Manganese in PDB 1wsf: Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+

All present enzymatic activity of Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+:
3.1.26.4;

The structure of Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+, PDB code: 1wsf was solved by Y.Tsunaka, K.Takano, H.Matsumura, Y.Yamagata, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.990, 80.089, 63.951, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 29

The binding sites of Manganese atom in the Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+ (pdb code 1wsf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+, PDB code: 1wsf:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:76.1 occ:1.00 OD2 A:ASP10 2.4 46.9 1.0 O A:HOH1037 2.5 53.5 1.0 OD2 A:ASP70 2.6 58.0 1.0 OD1 A:ASP10 2.8 44.5 1.0 CG A:ASP10 2.9 43.2 1.0 O A:HOH1022 3.2 55.6 1.0 CG A:ASP70 3.5 57.2 1.0 OD1 A:ASP70 3.7 60.4 1.0 O A:GLY11 3.9 36.9 1.0 O A:HOH1038 3.9 56.2 1.0 O A:HOH1039 4.3 76.4 1.0 CB A:ASP10 4.4 41.5 1.0 OE2 A:GLU48 4.7 61.6 1.0 N A:GLY11 4.7 34.6 1.0 C A:GLY11 4.9 33.7 1.0 CB A:ASP70 4.9 53.3 1.0 CB A:ALA134 5.0 38.0 1.0

Manganese binding site 2 out of 3 in the Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:75.5 occ:1.00 O B:HOH1003 2.5 62.6 1.0 O B:GLY11 2.5 46.8 1.0 OD1 B:ASP10 2.6 50.2 1.0 OD2 B:ASP10 2.7 49.7 1.0 O B:HOH1035 2.9 63.5 1.0 CG B:ASP10 3.0 46.9 1.0 CE1 B:HIS124 3.3 74.9 1.0 C B:GLY11 3.7 45.7 1.0 NE2 B:HIS124 3.7 74.7 1.0 N B:GLY11 4.0 45.7 1.0 O B:HOH1020 4.2 36.5 1.0 OD2 B:ASP70 4.2 58.7 1.0 CB B:ASP10 4.4 45.2 1.0 ND1 B:HIS124 4.5 74.5 1.0 CA B:GLY11 4.5 44.7 1.0 OD1 B:ASN44 4.6 54.3 1.0 N B:SER12 4.6 47.3 1.0 OD1 B:ASP70 4.6 59.2 1.0 CA B:SER12 4.6 48.5 1.0 CB B:ALA134 4.7 45.5 1.0 CB B:SER12 4.7 48.5 1.0 C B:ASP10 4.8 45.2 1.0 CG B:ASP70 4.9 58.1 1.0 CA B:ASP10 4.9 43.3 1.0

Manganese binding site 3 out of 3 in the Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Co-Crystal Structure of E.Coli Rnase Hi Active Site Mutant (D134A*) with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1003 b:83.8 occ:1.00 O D:HOH1016 2.3 63.7 1.0 OD2 D:ASP10 2.4 53.0 1.0 OD1 D:ASP70 2.9 64.3 1.0 O D:HOH1018 2.9 55.6 1.0 OD2 D:ASP70 2.9 62.1 1.0 CG D:ASP10 3.2 50.8 1.0 OE2 D:GLU48 3.3 65.3 1.0 CG D:ASP70 3.3 60.4 1.0 OD1 D:ASP10 3.4 51.9 1.0 O D:HOH1026 3.6 77.8 1.0 O D:HOH1027 3.6 58.4 1.0 O D:GLY11 4.0 54.9 1.0 N D:GLY11 4.2 51.5 1.0 CD D:GLU48 4.4 62.4 1.0 CB D:ASP10 4.5 50.0 1.0 ND2 D:ASN44 4.5 50.6 1.0 O D:HOH1032 4.6 81.4 1.0 CA D:ASP10 4.6 49.1 1.0 O D:HOH1022 4.7 60.7 1.0 C D:GLY11 4.7 54.0 1.0 CB D:ASP70 4.8 57.2 1.0 C D:ASP10 4.9 50.0 1.0 CG D:GLU48 4.9 55.9 1.0

Y.Tsunaka, K.Takano, H.Matsumura, Y.Yamagata, S.Kanaya. Identification of Single Mn(2+) Binding Sites Required For Activation of the Mutant Proteins of E.Coli Rnase Hi at GLU48 and/or ASP134 By X-Ray Crystallography J.Mol.Biol. V. 345 1171 2005.
ISSN: ISSN 0022-2836
PubMed: 15644213
DOI: 10.1016/J.JMB.2004.11.007