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Manganese in PDB 3isd: Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch

Enzymatic activity of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch, PDB code: 3isd was solved by W.A.Beard, D.D.Shock, V.K.Batra, 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) 21.19 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.700, 77.640, 55.220, 90.00, 113.67, 90.00
R / Rfree (%) 19.5 / 26.2

Other elements in 3isd:

The structure of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch (pdb code 3isd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch, PDB code: 3isd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3isd

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Manganese binding site 1 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


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 Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:28.9
occ:1.00
 OD2 A:ASP192 2.0 25.6 1.0
OD1 A:ASP190 2.1 24.8 1.0
O2B A:F2A412 2.1 23.7 1.0
O1A A:F2A412 2.3 18.2 1.0
O3G A:F2A412 2.4 26.0 1.0
O A:HOH442 2.7 19.3 1.0
CG A:ASP192 3.0 24.0 1.0
CG A:ASP190 3.1 24.0 1.0
PB A:F2A412 3.2 24.2 1.0
PA A:F2A412 3.4 22.9 1.0
OD2 A:ASP190 3.4 23.1 1.0
C3A A:F2A412 3.4 21.5 1.0
OD1 A:ASP192 3.5 23.2 1.0
PG A:F2A412 3.5 25.4 1.0
MN A:MN405 3.7 26.4 1.0
O3B A:F2A412 3.7 26.3 1.0
C5' A:F2A412 3.9 26.6 1.0
O2G A:F2A412 4.1 25.6 1.0
O5' A:F2A412 4.1 24.4 1.0
O A:ASP190 4.3 24.0 1.0
N A:ASP190 4.3 23.4 1.0
CB A:ASP192 4.3 21.9 1.0
C A:ASP190 4.4 23.0 1.0
CB A:ASP190 4.4 23.8 1.0
CA A:GLY179 4.4 21.6 1.0
O1B A:F2A412 4.5 22.8 1.0
N A:SER180 4.6 22.4 1.0
CA A:ASP190 4.6 23.1 1.0
O2A A:F2A412 4.6 22.8 1.0
O A:HOH379 4.6 22.9 1.0
OG A:SER180 4.6 21.9 1.0
O1G A:F2A412 4.6 26.1 1.0
O A:HOH458 4.7 22.9 1.0
N A:ASP192 4.8 19.4 1.0
N A:MET191 4.9 21.7 1.0

Manganese binding site 2 out of 8 in 3isd

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Manganese binding site 2 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


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 Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:26.4
occ:1.00
 OD1 A:ASP192 2.1 23.2 1.0
O3' P:DC10 2.3 72.0 1.0
O1A A:F2A412 2.4 18.2 1.0
OD2 A:ASP190 2.4 23.1 1.0
OD2 A:ASP256 2.5 20.1 1.0
CG A:ASP192 3.1 24.0 1.0
C3' P:DC10 3.2 73.6 1.0
CG A:ASP190 3.2 24.0 1.0
C5' P:DC10 3.4 69.2 1.0
PA A:F2A412 3.4 22.9 1.0
OD1 A:ASP190 3.5 24.8 1.0
OD2 A:ASP192 3.5 25.6 1.0
CG A:ASP256 3.6 22.1 1.0
C4' P:DC10 3.7 72.4 1.0
MN A:MN404 3.7 28.9 1.0
O2A A:F2A412 3.9 22.8 1.0
O5' A:F2A412 3.9 24.4 1.0
CB A:ASP256 4.0 22.2 1.0
O5' P:DC10 4.1 64.2 1.0
CB A:ASP192 4.4 21.9 1.0
C5' A:F2A412 4.4 26.6 1.0
CB A:ASP190 4.6 23.8 1.0
OD1 A:ASP256 4.6 24.6 1.0
C2' P:DC10 4.6 74.6 1.0
OP1 P:DC10 4.9 60.3 1.0

Manganese binding site 3 out of 8 in 3isd

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Manganese binding site 3 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


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 Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:44.1
occ:1.00
 O2 A:EDO413 2.1 30.5 1.0
OD1 A:ASP124 2.5 34.6 1.0
O A:HOH449 2.6 19.1 1.0
C2 A:EDO413 3.2 32.1 1.0
C1 A:EDO413 3.4 33.0 1.0
CG A:ASP124 3.4 31.7 1.0
OD2 A:ASP124 3.6 32.1 1.0
O A:HOH448 4.1 23.7 1.0
O A:HOH538 4.2 24.8 1.0
OG1 A:THR121 4.4 28.9 1.0
CB A:ASP124 4.8 32.4 1.0
O1 A:EDO413 4.8 35.7 1.0

