Atomistry » Manganese » PDB 5b4c-5cdm » 5bpc
Atomistry »
  Manganese »
    PDB 5b4c-5cdm »
      5bpc »

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

Go back to Manganese Binding Sites List in 5bpc
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy