Manganese in PDB 2id0: Escherichia Coli Rnase II

All present enzymatic activity of Escherichia Coli Rnase II:
3.1.13.1;

The structure of Escherichia Coli Rnase II, PDB code: 2id0 was solved by Y.Zuo, J.Zhang, Y.Wang, A.Malhotra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.95 / 2.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.760, 118.430, 122.380, 107.80, 98.36, 91.40
R / Rfree (%)	22.3 / 28.6

The binding sites of Manganese atom in the Escherichia Coli Rnase II (pdb code 2id0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Escherichia Coli Rnase II, PDB code: 2id0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Escherichia Coli Rnase II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Escherichia Coli Rnase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:0.3 occ:1.00 OD1 A:ASP201 2.0 84.3 1.0 OD1 A:ASP210 2.2 76.8 1.0 CG A:ASP210 3.1 76.5 1.0 CG A:ASP201 3.1 83.9 1.0 OD1 A:ASP209 3.3 80.2 1.0 OD2 A:ASP210 3.4 77.7 1.0 OD2 A:ASP201 3.7 83.7 1.0 CG A:ASP209 4.2 79.6 1.0 N A:ASP209 4.2 80.7 1.0 CB A:ASP210 4.3 75.8 1.0 CB A:ASP201 4.3 83.4 1.0 O A:ILE200 4.3 81.1 1.0 N A:ASP210 4.4 76.6 1.0 OD2 A:ASP209 4.7 79.9 1.0 CA A:MSE208 4.7 83.7 1.0 CA A:ASP201 4.9 83.3 1.0 CA A:ASP210 4.9 75.5 1.0 C A:MSE208 5.0 82.2 1.0 O A:ASP210 5.0 74.7 1.0

Manganese binding site 2 out of 4 in the Escherichia Coli Rnase II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Escherichia Coli Rnase II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:83.5 occ:1.00 OD1 B:ASP210 2.0 59.3 1.0 OD1 B:ASP201 2.3 66.3 1.0 CG B:ASP210 3.1 61.1 1.0 CG B:ASP201 3.2 66.5 1.0 OD2 B:ASP201 3.4 67.0 1.0 OD1 B:ASP209 3.6 68.2 1.0 N B:ASP210 3.7 62.6 1.0 CB B:ASP210 3.8 60.6 1.0 N B:ASP209 3.8 69.8 1.0 OD2 B:ASP210 4.0 61.4 1.0 O B:ASP210 4.1 59.0 1.0 CA B:MSE208 4.2 75.3 1.0 CA B:ASP210 4.2 60.7 1.0 CG B:ASP209 4.4 68.5 1.0 CB B:ASP201 4.4 66.1 1.0 O B:ILE200 4.5 63.0 1.0 C B:MSE208 4.5 72.2 1.0 C B:ASP210 4.6 59.1 1.0 C B:ASP209 4.7 64.8 1.0 CA B:ASP209 4.8 67.2 1.0 N B:MSE208 4.8 75.2 1.0 OD2 B:ASP209 4.9 68.8 1.0

Manganese binding site 3 out of 4 in the Escherichia Coli Rnase II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Escherichia Coli Rnase II within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1003 b:88.7 occ:1.00 OD1 C:ASP210 2.1 57.3 1.0 OD1 C:ASP201 2.4 63.2 1.0 CG C:ASP210 3.1 55.9 1.0 OD1 C:ASP209 3.2 66.5 1.0 CG C:ASP201 3.3 63.7 1.0 OD2 C:ASP201 3.5 61.8 1.0 OD2 C:ASP210 3.5 55.4 1.0 N C:ASP210 3.9 58.8 1.0 N C:ASP209 3.9 66.2 1.0 O C:ASP210 4.2 55.0 1.0 CB C:ASP210 4.3 56.7 1.0 CG C:ASP209 4.4 64.0 1.0 O C:ILE200 4.4 61.2 1.0 CA C:ASP210 4.6 56.6 1.0 CA C:MSE208 4.6 72.8 1.0 CB C:ASP201 4.7 64.6 1.0 C C:ASP209 4.8 61.0 1.0 CA C:ASP209 4.8 63.1 1.0 C C:MSE208 4.8 69.8 1.0 C C:ASP210 4.9 55.3 1.0

Manganese binding site 4 out of 4 in the Escherichia Coli Rnase II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Escherichia Coli Rnase II within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1004 b:94.4 occ:1.00 OD1 D:ASP201 2.1 59.3 1.0 OD1 D:ASP210 2.3 45.5 1.0 OD1 D:ASP209 2.4 53.5 1.0 CG D:ASP201 3.0 58.3 1.0 CG D:ASP209 3.2 54.8 1.0 CG D:ASP210 3.2 47.0 1.0 OD2 D:ASP201 3.3 58.6 1.0 OD2 D:ASP209 3.4 56.8 1.0 OD2 D:ASP210 3.6 48.0 1.0 O D:ILE200 4.0 55.3 1.0 N D:ASP210 4.0 48.5 1.0 O D:HOH1058 4.2 43.5 1.0 O D:ASP210 4.2 43.4 1.0 N D:ASP209 4.3 55.8 1.0 CB D:ASP210 4.4 46.5 1.0 CB D:ASP201 4.4 58.5 1.0 CB D:ASP209 4.5 53.6 1.0 CA D:ASP210 4.6 46.4 1.0 CA D:ASP209 4.7 53.1 1.0 C D:ASP210 4.8 44.8 1.0 C D:ASP209 4.8 50.8 1.0 C D:ILE200 4.9 55.3 1.0

Y.Zuo, H.A.Vincent, J.Zhang, Y.Wang, M.P.Deutscher, A.Malhotra. Structural Basis For Processivity and Single-Strand Specificity of Rnase II. Mol.Cell V. 24 149 2006.
ISSN: ISSN 1097-2765
PubMed: 16996291
DOI: 10.1016/J.MOLCEL.2006.09.004