Manganese binding site 4 out of 8 in 3isd

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Manganese binding site 4 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


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 Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn408

b:57.9
occ:1.00
 ND1 A:HIS285 2.5 49.2 1.0
OE1 A:GLU288 2.7 45.2 1.0
CE1 A:HIS285 3.3 49.9 1.0
CG A:HIS285 3.6 48.6 1.0
CD A:GLU288 3.7 47.0 1.0
CB A:HIS285 3.9 46.0 1.0
OE2 A:GLU288 4.1 47.4 1.0
CA A:HIS285 4.3 45.2 1.0
NE2 A:HIS285 4.4 50.6 1.0
CD2 A:HIS285 4.6 50.0 1.0
NE1 A:TRP325 4.6 54.7 1.0
O A:HOH525 4.9 31.0 1.0

Manganese binding site 5 out of 8 in 3isd

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Manganese binding site 5 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


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 Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:53.8
occ:1.00
 NE2 A:HIS51 2.3 27.2 1.0
O A:HOH516 3.0 28.4 1.0
CE1 A:HIS51 3.2 27.4 1.0
CD2 A:HIS51 3.3 25.5 1.0
ND1 A:HIS51 4.4 25.5 1.0
CG A:HIS51 4.4 25.9 1.0

Manganese binding site 6 out of 8 in 3isd

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Manganese binding site 6 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


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 Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn410

b:87.4
occ:1.00
 CE1 A:HIS252 2.6 36.8 1.0
NE2 A:HIS252 2.6 37.6 1.0
OE2 A:GLU249 3.6 53.5 1.0
OE1 A:GLU249 3.8 52.1 1.0
ND1 A:HIS252 3.9 36.2 1.0
CD A:GLU249 4.0 52.1 1.0
CD2 A:HIS252 4.0 35.5 1.0
OE1 A:GLN240 4.2 32.0 1.0
NE2 A:GLN240 4.3 32.9 1.0
CD A:GLN240 4.6 32.5 1.0
CG A:HIS252 4.6 35.3 1.0

Manganese binding site 7 out of 8 in 3isd

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Manganese binding site 7 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


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 Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn411

b:88.6
occ:1.00
 O A:HOH487 2.3 40.4 1.0
NE2 A:HIS222 2.7 39.8 1.0
CE1 A:HIS222 3.0 41.2 1.0
CD2 A:HIS222 3.9 39.2 1.0
O A:HOH488 4.1 29.8 1.0
ND1 A:HIS222 4.3 40.4 1.0
CG A:HIS222 4.8 38.7 1.0

Manganese binding site 8 out of 8 in 3isd

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Manganese binding site 8 out of 8 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn406

b:36.0
occ:1.00
 O D:HOH10 2.1 13.1 1.0
O T:HOH147 2.3 15.5 1.0
O T:HOH144 2.4 20.7 1.0
O T:HOH150 2.4 18.7 1.0
N7 T:DG3 2.5 38.2 1.0
C8 T:DG3 3.2 39.2 1.0
C5 T:DG3 3.7 36.6 1.0
O6 T:DG3 4.1 34.7 1.0
C6 T:DG3 4.3 36.2 1.0
O4 D:DT2 4.4 18.7 1.0
N9 T:DG3 4.5 39.7 1.0
O T:HOH123 4.7 26.2 1.0
C4 T:DG3 4.7 37.8 1.0
C6 T:DC2 4.8 43.5 1.0
N6 T:DA4 4.8 27.5 1.0
C2' T:DC2 4.8 44.6 1.0
OP2 T:DC2 4.9 59.7 1.0
C5 T:DC2 5.0 42.8 1.0

Reference:

W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson. Dna Polymerase Beta Substrate Specificity: Side Chain Modulation of the "A-Rule". J.Biol.Chem. V. 284 31680 2009.
ISSN: ISSN 0021-9258
PubMed: 19759017
DOI: 10.1074/JBC.M109.029843
Page generated: Sat Oct 5 16:36:15 2024

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