP292 4.8 21.3 1.0 H A:ASP292 4.8 28.6 1.0 H A:SER291 4.8 29.6 1.0 CA A:ASP254 4.8 22.6 1.0 O A:ASP254 4.8 22.7 1.0 HB3 A:ASN255 4.9 32.1 1.0

Manganese binding site 2 out of 3 in the Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:38.6 occ:0.90 O1 B:PO4502 2.1 49.9 1.0 OD1 B:ASP254 2.2 32.7 1.0 O B:HOH608 2.2 34.1 1.0 OD1 B:ASN255 2.2 28.7 1.0 OD1 B:ASP292 2.3 29.2 1.0 O B:HOH628 2.3 27.9 1.0 P B:PO4502 3.2 48.2 1.0 CG B:ASN255 3.2 28.7 1.0 O3 B:PO4502 3.2 46.4 1.0 CG B:ASP254 3.2 32.7 1.0 HD21 B:ASN255 3.3 34.7 1.0 CG B:ASP292 3.4 29.0 1.0 OD2 B:ASP254 3.6 33.1 1.0 ND2 B:ASN255 3.6 28.9 1.0 HB3 B:MET289 3.7 43.0 1.0 OD2 B:ASP292 3.8 29.3 1.0 HB2 B:MET289 3.9 43.0 1.0 HG B:SER291 3.9 43.6 1.0 O B:HOH603 4.0 30.4 1.0 O4 B:PO4502 4.0 49.5 1.0 CB B:MET289 4.2 35.9 1.0 HA B:ASN255 4.2 33.4 1.0 N B:ASN255 4.3 27.4 1.0 HA B:ASP292 4.3 35.0 1.0 O2 B:PO4502 4.3 52.1 1.0 HG3 B:MET289 4.3 43.1 1.0 C B:ASP254 4.4 31.8 1.0 H B:ASN255 4.4 32.9 1.0 CB B:ASN255 4.5 28.7 1.0 HA B:ASP254 4.5 38.4 1.0 HD22 B:ASN255 4.5 34.7 1.0 CB B:ASP254 4.5 32.4 1.0 CA B:ASN255 4.6 27.9 1.0 O1 B:PO4503 4.6 57.2 1.0 O B:MET289 4.6 37.3 1.0 OG B:SER291 4.6 36.3 1.0 CB B:ASP292 4.6 28.8 1.0 CA B:ASP254 4.7 32.0 1.0 O B:ASP254 4.8 31.8 1.0 CA B:ASP292 4.8 29.1 1.0 N B:ASP292 4.8 30.1 1.0 CG B:MET289 4.8 35.9 1.0 H B:ASP292 4.9 36.1 1.0 O B:HOH634 5.0 39.0 1.0 HB3 B:ASN255 5.0 34.4 1.0 H B:SER291 5.0 43.5 1.0

Manganese binding site 3 out of 3 in the Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Mn Bound DUF89 From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn501 b:48.6 occ:0.96 O2 C:PO4502 2.1 70.6 1.0 O C:HOH609 2.1 39.2 1.0 OD1 C:ASP292 2.3 46.1 1.0 O C:HOH608 2.3 35.3 1.0 OD1 C:ASN255 2.3 49.4 1.0 OD1 C:ASP254 2.4 46.8 1.0 CG C:ASN255 3.0 50.0 1.0 HD21 C:ASN255 3.1 60.1 1.0 CG C:ASP254 3.3 47.7 1.0 ND2 C:ASN255 3.3 50.1 1.0 P C:PO4502 3.4 68.9 1.0 CG C:ASP292 3.4 45.1 1.0 O4 C:PO4502 3.5 64.5 1.0 OD2 C:ASP254 3.7 48.8 1.0 HB3 C:MET289 3.7 49.9 1.0 HG C:SER291 3.7 53.5 1.0 HB2 C:MET289 3.8 49.9 1.0 OD2 C:ASP292 4.0 44.1 1.0 HA C:ASN255 4.0 59.4 1.0 HD22 C:ASN255 4.1 60.1 1.0 N C:ASN255 4.1 48.6 1.0 HA C:ASP292 4.2 55.6 1.0 CB C:MET289 4.2 41.6 1.0 CB C:ASN255 4.2 50.7 1.0 O3 C:PO4502 4.2 68.3 1.0 H C:ASN255 4.3 58.4 1.0 C C:ASP254 4.3 49.0 1.0 CA C:ASN255 4.4 49.5 1.0 O C:MET289 4.4 43.9 1.0 O1 C:PO4502 4.4 72.2 1.0 OG C:SER291 4.4 44.6 1.0 HA C:ASP254 4.5 58.0 1.0 HG3 C:MET289 4.6 48.8 1.0 CB C:ASP254 4.6 47.6 1.0 CB C:ASP292 4.6 45.1 1.0 HB3 C:ASN255 4.7 60.8 1.0 O C:ASP254 4.7 48.4 1.0 O3 C:PO4503 4.7 75.1 1.0 CA C:ASP254 4.7 48.4 1.0 N C:ASP292 4.7 46.9 1.0 CA C:ASP292 4.7 46.4 1.0 H C:SER291 4.8 51.2 1.0 H C:ASP292 4.8 56.2 1.0 HB2 C:ASN255 4.9 60.8 1.0 HB2 C:ASP292 4.9 54.1 1.0 CG C:MET289 5.0 40.7 1.0 C C:SER291 5.0 42.7 1.0

L.Huang, A.Khusnutdinova, B.Nocek, G.Brown, X.Xu, H.Cui, P.Petit, R.Flick, R.Zallot, K.Balmant, M.J.Ziemak, J.Shanklin, V.De Crecy-Lagard, O.Fiehn, J.F.Gregory, A.Joachimiak, A.Savchenko, A.F.Yakunin, A.D.Hanson. A Family of Metal-Dependent Phosphatases Implicated in Metabolite Damage-Control. Nat.Chem.Biol. V. 12 621 2016.
ISSN: ESSN 1552-4469
PubMed: 27322068
DOI: 10.1038/NCHEMBIO.2108