Manganese in PDB 4m0v: Crystal Structure of E.Coli Sbcd with MN2+

The structure of Crystal Structure of E.Coli Sbcd with MN2+, PDB code: 4m0v was solved by S.Liu, L.F.Tian, X.X.Yan, D.C.Liang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.83
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.162, 69.229, 95.187, 72.24, 84.00, 83.48
R / Rfree (%)	16.2 / 19.9

The binding sites of Manganese atom in the Crystal Structure of E.Coli Sbcd with MN2+ (pdb code 4m0v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of E.Coli Sbcd with MN2+, PDB code: 4m0v:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


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 E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:63.8 occ:0.80 NE2 A:HIS10 2.1 21.6 1.0 OD1 A:ASP8 2.2 21.4 1.0 OD2 A:ASP48 2.3 24.2 1.0 O A:HOH664 2.4 58.1 0.8 NE2 A:HIS224 2.8 24.1 1.0 CE1 A:HIS10 3.0 24.0 1.0 CD2 A:HIS10 3.1 20.4 1.0 CG A:ASP8 3.2 23.8 1.0 CG A:ASP48 3.3 21.7 1.0 MN A:MN403 3.4 68.0 0.8 CB A:ASP48 3.5 20.7 1.0 CD2 A:HIS224 3.6 23.3 1.0 CB A:ASP8 3.7 18.4 1.0 CE1 A:HIS224 3.8 29.8 1.0 O A:HIS222 3.9 22.1 1.0 O A:HOH663 3.9 33.4 1.0 ND1 A:HIS10 4.2 27.1 1.0 CA A:ASP8 4.2 16.6 1.0 CG A:HIS10 4.3 22.5 1.0 OD2 A:ASP8 4.3 21.3 1.0 CD2 A:HIS84 4.4 25.8 1.0 OD1 A:ASP48 4.4 20.1 1.0 CA A:HIS222 4.5 18.8 1.0 C A:HIS222 4.6 20.3 1.0 NE2 A:HIS84 4.6 31.5 1.0 ND1 A:HIS222 4.7 29.7 1.0 CE1 A:HIS184 4.7 17.0 1.0 CG A:HIS224 4.8 26.1 1.0 ND1 A:HIS224 4.9 34.4 1.0 NE2 A:HIS184 4.9 18.4 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


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 E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:68.0 occ:0.75 OD2 A:ASP48 2.2 24.2 1.0 ND1 A:HIS222 2.2 29.7 1.0 OD1 A:ASN83 2.3 20.4 1.0 NE2 A:HIS184 2.5 18.4 1.0 O A:HOH664 2.6 58.1 0.8 CG A:ASP48 3.1 21.7 1.0 CE1 A:HIS222 3.1 33.1 1.0 CE1 A:HIS184 3.2 17.0 1.0 CG A:HIS222 3.3 25.7 1.0 MN A:MN402 3.4 63.8 0.8 OD1 A:ASP48 3.4 20.1 1.0 CG A:ASN83 3.5 37.7 1.0 CD2 A:HIS184 3.6 18.1 1.0 CA A:HIS222 3.7 18.8 1.0 CB A:HIS222 3.7 19.4 1.0 OD1 A:ASP8 3.9 21.4 1.0 CD2 A:HIS84 3.9 25.8 1.0 O A:HOH663 4.1 33.4 1.0 O A:HIS222 4.1 22.1 1.0 ND2 A:ASN83 4.2 25.6 1.0 NE2 A:HIS222 4.2 27.1 1.0 CB A:ASP48 4.3 20.7 1.0 N A:ASN83 4.3 18.6 1.0 CD2 A:HIS222 4.4 23.6 1.0 ND1 A:HIS184 4.4 15.8 1.0 C A:HIS222 4.4 20.3 1.0 NE2 A:HIS84 4.6 31.5 1.0 CG A:HIS184 4.6 16.4 1.0 CB A:ASN83 4.6 22.3 1.0 N A:HIS222 4.7 17.1 1.0 N A:HIS84 4.9 16.2 1.0 NE2 A:HIS10 5.0 21.6 1.0 CA A:ASN83 5.0 21.9 1.0 CG A:HIS84 5.0 22.1 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


