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Manganese in PDB 2ido: Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex

Enzymatic activity of Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex

All present enzymatic activity of Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex:
2.7.7.7;

Protein crystallography data

The structure of Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex, PDB code: 2ido was solved by T.W.Kirby, S.Harvey, E.F.Derose, S.Chalov, A.K.Chikova, F.W.Perrino, R.M.Schaaper, R.E.London, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.76 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.289, 77.289, 212.978, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex (pdb code 2ido). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex, PDB code: 2ido:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 2ido

Go back to Manganese Binding Sites List in 2ido
Manganese binding site 1 out of 5 in the Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex


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 E. Coli Pol III Epsilon-Hot Proofreading Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:22.3
occ:1.00
 OD1 A:ASP12 2.1 21.4 1.0
O A:HOH2081 2.2 21.1 1.0
O A:HOH2016 2.2 18.9 1.0
O1P A:TMP2001 2.3 28.5 1.0
O A:HOH2003 2.3 17.1 1.0
O3P A:TMP2001 2.4 22.1 1.0
P A:TMP2001 2.8 25.9 1.0
CG A:ASP12 3.1 24.7 1.0
OD2 A:ASP12 3.5 22.5 1.0
MN A:MN1002 3.8 22.1 1.0
O5' A:TMP2001 3.9 24.1 1.0
C5' A:TMP2001 4.0 22.6 1.0
O2P A:TMP2001 4.0 26.9 1.0
O A:HOH2015 4.1 17.6 1.0
OD2 A:ASP103 4.1 17.0 1.0
O A:THR13 4.2 20.3 1.0
OD1 A:ASP103 4.2 17.7 1.0
O A:HOH2074 4.2 30.4 1.0
O A:HOH2027 4.3 24.4 1.0
CB A:ASP12 4.4 22.0 1.0
O A:HOH2051 4.4 54.1 1.0
O A:HIS98 4.6 21.8 1.0
CG A:ASP103 4.6 19.3 1.0
N A:THR13 4.7 22.5 1.0
CA A:ASP12 4.9 21.9 1.0
CD2 A:PHE102 5.0 23.0 1.0

Manganese binding site 2 out of 5 in 2ido

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Manganese binding site 2 out of 5 in the Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex


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 E. Coli Pol III Epsilon-Hot Proofreading Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1002

b:22.1
occ:1.00
 O3P A:TMP2001 2.0 22.1 1.0
OD2 A:ASP167 2.1 21.2 1.0
OE2 A:GLU14 2.1 19.9 1.0
O A:HOH2017 2.2 29.3 1.0
OD2 A:ASP12 2.2 22.5 1.0
CD A:GLU14 3.1 20.8 1.0
CG A:ASP167 3.1 25.4 1.0
CG A:ASP12 3.3 24.7 1.0
P A:TMP2001 3.3 25.9 1.0
OE1 A:GLU14 3.4 20.1 1.0
CB A:ASP167 3.6 23.7 1.0
OD1 A:ASP12 3.7 21.4 1.0
MN A:MN1001 3.8 22.3 1.0
O2P A:TMP2001 3.8 26.9 1.0
O A:THR13 4.0 20.3 1.0
O A:GLY163 4.0 31.4 1.0
O A:HOH2081 4.0 21.1 1.0
O5' A:TMP2001 4.1 24.1 1.0
NH2 A:ARG159 4.1 34.2 0.5
OD1 A:ASP167 4.2 28.3 1.0
C5' A:TMP2001 4.3 22.6 1.0
C A:GLY163 4.3 33.4 1.0
O1P A:TMP2001 4.5 28.5 1.0
CG A:GLU14 4.5 18.6 1.0
CB A:HIS162 4.6 51.2 1.0
CA A:ALA164 4.6 27.6 1.0
N A:ALA164 4.6 29.0 1.0
CB A:ASP12 4.6 22.0 1.0
O A:HOH2003 4.6 17.1 1.0
O A:HOH2074 4.6 30.4 1.0
N A:GLY163 4.8 43.1 1.0
C A:THR13 4.8 20.5 1.0

