Manganese in PDB 1zth: Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion

The structure of Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion, PDB code: 1zth was solved by A.Wlodawer, N.Laronde-Leblanc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.414, 80.084, 121.056, 90.00, 90.17, 90.00
R / Rfree (%)	18.9 / 26.2

The binding sites of Manganese atom in the Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion (pdb code 1zth). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion, PDB code: 1zth:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion


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 A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn902 b:21.6 occ:1.00 O A:HOH942 1.9 32.3 1.0 O A:HOH1073 1.9 24.9 1.0 OD2 A:ASP212 2.0 24.7 1.0 O1B A:ADP901 2.1 27.6 1.0 OD1 A:ASN201 2.1 26.2 1.0 O2A A:ADP901 2.2 20.1 1.0 CG A:ASP212 3.0 18.1 1.0 CG A:ASN201 3.1 22.6 1.0 PB A:ADP901 3.3 24.1 1.0 PA A:ADP901 3.3 20.9 1.0 CB A:ASP212 3.5 21.2 1.0 ND2 A:ASN201 3.5 22.0 1.0 O3A A:ADP901 3.5 20.7 1.0 OD1 A:ASP212 4.0 22.6 1.0 O2B A:ADP901 4.3 22.5 1.0 O1A A:ADP901 4.3 19.2 1.0 O A:TYR200 4.3 17.6 1.0 O3B A:ADP901 4.4 24.6 1.0 O5' A:ADP901 4.5 25.7 1.0 CB A:ASN201 4.5 20.4 1.0 C5' A:ADP901 4.7 21.3 1.0 CA A:ASP212 4.9 21.4 1.0 CA A:ASN201 4.9 21.3 1.0 OD1 A:ASP196 5.0 33.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion


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 A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn904 b:22.0 occ:1.00 O1B B:ADP903 2.0 25.8 1.0 O B:HOH1090 2.1 29.3 1.0 O2A B:ADP903 2.1 19.3 1.0 OD2 B:ASP212 2.1 22.2 1.0 OD1 B:ASN201 2.2 25.3 1.0 O B:HOH911 2.3 28.2 1.0 CG B:ASP212 3.1 19.7 1.0 CG B:ASN201 3.2 21.6 1.0 PB B:ADP903 3.3 22.9 1.0 PA B:ADP903 3.3 20.9 1.0 O3A B:ADP903 3.6 18.7 1.0 ND2 B:ASN201 3.6 23.6 1.0 CB B:ASP212 3.6 22.1 1.0 O B:HOH1059 3.9 39.5 1.0 O B:HOH1037 4.0 46.7 1.0 OD1 B:ASP212 4.2 22.5 1.0 O A:HOH952 4.2 40.6 1.0 O3B B:ADP903 4.2 23.0 1.0 O2B B:ADP903 4.3 22.7 1.0 O1A B:ADP903 4.4 17.7 1.0 O B:TYR200 4.4 22.6 1.0 O5' B:ADP903 4.5 22.3 1.0 CB B:ASN201 4.5 13.0 1.0 O B:HOH1009 4.7 45.2 1.0 C5' B:ADP903 4.8 22.3 1.0 OD2 B:ASP196 4.9 34.6 1.0 CA B:ASN201 4.9 17.4 1.0 O B:HOH905 5.0 22.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion


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 A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn906 b:21.7 occ:1.00 O1B C:ADP905 2.0 24.0 1.0 O2A C:ADP905 2.1 23.0 1.0 O C:HOH1063 2.1 29.8 1.0 OD1 C:ASN201 2.2 22.0 1.0 OD2 C:ASP212 2.2 22.8 1.0 CG C:ASN201 3.2 22.0 1.0 CG C:ASP212 3.2 22.4 1.0 PB C:ADP905 3.3 24.7 1.0 PA C:ADP905 3.3 21.2 1.0 O3A C:ADP905 3.5 21.8 1.0 ND2 C:ASN201 3.5 22.6 1.0 CB C:ASP212 3.6 20.8 1.0 O C:HOH928 3.7 27.6 1.0 O C:HOH1046 4.0 43.1 1.0 O1A C:ADP905 4.2 21.0 1.0 O2B C:ADP905 4.2 24.9 1.0 OD1 C:ASP212 4.3 23.7 1.0 O3B C:ADP905 4.3 25.0 1.0 O C:HOH1013 4.4 34.0 1.0 O5' C:ADP905 4.5 18.8 1.0 O C:TYR200 4.5 23.8 1.0 CB C:ASN201 4.5 18.2 1.0 C5' C:ADP905 4.7 18.9 1.0 O C:HOH912 4.8 25.8 1.0 CA C:ASN201 4.9 22.0 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion


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 A.Fulgidus RIO1 Serine Protein Kinase Bound to Adp and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn908 b:22.7 occ:1.00 O D:HOH1049 1.9 28.1 1.0 OD1 D:ASN201 2.0 25.9 1.0 O D:HOH948 2.2 29.0 1.0 OD2 D:ASP212 2.2 23.8 1.0 O1B D:ADP907 2.2 30.4 1.0 O2A D:ADP907 2.2 22.6 1.0 CG D:ASN201 3.1 26.6 1.0 CG D:ASP212 3.2 22.6 1.0 PA D:ADP907 3.3 20.5 1.0 PB D:ADP907 3.4 25.9 1.0 O D:HOH1033 3.4 50.4 1.0 ND2 D:ASN201 3.5 27.6 1.0 O3A D:ADP907 3.5 19.2 1.0 O D:HOH924 3.5 28.6 1.0 CB D:ASP212 3.6 20.6 1.0 O D:HOH1029 4.0 39.9 1.0 OD1 D:ASP212 4.2 25.4 1.0 O1A D:ADP907 4.3 22.8 1.0 O D:HOH993 4.3 29.8 1.0 O2B D:ADP907 4.4 24.8 1.0 O D:TYR200 4.4 20.4 1.0 CB D:ASN201 4.5 20.9 1.0 O3B D:ADP907 4.5 23.9 1.0 O D:HOH1077 4.5 66.2 1.0 O5' D:ADP907 4.5 22.5 1.0 C5' D:ADP907 4.7 20.7 1.0 CA D:ASN201 4.8 23.6 1.0 OE2 C:GLU249 4.9 46.6 1.0 OD1 D:ASP196 4.9 36.5 1.0

N.Laronde-Leblanc, T.Guszczynski, T.Copeland, A.Wlodawer. Structure and Activity of the Atypical Serine Kinase RIO1. Febs J. V. 272 3698 2005.
ISSN: ISSN 1742-464X
PubMed: 16008568
DOI: 10.1111/J.1742-4658.2005.04796.X