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 E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:67.2 occ:0.80 NE2 B:HIS10 2.1 18.5 1.0 OD1 B:ASP8 2.2 17.0 1.0 O B:HOH694 2.3 44.6 0.8 OD2 B:ASP48 2.4 18.3 1.0 NE2 B:HIS224 2.9 20.2 1.0 CE1 B:HIS10 2.9 21.4 1.0 CD2 B:HIS10 3.2 16.6 1.0 CG B:ASP8 3.2 18.6 1.0 MN B:MN403 3.3 82.7 0.5 CG B:ASP48 3.4 17.9 1.0 CB B:ASP48 3.6 17.9 1.0 CD2 B:HIS224 3.7 18.3 1.0 CB B:ASP8 3.7 16.0 1.0 O B:HIS222 3.8 16.8 1.0 CE1 B:HIS224 4.0 26.4 1.0 O B:HOH693 4.0 25.6 1.0 ND1 B:HIS10 4.1 22.3 1.0 CA B:ASP8 4.2 14.0 1.0 CG B:HIS10 4.3 15.1 1.0 OD2 B:ASP8 4.3 20.9 1.0 CA B:HIS222 4.3 15.2 1.0 C B:HIS222 4.4 16.5 1.0 CD2 B:HIS84 4.4 16.6 1.0 ND1 B:HIS222 4.5 17.7 1.0 OD1 B:ASP48 4.5 16.8 1.0 NE2 B:HIS84 4.6 20.1 1.0 CE1 B:HIS184 4.8 18.3 1.0 NE2 B:HIS184 4.9 14.1 1.0 CG B:HIS224 4.9 21.0 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