Manganese binding site 3 out of 5 in 2ido

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Manganese binding site 3 out of 5 in the Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1003

b:23.5
occ:1.00
 O3P C:TMP2002 2.0 22.4 1.0
OD2 C:ASP167 2.0 17.5 1.0
OE2 C:GLU14 2.1 23.9 1.0
OD2 C:ASP12 2.3 17.9 1.0
O C:HOH2008 2.4 19.6 1.0
CD C:GLU14 3.1 22.7 1.0
CG C:ASP167 3.1 18.6 1.0
CG C:ASP12 3.3 16.9 1.0
P C:TMP2002 3.3 22.8 1.0
OE1 C:GLU14 3.4 25.1 1.0
OD1 C:ASP12 3.6 18.0 1.0
CB C:ASP167 3.6 18.4 1.0
O2P C:TMP2002 3.7 24.8 1.0
MN C:MN1004 3.8 22.4 1.0
O C:THR13 4.0 22.2 1.0
O C:HOH2090 4.0 17.2 1.0
O5' C:TMP2002 4.0 23.0 1.0
O C:HOH2037 4.2 37.4 1.0
OD1 C:ASP167 4.2 18.7 1.0
O C:HOH2044 4.3 26.1 1.0
C5' C:TMP2002 4.3 24.5 1.0
CA C:ALA164 4.4 20.5 1.0
O C:HOH2064 4.4 33.5 1.0
CG C:GLU14 4.4 21.9 1.0
O1P C:TMP2002 4.5 20.2 1.0
O C:HOH2003 4.5 19.4 1.0
O C:GLY163 4.5 21.9 1.0
CB C:ASP12 4.6 17.5 1.0
N C:ALA164 4.7 22.4 1.0
C C:GLY163 4.7 23.9 1.0
C C:THR13 4.8 22.2 1.0
O C:HOH2051 4.9 29.9 1.0
O C:HOH2135 5.0 43.9 1.0

Manganese binding site 4 out of 5 in 2ido

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Manganese binding site 4 out of 5 in the Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1004

b:22.4
occ:1.00
 O C:HOH2089 2.1 17.0 1.0
OD1 C:ASP12 2.1 18.0 1.0
O C:HOH2003 2.2 19.4 1.0
O C:HOH2090 2.2 17.2 1.0
O3P C:TMP2002 2.3 22.4 1.0
O1P C:TMP2002 2.4 20.2 1.0
P C:TMP2002 2.8 22.8 1.0
CG C:ASP12 3.2 16.9 1.0
OD2 C:ASP12 3.6 17.9 1.0
MN C:MN1003 3.8 23.5 1.0
O5' C:TMP2002 3.9 23.0 1.0
O C:HOH2011 4.0 16.8 1.0
O2P C:TMP2002 4.0 24.8 1.0
OD2 C:ASP103 4.0 24.3 1.0
C5' C:TMP2002 4.0 24.5 1.0
O C:HOH2044 4.1 26.1 1.0
OD1 C:ASP103 4.2 26.4 1.0
C2 C:EDO1000 4.2 27.0 1.0
O C:THR13 4.2 22.2 1.0
O2 C:EDO1000 4.4 30.2 1.0
O C:HOH2033 4.4 24.6 1.0
CB C:ASP12 4.5 17.5 1.0
O C:HIS98 4.5 22.4 1.0
CG C:ASP103 4.6 25.8 1.0
O C:HOH2027 4.6 43.6 1.0
N C:THR13 4.8 19.0 1.0
CA C:ASP12 4.9 17.8 1.0

Manganese binding site 5 out of 5 in 2ido

Go back to Manganese Binding Sites List in 2ido
Manganese binding site 5 out of 5 in the Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of the E. Coli Pol III Epsilon-Hot Proofreading Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1005

b:71.3
occ:1.00
 O C:HOH2150 2.3 45.5 1.0
NE2 C:HIS162 2.3 37.8 1.0
O C:HOH2151 2.6 56.0 1.0
O C:HOH2149 2.9 46.6 1.0
CE1 C:HIS162 2.9 36.7 1.0
CD2 C:HIS162 3.5 34.1 1.0
O D:HOH102 3.8 37.8 1.0
ND1 C:HIS162 4.2 36.6 1.0
O D:HOH98 4.2 42.7 1.0
O D:HOH90 4.3 27.6 1.0
CG C:HIS162 4.5 33.9 1.0
O C:HOH2137 4.5 49.3 1.0
O C:HOH2074 4.5 26.7 1.0
O C:ARG159 4.8 29.8 1.0

Reference:

T.W.Kirby, S.Harvey, E.F.Derose, S.Chalov, A.K.Chikova, F.W.Perrino, R.M.Schaaper, R.E.London, L.C.Pedersen. Structure of the Escherichia Coli Dna Polymerase III Epsilon-Hot Proofreading Complex. J.Biol.Chem. V. 281 38466 2006.
ISSN: ISSN 0021-9258
PubMed: 16973612
DOI: 10.1074/JBC.M606917200
Page generated: Sat Oct 5 14:27:03 2024

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