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Manganese in PDB 5bpc: Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog

Enzymatic activity of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog

All present enzymatic activity of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog, PDB code: 5bpc was solved by B.D.Freudenthal, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.83 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.654, 78.635, 55.077, 90.00, 113.22, 90.00
R / Rfree (%) 21 / 25.9

Other elements in 5bpc:

The structure of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog (pdb code 5bpc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog, PDB code: 5bpc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5bpc

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Manganese binding site 1 out of 4 in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:28.5
occ:1.00
 OD1 A:ASP192 2.1 30.2 1.0
OD2 A:ASP190 2.2 25.6 1.0
O P:HOH105 2.2 24.4 1.0
O1A A:F2A405 2.2 21.4 1.0
OD2 A:ASP256 2.2 30.4 1.0
O P:HOH101 2.3 29.5 1.0
CG A:ASP190 3.1 27.8 1.0
CG A:ASP192 3.2 27.6 1.0
CG A:ASP256 3.4 30.9 1.0
OD1 A:ASP190 3.4 24.9 1.0
PA A:F2A405 3.4 29.0 1.0
O2A A:F2A405 3.6 30.2 1.0
MN A:MN402 3.7 26.1 1.0
OD2 A:ASP192 3.7 29.6 1.0
CB A:ASP256 4.0 28.0 1.0
O5' A:F2A405 4.0 39.4 1.0
O3' P:DC10 4.1 44.2 1.0
O P:HOH108 4.3 36.2 1.0
C5' A:F2A405 4.4 32.7 1.0
OD1 A:ASP256 4.4 28.4 1.0
OP1 P:DC10 4.4 33.6 1.0
CB A:ASP192 4.5 21.8 1.0
CB A:ASP190 4.5 26.7 1.0
C5' P:DC10 4.6 35.3 1.0
O5' P:DC10 5.0 35.4 1.0
O3G A:F2A405 5.0 26.8 1.0
C3A A:F2A405 5.0 22.1 1.0
CA A:ASP192 5.0 21.8 1.0

Manganese binding site 2 out of 4 in 5bpc

Go back to Manganese Binding Sites List in 5bpc
Manganese binding site 2 out of 4 in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:26.1
occ:1.00
 OD1 A:ASP190 2.0 24.9 1.0
O2B A:F2A405 2.0 26.9 1.0
OD2 A:ASP192 2.1 29.6 1.0
O A:HOH579 2.2 31.5 1.0
O1A A:F2A405 2.2 21.4 1.0
O3G A:F2A405 2.3 26.8 1.0
CG A:ASP192 3.1 27.6 1.0
CG A:ASP190 3.1 27.8 1.0
PB A:F2A405 3.1 27.6 1.0
PA A:F2A405 3.3 29.0 1.0
OD1 A:ASP192 3.4 30.2 1.0
PG A:F2A405 3.4 31.0 1.0
C3A A:F2A405 3.5 22.1 1.0
OD2 A:ASP190 3.5 25.6 1.0
O3B A:F2A405 3.7 35.9 1.0
MN A:MN401 3.7 28.5 1.0
O1G A:F2A405 4.1 30.8 1.0
O A:ASP190 4.1 28.8 1.0
C5' A:F2A405 4.2 32.7 1.0
O5' A:F2A405 4.2 39.4 1.0
N A:ASP190 4.4 21.9 1.0
C A:ASP190 4.4 22.3 1.0
O A:HOH548 4.4 23.8 1.0
CB A:ASP190 4.4 26.7 1.0
CB A:ASP192 4.4 21.8 1.0
N A:SER180 4.4 31.7 1.0
OG A:SER180 4.5 29.6 1.0
O1B A:F2A405 4.5 26.3 1.0
CA A:GLY179 4.5 28.6 1.0
O2A A:F2A405 4.5 30.2 1.0
O2G A:F2A405 4.6 24.8 1.0
CA A:ASP190 4.6 20.5 1.0
O P:HOH101 4.8 29.5 1.0
N A:ASP192 4.8 18.4 1.0
O P:HOH105 4.9 24.4 1.0

Manganese binding site 3 out of 4 in 5bpc

Go back to Manganese Binding Sites List in 5bpc
Manganese binding site 3 out of 4 in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:63.5
occ:1.00
 O A:HOH633 2.3 41.5 1.0
O P:HOH108 3.9 36.2 1.0
O2G A:F2A405 4.3 24.8 1.0
O P:HOH101 4.7 29.5 1.0
O3G A:F2A405 4.7 26.8 1.0
O A:HOH587 4.8 35.8 1.0
CA A:GLY189 4.8 27.9 1.0
OP2 P:DC10 4.8 31.9 1.0
O A:GLY189 4.9 25.2 1.0
C A:GLY189 4.9 27.6 1.0

Manganese binding site 4 out of 4 in 5bpc

Go back to Manganese Binding Sites List in 5bpc
Manganese binding site 4 out of 4 in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:71.4
occ:1.00
 OE2 A:GLU295 2.2 69.1 1.0
O2 T:4U36 2.6 53.7 1.0
O A:HOH502 3.0 55.7 1.0
CD A:GLU295 3.3 58.7 1.0
N3 T:DG7 3.6 43.7 1.0
O4' T:DG7 3.7 52.5 1.0
OE1 A:GLU295 3.8 55.3 1.0
C2 T:4U36 3.8 55.0 1.0
C1' T:DG7 4.1 52.0 1.0
N2 T:DG7 4.1 49.9 1.0
O4' T:DC8 4.2 52.8 1.0
C2 T:DG7 4.2 45.1 1.0
C4' T:DG7 4.3 56.7 1.0
C4 T:DG7 4.5 51.9 1.0
N3 T:4U36 4.5 54.1 1.0
CG A:GLU295 4.6 47.1 1.0
N9 T:DG7 4.7 52.8 1.0
O3' T:DG7 4.7 62.2 1.0
C4' T:DC8 4.8 47.1 1.0
C5' T:DC8 4.8 55.5 1.0
N1 T:4U36 4.8 55.3 1.0
C1' T:4U36 4.9 55.8 1.0

Reference:

B.I.Fedeles, B.D.Freudenthal, E.Yau, V.Singh, S.C.Chang, D.Li, J.C.Delaney, S.H.Wilson, J.M.Essigmann. Intrinsic Mutagenic Properties of 5-Chlorocytosine: A Mechanistic Connection Between Chronic Inflammation and Cancer. Proc.Natl.Acad.Sci.Usa V. 112 E4571 2015.
ISSN: ESSN 1091-6490
PubMed: 26243878
DOI: 10.1073/PNAS.1507709112
Page generated: Sat Oct 5 23:37:53 2024

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