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 E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:82.7 occ:0.50 OD2 B:ASP48 2.1 18.3 1.0 ND1 B:HIS222 2.2 17.7 1.0 OD1 B:ASN83 2.2 16.0 1.0 NE2 B:HIS184 2.5 14.1 1.0 O B:HOH694 2.9 44.6 0.8 CG B:ASP48 3.0 17.9 1.0 CE1 B:HIS222 3.0 23.7 1.0 OD1 B:ASP48 3.3 16.8 1.0 CG B:HIS222 3.3 15.2 1.0 CE1 B:HIS184 3.3 18.3 1.0 MN B:MN402 3.3 67.2 0.8 CG B:ASN83 3.4 26.1 1.0 CD2 B:HIS184 3.6 17.0 1.0 CB B:HIS222 3.7 12.8 1.0 CA B:HIS222 3.7 15.2 1.0 CD2 B:HIS84 3.8 16.6 1.0 OD1 B:ASP8 4.0 17.0 1.0 ND2 B:ASN83 4.1 18.0 1.0 NE2 B:HIS222 4.2 22.2 1.0 N B:ASN83 4.2 14.2 1.0 CB B:ASP48 4.2 17.9 1.0 O B:HIS222 4.3 16.8 1.0 CD2 B:HIS222 4.3 15.3 1.0 O B:HOH693 4.4 25.6 1.0 NE2 B:HIS84 4.4 20.1 1.0 ND1 B:HIS184 4.5 14.5 1.0 CB B:ASN83 4.5 19.6 1.0 C B:HIS222 4.5 16.5 1.0 CG B:HIS184 4.7 18.2 1.0 N B:HIS84 4.7 14.8 1.0 N B:HIS222 4.8 14.3 1.0 CG B:HIS84 4.8 20.0 1.0 CA B:ASN83 4.8 15.3 1.0 NE2 B:HIS10 4.9 18.5 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:69.2 occ:0.20 OD1 C:ASN83 1.9 14.8 1.0 NE2 C:HIS184 2.0 12.5 1.0 OD2 C:ASP48 2.1 15.3 1.0 ND1 C:HIS222 2.4 17.8 1.0 CG C:ASP48 2.7 14.8 1.0 OD1 C:ASP48 2.8 13.6 1.0 CE1 C:HIS184 3.0 10.9 1.0 CD2 C:HIS184 3.1 11.8 1.0 CG C:ASN83 3.1 16.1 1.0 CE1 C:HIS222 3.3 11.9 1.0 CG C:HIS222 3.4 11.1 1.0 N C:ASN83 3.5 12.8 1.0 O C:HOH736 3.6 76.9 0.9 CB C:HIS222 3.8 12.0 1.0 CD2 C:HIS84 4.0 13.3 1.0 CA C:HIS222 4.0 11.6 1.0 MN C:MN403 4.0 23.1 0.3 CB C:ASN83 4.0 14.8 1.0 CB C:ASP48 4.1 18.2 1.0 ND2 C:ASN83 4.1 13.9 1.0 ND1 C:HIS184 4.1 12.4 1.0 CG C:HIS184 4.2 11.4 1.0 CA C:ASN83 4.2 14.3 1.0 N C:HIS84 4.3 12.8 1.0 OD1 C:ASP8 4.3 15.1 1.0 CA C:GLY82 4.3 11.2 1.0 C C:GLY82 4.4 12.3 1.0 NE2 C:HIS222 4.4 19.0 1.0 CD2 C:HIS222 4.5 10.8 1.0 NE2 C:HIS84 4.7 14.8 1.0 C C:ASN83 4.8 18.4 1.0 O C:HOH735 4.8 16.9 1.0 N C:HIS222 4.8 12.9 1.0 CG C:HIS84 4.8 12.9 1.0 O C:HIS222 4.9 13.2 1.0 C C:HIS222 5.0 14.7 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn403 b:23.1 occ:0.35 O C:HOH736 1.9 76.9 0.9 O C:HIS222 2.3 13.2 1.0 O C:HOH735 2.6 16.9 1.0 ND1 C:HIS222 3.0 17.8 1.0 NE2 C:HIS224 3.1 14.0 1.0 CE1 C:HIS222 3.2 11.9 1.0 C C:HIS222 3.3 14.7 1.0 OD1 C:ASP8 3.5 15.1 1.0 CG C:HIS222 3.6 11.1 1.0 OD2 C:ASP48 3.6 15.3 1.0 CA C:VAL196 3.7 14.6 1.0 CG1 C:VAL196 3.7 14.4 1.0 CD2 C:HIS224 3.7 17.2 1.0 CA C:HIS222 3.8 11.6 1.0 CE1 C:HIS224 3.8 18.6 1.0 NE2 C:HIS222 3.9 19.0 1.0 MN C:MN402 4.0 69.2 0.2 CB C:VAL196 4.0 18.9 1.0 CG2 C:VAL196 4.0 14.2 1.0 NE2 C:HIS10 4.1 15.0 1.0 CD2 C:HIS222 4.1 10.8 1.0 N C:ARG197 4.2 14.7 1.0 O C:ALA195 4.3 16.5 1.0 CB C:HIS222 4.3 12.0 1.0 C C:VAL196 4.5 18.5 1.0 CE1 