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Manganese in PDB 3c2m: Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site, PDB code: 3c2m was solved by V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.35 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.750, 78.370, 55.170, 90.00, 113.36, 90.00
R / Rfree (%) 21.4 / 27

Other elements in 3c2m:

The structure of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site (pdb code 3c2m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site, PDB code: 3c2m:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 3c2m

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Manganese binding site 1 out of 7 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn342

b:49.5
occ:0.50
 O T:HOH22 1.8 52.8 1.0
O1 D:EDO361 1.9 40.9 1.0
C2 D:EDO361 2.1 44.0 1.0
C1 D:EDO361 2.4 44.4 1.0
O T:HOH284 2.9 58.5 1.0
O D:HOH75 3.2 47.8 1.0
O6 T:DG3 3.2 44.6 1.0
O2 D:EDO361 3.6 47.5 1.0
N7 T:DG3 3.6 46.2 1.0
C6 T:DG3 4.1 44.9 1.0
C5 T:DG3 4.2 46.0 1.0
C5 T:DC2 4.3 49.4 1.0
O4 D:DT2 4.3 22.1 1.0
C6 T:DC2 4.5 51.0 1.0
OP2 T:DC2 4.7 70.5 1.0
C7 D:DT2 4.8 19.4 1.0
C8 T:DG3 4.8 48.1 1.0

Manganese binding site 2 out of 7 in 3c2m

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Manganese binding site 2 out of 7 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn339

b:23.8
occ:1.00
 OD1 A:ASP190 1.8 23.2 1.0
O2B A:F2A338 2.1 21.2 1.0
OD2 A:ASP192 2.2 21.4 1.0
O1A A:F2A338 2.2 11.0 1.0
O A:HOH368 2.3 23.8 1.0
O3G A:F2A338 2.4 27.2 1.0
CG A:ASP190 2.9 23.3 1.0
PB A:F2A338 3.2 25.7 1.0
CG A:ASP192 3.2 22.2 1.0
OD2 A:ASP190 3.2 20.8 1.0
PA A:F2A338 3.3 21.2 1.0
C3A A:F2A338 3.5 21.1 1.0
PG A:F2A338 3.5 29.0 1.0
OD1 A:ASP192 3.5 22.7 1.0
MN A:MN340 3.5 23.1 1.0
O3B A:F2A338 3.7 24.8 1.0
O2G A:F2A338 3.8 27.6 1.0
O A:ASP190 4.0 16.4 1.0
C5' A:F2A338 4.0 26.3 1.0
O5' A:F2A338 4.2 22.2 1.0
C A:ASP190 4.2 19.2 1.0
CB A:ASP190 4.2 20.4 1.0
N A:ASP190 4.3 19.7 1.0
O A:HOH395 4.4 9.7 1.0
CA A:ASP190 4.4 20.4 1.0
O1B A:F2A338 4.5 21.3 1.0
CB A:ASP192 4.5 20.9 1.0
O2A A:F2A338 4.5 22.5 1.0
CA A:GLY179 4.5 25.4 1.0
N A:SER180 4.5 27.3 1.0
O1G A:F2A338 4.7 29.8 1.0
N A:MET191 4.8 19.4 1.0
O P:HOH359 4.8 17.1 1.0
N A:ASP192 4.8 19.0 1.0
OG A:SER180 4.8 29.6 1.0
O P:HOH358 5.0 23.4 1.0

Manganese binding site 3 out of 7 in 3c2m

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Manganese binding site 3 out of 7 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn340

b:23.1
occ:1.00
 OD1 A:ASP192 2.1 22.7 1.0
OD2 A:ASP190 2.1 20.8 1.0
OD2 A:ASP256 2.2 21.3 1.0
O1A A:F2A338 2.3 11.0 1.0
O P:HOH358 2.4 23.4 1.0
O P:HOH359 2.5 17.1 1.0
CG A:ASP190 3.1 23.3 1.0
CG A:ASP192 3.1 22.2 1.0
PA A:F2A338 3.4 21.2 1.0
CG A:ASP256 3.4 19.0 1.0
OD1 A:ASP190 3.4 23.2 1.0
OD2 A:ASP192 3.4 21.4 1.0
MN A:MN339 3.5 23.8 1.0
O2A A:F2A338 3.8 22.5 1.0
O5' A:F2A338 3.9 22.2 1.0
CB A:ASP256 4.0 18.4 1.0
O P:HOH374 4.3 35.4 1.0
OD1 A:ASP256 4.4 20.0 1.0
C3' P:DC10 4.4 45.2 1.0
CB A:ASP190 4.4 20.4 1.0
CB A:ASP192 4.4 20.9 1.0
C5' A:F2A338 4.4 26.3 1.0
OP1 P:DC10 4.5 30.6 1.0
O3' P:DC10 4.5 46.5 1.0
C5' P:DC10 4.7 40.7 1.0
C4' P:DC10 4.8 43.8 1.0
O5' P:DC10 4.9 37.0 1.0
C3A A:F2A338 4.9 21.1 1.0
O3G A:F2A338 4.9 27.2 1.0

