Manganese in PDB 1j54: Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8

All present enzymatic activity of Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8:
2.7.7.7;

The structure of Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8, PDB code: 1j54 was solved by S.Hamdan, P.D.Carr, S.E.Brown, D.L.Ollis, N.E.Dixon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.800, 60.800, 111.100, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.4

The binding sites of Manganese atom in the Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8 (pdb code 1j54). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8, PDB code: 1j54:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn3000 b:19.1 occ:1.00 O3P A:TMP2000 2.1 24.9 0.8 OE2 A:GLU14 2.1 18.8 1.0 OD2 A:ASP167 2.1 18.6 1.0 O3P A:TMP2000 2.1 19.1 0.1 OD2 A:ASP12 2.2 16.9 1.0 O2P A:TMP2000 2.5 26.5 0.8 P A:TMP2000 2.8 25.4 0.8 CD A:GLU14 3.0 20.4 1.0 CG A:ASP167 3.1 20.4 1.0 CG A:ASP12 3.2 16.7 1.0 OE1 A:GLU14 3.4 21.7 1.0 OD1 A:ASP12 3.5 16.9 1.0 P A:TMP2000 3.6 17.5 0.1 CB A:ASP167 3.6 18.2 1.0 MN A:MN3001 3.7 17.8 1.0 O A:THR13 3.9 16.3 1.0 C5' A:TMP2000 4.0 25.8 0.8 O5' A:TMP2000 4.0 24.5 0.8 CB A:HIS162 4.1 25.5 1.0 O A:GLY163 4.1 20.0 1.0 O1P A:TMP2000 4.1 25.2 0.8 C5' A:TMP2000 4.1 20.2 0.1 O2P A:TMP2000 4.1 19.4 0.1 OD1 A:ASP167 4.2 20.8 1.0 O A:HOH6003 4.2 23.1 1.0 CG A:GLU14 4.3 19.2 1.0 C A:GLY163 4.4 19.5 1.0 O A:HOH6001 4.4 13.3 1.0 NH2 A:ARG159 4.5 21.9 1.0 O5' A:TMP2000 4.5 19.8 0.1 CB A:ASP12 4.5 15.1 1.0 N A:GLY163 4.6 21.9 1.0 CA A:ALA164 4.6 16.3 1.0 ND1 A:HIS162 4.6 27.4 1.0 N A:ALA164 4.6 17.2 1.0 C A:THR13 4.7 15.5 1.0 CG A:HIS162 4.8 26.9 1.0 O1P A:TMP2000 4.8 19.1 0.1 O A:HOH6035 4.9 28.2 1.0 C A:HIS162 5.0 23.7 1.0

Manganese binding site 2 out of 2 in the Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the N-Terminal Exonuclease Domain of the Epsilon Subunit of E.Coli Dna Polymerase III at pH 5.8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn3001 b:17.8 occ:1.00 OD1 A:ASP12 2.0 16.9 1.0 O3P A:TMP2000 2.1 24.9 0.8 O3P A:TMP2000 2.2 19.1 0.1 O A:HOH6002 2.2 17.4 1.0 O A:HOH6001 2.2 13.3 1.0 O A:HOH6003 2.2 23.1 1.0 O A:HOH6004 2.4 36.7 0.8 O1P A:TMP2000 2.4 19.1 0.1 P A:TMP2000 2.8 17.5 0.1 CG A:ASP12 3.1 16.7 1.0 P A:TMP2000 3.4 25.4 0.8 OD2 A:ASP12 3.6 16.9 1.0 O5' A:TMP2000 3.7 19.8 0.1 MN A:MN3000 3.7 19.1 1.0 O1P A:TMP2000 3.8 25.2 0.8 O2P A:TMP2000 4.0 19.4 0.1 O5' A:TMP2000 4.0 24.5 0.8 O A:HOH6013 4.1 15.4 1.0 OD2 A:ASP103 4.1 18.9 1.0 C5' A:TMP2000 4.1 20.2 0.1 OD1 A:ASP103 4.2 18.6 1.0 O A:THR13 4.2 16.3 1.0 O A:HOH6072 4.3 45.0 1.0 CB A:ASP12 4.4 15.1 1.0 O A:HOH6035 4.4 28.2 1.0 O A:HIS98 4.4 20.7 1.0 C5' A:TMP2000 4.5 25.8 0.8 O A:HOH6017 4.5 21.7 1.0 CG A:ASP103 4.6 17.9 1.0 N A:THR13 4.7 14.2 1.0 O2P A:TMP2000 4.7 26.5 0.8 CA A:ASP12 4.8 13.6 1.0 OD2 A:ASP167 5.0 18.6 1.0

S.Hamdan, P.D.Carr, S.E.Brown, D.L.Ollis, N.E.Dixon. Structural Basis For Proofreading During Replication of the Escherichia Coli Chromosome Structure V. 10 535 2002.
ISSN: ISSN 0969-2126
PubMed: 11937058
DOI: 10.1016/S0969-2126(02)00738-4