C:HIS10 4.5 16.9 1.0 N C:ILE223 4.5 17.6 0.4 N C:ILE223 4.5 17.2 0.6 CG C:ASP8 4.6 18.5 1.0 N C:VAL196 4.7 16.1 1.0 CG C:HIS224 4.7 15.9 1.0 ND1 C:HIS224 4.7 19.5 1.0 CD2 C:HIS84 4.8 13.3 1.0 NE2 C:HIS84 4.8 14.8 1.0 C C:ALA195 4.9 20.2 1.0 CG C:ASP48 4.9 14.8 1.0 OD1 C:ASN83 4.9 14.8 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:57.8 occ:0.15 ND1 D:HIS222 2.0 19.4 1.0 OD2 D:ASP48 2.0 12.6 1.0 OD1 D:ASN83 2.2 13.1 1.0 NE2 D:HIS184 2.4 12.5 1.0 CE1 D:HIS222 2.9 13.4 1.0 CG D:ASP48 2.9 13.3 1.0 CG D:HIS222 3.1 13.5 1.0 O D:HOH742 3.1 68.9 0.9 CE1 D:HIS184 3.1 14.9 1.0 MN D:MN403 3.3 19.4 0.3 OD1 D:ASP48 3.3 11.5 1.0 CG D:ASN83 3.4 17.5 1.0 CD2 D:HIS184 3.5 12.6 1.0 CB D:HIS222 3.6 11.9 1.0 CA D:HIS222 3.6 15.0 1.0 CD2 D:HIS84 3.9 10.8 1.0 OD1 D:ASP8 3.9 15.1 1.0 NE2 D:HIS222 4.0 19.4 1.0 CD2 D:HIS222 4.2 13.3 1.0 ND2 D:ASN83 4.2 12.8 1.0 CB D:ASP48 4.2 13.4 1.0 N D:ASN83 4.2 12.6 1.0 O D:HOH741 4.2 16.7 1.0 O D:HIS222 4.3 14.9 1.0 ND1 D:HIS184 4.3 14.1 1.0 C D:HIS222 4.4 15.4 1.0 CB D:ASN83 4.5 13.2 1.0 CG D:HIS184 4.5 12.2 1.0 NE2 D:HIS84 4.5 13.4 1.0 N D:HIS222 4.6 12.1 1.0 N D:HIS84 4.8 14.8 1.0 NE2 D:HIS10 4.9 14.7 1.0 CA D:ASN83 4.9 13.3 1.0 CG D:HIS84 4.9 10.5 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of E.Coli Sbcd with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of E.Coli Sbcd with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn403 b:19.4 occ:0.30 O D:HOH742 1.8 68.9 0.9 O D:HOH741 2.4 16.7 1.0 O D:HIS222 2.6 14.9 1.0 NE2 D:HIS224 2.9 18.3 1.0 ND1 D:HIS222 3.2 19.4 1.0 MN D:MN402 3.3 57.8 0.1 CE1 D:HIS222 3.4 13.4 1.0 OD1 D:ASP8 3.5 15.1 1.0 OD2 D:ASP48 3.5 12.6 1.0 C D:HIS222 3.7 15.4 1.0 CE1 D:HIS224 3.7 24.8 1.0 CD2 D:HIS224 3.7 17.8 1.0 NE2 D:HIS10 3.8 14.7 1.0 CA D:VAL196 3.8 14.5 1.0 CG D:HIS222 3.9 13.5 1.0 CA D:HIS222 4.0 15.0 1.0 CG1 D:VAL196 4.0 14.4 1.0 CE1 D:HIS10 4.1 18.0 1.0 O D:ALA195 4.1 15.3 1.0 N D:ARG197 4.2 13.9 1.0 NE2 D:HIS222 4.2 19.4 1.0 CG2 D:VAL196 4.3 14.0 1.0 CB D:VAL196 4.3 16.8 1.0 CD2 D:HIS84 4.5 10.8 1.0 CD2 D:HIS222 4.5 13.3 1.0 C D:VAL196 4.5 15.7 1.0 NE2 D:HIS84 4.6 13.4 1.0 CG D:ASP8 4.6 19.2 1.0 CB D:HIS222 4.6 11.9 1.0 N D:VAL196 4.7 15.1 1.0 ND1 D:HIS224 4.7 21.6 1.0 CG D:HIS224 4.8 20.8 1.0 CG D:ASP48 4.8 13.3 1.0 C D:ALA195 4.8 16.4 1.0 N D:ILE223 4.9 13.5 0.6 N D:ILE223 4.9 14.2 0.4 OD1 D:ASN83 4.9 13.1 1.0

S.Liu, L.F.Tian, Y.P.Liu, X.M.An, Q.Tang, X.X.Yan, D.C.Liang. Structural Basis For Dna Recognition and Nuclease Processing By the MRE11 Homologue Sbcd in Double-Strand Breaks Repair. Acta Crystallogr.,Sect.D V. 70 299 2014.
ISSN: ISSN 0907-4449
PubMed: 24531464
DOI: 10.1107/S139900471302693X