Manganese binding site 4 out of 7 in 3c2m

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Manganese binding site 4 out of 7 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn341

b:36.6
occ:1.00
 O A:HOH459 1.8 31.6 1.0
O2 A:EDO360 2.0 45.9 1.0
O A:HOH592 2.1 29.4 1.0
O A:HOH575 2.3 32.1 1.0
OD1 A:ASP124 2.3 29.3 1.0
O A:HOH400 2.5 26.9 1.0
C2 A:EDO360 3.1 45.7 1.0
CG A:ASP124 3.2 29.5 1.0
C1 A:EDO360 3.2 45.0 1.0
OD2 A:ASP124 3.3 30.3 1.0
O A:HOH460 3.7 45.3 1.0
OG1 A:THR121 3.9 22.8 1.0
O A:HOH446 4.2 35.7 1.0
CB A:ASP124 4.6 29.1 1.0
O1 A:EDO360 4.6 48.4 1.0
N A:ASP124 4.9 26.8 1.0
CA A:ASP124 5.0 28.6 1.0

Manganese binding site 5 out of 7 in 3c2m

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Manganese binding site 5 out of 7 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn343

b:30.8
occ:0.50
 O A:HOH569 2.0 41.6 1.0
NE2 A:HIS51 2.1 32.0 1.0
O A:HOH568 2.3 41.4 1.0
O A:HOH567 2.8 46.6 1.0
O A:HOH566 2.8 48.2 1.0
CE1 A:HIS51 3.0 31.3 1.0
CD2 A:HIS51 3.1 31.2 1.0
ND1 A:HIS51 4.1 30.3 1.0
CG A:HIS51 4.2 31.7 1.0
CG A:PRO50 4.9 30.5 1.0

Manganese binding site 6 out of 7 in 3c2m

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Manganese binding site 6 out of 7 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn344

b:51.6
occ:0.50
 O A:HOH550 3.3 45.5 1.0
NH2 A:ARG112 3.5 26.4 1.0
NH1 A:ARG112 3.7 31.8 1.0
CG1 A:VAL29 4.1 18.5 1.0
CZ A:ARG112 4.1 31.2 1.0
CG2 A:THR93 4.2 27.4 1.0
CB A:THR93 5.0 27.5 1.0

Manganese binding site 7 out of 7 in 3c2m

Go back to Manganese Binding Sites List in 3c2m
Manganese binding site 7 out of 7 in the Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Ternary Complex of Dna Polymerase Beta with A G:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn345

b:46.0
occ:0.50
 OE1 A:GLU288 2.1 49.9 1.0
ND1 A:HIS285 2.4 45.7 1.0
O A:HOH375 2.4 42.3 1.0
CE1 A:HIS285 3.2 46.4 1.0
O A:HOH563 3.3 44.1 1.0
CD A:GLU288 3.3 49.9 1.0
CG A:HIS285 3.4 45.0 1.0
CB A:HIS285 3.7 42.3 1.0
OE2 A:GLU288 3.9 49.7 1.0
CA A:HIS285 4.0 40.7 1.0
NE2 A:HIS285 4.4 45.8 1.0
CG A:GLU288 4.5 47.7 1.0
CD2 A:HIS285 4.5 45.8 1.0
CB A:GLU288 4.8 45.3 1.0
N A:HIS285 4.9 39.1 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Beta with Active-Site Mismatches Suggest A Transient Abasic Site Intermediate During Misincorporation. Mol.Cell V. 30 315 2008.
ISSN: ISSN 1097-2765
PubMed: 18471977
DOI: 10.1016/J.MOLCEL.2008.02.025
Page generated: Sat Oct 5 16:00:05 2024

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