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Manganese in PDB 3c2l: Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site

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

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

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site, PDB code: 3c2l 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) 23.14 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.470, 78.280, 54.890, 90.00, 113.18, 90.00
R / Rfree (%) 22.4 / 30.6

Other elements in 3c2l:

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

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site (pdb code 3c2l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site, PDB code: 3c2l:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3c2l

Go back to Manganese Binding Sites List in 3c2l
Manganese binding site 1 out of 6 in the Ternary Complex of Dna Polymerase Beta with A C: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 1 of Ternary Complex of Dna Polymerase Beta with A C:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn339

b:30.4
occ:1.00
 O2B A:F2A338 2.0 37.1 1.0
OD1 A:ASP190 2.0 25.6 1.0
O3G A:F2A338 2.1 34.3 1.0
OD2 A:ASP192 2.2 27.9 1.0
O1A A:F2A338 2.3 36.4 1.0
O A:HOH402 2.5 23.8 1.0
C3A A:F2A338 2.8 37.7 1.0
PB A:F2A338 2.9 40.8 1.0
CG A:ASP190 3.1 24.3 1.0
CG A:ASP192 3.1 29.1 1.0
PA A:F2A338 3.1 40.3 1.0
OD1 A:ASP192 3.2 32.6 1.0
PG A:F2A338 3.4 36.1 1.0
OD2 A:ASP190 3.4 23.5 1.0
MN A:MN340 3.5 30.7 1.0
O3B A:F2A338 3.5 38.2 1.0
O2G A:F2A338 4.0 33.0 1.0
C5' A:F2A338 4.1 45.4 1.0
O5' A:F2A338 4.1 42.7 1.0
O1B A:F2A338 4.2 39.0 1.0
O A:HOH369 4.2 39.1 1.0
O A:ASP190 4.3 25.6 1.0
O2A A:F2A338 4.3 41.4 1.0
N A:ASP190 4.4 26.4 1.0
CB A:ASP190 4.4 24.8 1.0
O1G A:F2A338 4.4 35.3 1.0
C A:ASP190 4.5 25.5 1.0
CB A:ASP192 4.5 26.7 1.0
CA A:ASP190 4.6 26.7 1.0
CA A:GLY179 4.7 33.2 1.0
N A:SER180 4.9 35.3 1.0
N A:ASP192 5.0 25.7 1.0

Manganese binding site 2 out of 6 in 3c2l

Go back to Manganese Binding Sites List in 3c2l
Manganese binding site 2 out of 6 in the Ternary Complex of Dna Polymerase Beta with A C: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 C:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn340

b:30.7
occ:1.00
 OD1 A:ASP192 1.9 32.6 1.0
O A:HOH369 2.1 39.1 1.0
O1A A:F2A338 2.2 36.4 1.0
OD2 A:ASP256 2.2 22.5 1.0
OD2 A:ASP190 2.3 23.5 1.0
O P:HOH86 2.6 28.5 1.0
CG A:ASP192 3.0 29.1 1.0
CG A:ASP190 3.3 24.3 1.0
CG A:ASP256 3.4 23.6 1.0
MN A:MN339 3.5 30.4 1.0
PA A:F2A338 3.5 40.3 1.0
OD1 A:ASP190 3.5 25.6 1.0
OD2 A:ASP192 3.6 27.9 1.0
CB A:ASP256 4.0 23.9 1.0
O2A A:F2A338 4.1 41.4 1.0
O5' A:F2A338 4.2 42.7 1.0
CB A:ASP192 4.2 26.7 1.0
C3' P:DC10 4.3 55.4 1.0
OP1 P:DC10 4.3 45.4 1.0
OD1 A:ASP256 4.4 21.8 1.0
O3' P:DC10 4.4 53.6 1.0
C5' P:DC10 4.4 52.0 1.0
C5' A:F2A338 4.6 45.4 1.0
C4' P:DC10 4.6 54.5 1.0
CB A:ASP190 4.6 24.8 1.0
O5' P:DC10 4.7 48.9 1.0
CA A:ASP192 4.8 26.1 1.0
C3A A:F2A338 4.8 37.7 1.0

Manganese binding site 3 out of 6 in 3c2l

Go back to Manganese Binding Sites List in 3c2l
Manganese binding site 3 out of 6 in the Ternary Complex of Dna Polymerase Beta with A C: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 C:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn341

b:46.9
occ:1.00
 O A:HOH421 2.1 15.3 1.0
O A:HOH420 2.3 23.4 1.0
OD1 A:ASP124 2.9 40.2 1.0
OD2 A:ASP124 3.3 44.0 1.0
CG A:ASP124 3.5 41.7 1.0
O A:HOH371 4.2 29.7 1.0
OG1 A:THR121 4.4 31.2 1.0
CB A:ASP124 4.9 42.0 1.0

Manganese binding site 4 out of 6 in 3c2l

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Manganese binding site 4 out of 6 in the Ternary Complex of Dna Polymerase Beta with A C: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 C:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn344

b:0.9
occ:1.00
 NE2 A:HIS51 2.4 49.4 1.0
CD2 A:HIS51 3.3 48.9 1.0
CE1 A:HIS51 3.3 49.5 1.0
ND1 A:HIS51 4.4 48.2 1.0
CG A:HIS51 4.4 47.4 1.0
CG A:PRO50 4.5 42.9 1.0

Manganese binding site 5 out of 6 in 3c2l

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Manganese binding site 5 out of 6 in the Ternary Complex of Dna Polymerase Beta with A C: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 C:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn342

b:70.3
occ:1.00
 O T:HOH356 2.4 22.2 1.0
O T:HOH355 2.6 38.8 1.0
N7 T:DG3 3.1 59.8 1.0
O6 T:DG3 3.4 58.0 1.0
O T:HOH348 3.9 27.9 1.0
C5 T:DG3 3.9 58.7 1.0
C6 T:DG3 4.0 58.0 1.0
C8 T:DG3 4.2 61.0 1.0
O4 D:DT2 4.5 40.3 1.0
C6 T:DC2 4.7 61.2 1.0
C2' T:DC2 4.8 66.7 1.0
N6 T:DA4 4.8 53.1 1.0
C5 T:DC2 4.9 60.6 1.0

Manganese binding site 6 out of 6 in 3c2l

Go back to Manganese Binding Sites List in 3c2l
Manganese binding site 6 out of 6 in the Ternary Complex of Dna Polymerase Beta with A C: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 C:Dapcpp Mismatch in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn343

b:73.6
occ:1.00
 N7 P:DG4 3.2 41.8 1.0
O6 P:DG4 4.0 40.0 1.0
C8 P:DG4 4.1 42.8 1.0
C5 P:DG4 4.1 40.8 1.0
N6 P:DA5 4.4 37.6 1.0
C6 P:DG4 4.4 39.9 1.0
C2' P:DT3 4.5 43.9 1.0
OP2 P:DG4 4.8 46.8 1.0
O4 T:DT12 4.9 26.1 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 15:59:55 2024

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