Atomistry » Manganese » PDB 4gwc-4ilk » 4gxk
Atomistry »
  Manganese »
    PDB 4gwc-4ilk »
      4gxk »

Manganese in PDB 4gxk: R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog

Enzymatic activity of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog

All present enzymatic activity of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog, PDB code: 4gxk was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.89 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.861, 78.791, 55.151, 90.00, 112.65, 90.00
R / Rfree (%) 21.9 / 27.8

Other elements in 4gxk:

The structure of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog also contains other interesting chemical elements:

Sodium (Na) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog (pdb code 4gxk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog, PDB code: 4gxk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4gxk

Go back to Manganese Binding Sites List in 4gxk
Manganese binding site 1 out of 4 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG 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 R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:26.1
occ:1.00
 O A:HOH505 2.0 24.5 1.0
OD2 A:ASP256 2.0 31.3 1.0
O A:HOH514 2.0 29.2 1.0
OD1 A:ASP192 2.1 19.9 1.0
OD2 A:ASP190 2.1 23.0 1.0
O1A A:F2A404 2.1 27.1 0.9
CG A:ASP190 3.1 28.3 1.0
CG A:ASP192 3.2 21.5 1.0
CG A:ASP256 3.2 27.9 1.0
PA A:F2A404 3.4 25.3 0.9
OD1 A:ASP190 3.5 27.3 1.0
MN A:MN402 3.5 29.6 1.0
OD2 A:ASP192 3.6 21.1 1.0
O2A A:F2A404 3.7 24.5 0.9
CB A:ASP256 3.9 22.7 1.0
O P:HOH204 4.0 31.1 1.0
O5' A:F2A404 4.1 28.4 0.9
O A:HOH580 4.2 29.0 1.0
OD1 A:ASP256 4.2 33.0 1.0
CB A:ASP192 4.4 23.0 1.0
C5' A:F2A404 4.4 30.6 0.9
OP1 P:DA10 4.4 31.6 1.0
CB A:ASP190 4.4 23.5 1.0
O3' P:DA10 4.5 39.6 1.0
C5' P:DA10 4.5 35.4 1.0
CA A:ASP192 4.9 18.4 1.0
O A:MET191 5.0 20.4 1.0
O1B A:F2A404 5.0 29.7 0.9

Manganese binding site 2 out of 4 in 4gxk

Go back to Manganese Binding Sites List in 4gxk
Manganese binding site 2 out of 4 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG 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 R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:29.6
occ:1.00
 O1B A:F2A404 2.0 29.7 0.9
OD1 A:ASP190 2.0 27.3 1.0
O A:HOH506 2.1 27.3 1.0
O3G A:F2A404 2.2 24.3 0.9
OD2 A:ASP192 2.2 21.1 1.0
O1A A:F2A404 2.2 27.1 0.9
CG A:ASP190 3.0 28.3 1.0
PB A:F2A404 3.1 30.0 0.9
CG A:ASP192 3.1 21.5 1.0
PA A:F2A404 3.2 25.3 0.9
OD2 A:ASP190 3.3 23.0 1.0
OD1 A:ASP192 3.3 19.9 1.0
PG A:F2A404 3.4 31.6 0.9
C3A A:F2A404 3.4 32.7 0.9
MN A:MN401 3.5 26.1 1.0
O A:HOH580 3.6 29.0 1.0
O3B A:F2A404 3.6 34.2 0.9
C5' A:F2A404 4.0 30.6 0.9
O5' A:F2A404 4.1 28.4 0.9
O A:ASP190 4.1 25.7 1.0
O2G A:F2A404 4.2 32.1 0.9
CB A:ASP190 4.3 23.5 1.0
C A:ASP190 4.4 22.0 1.0
O A:HOH514 4.4 29.2 1.0
N A:ASP190 4.4 21.5 1.0
O A:HOH509 4.4 22.5 1.0
O2B A:F2A404 4.4 26.4 0.9
O1G A:F2A404 4.5 27.8 0.9
O2A A:F2A404 4.5 24.5 0.9
CA A:GLY179 4.5 29.6 1.0
N A:SER180 4.5 34.8 1.0
CB A:ASP192 4.6 23.0 1.0
CA A:ASP190 4.6 22.7 1.0
OG A:SER180 4.7 28.0 1.0
O A:HOH505 4.7 24.5 1.0
N A:ASP192 4.9 22.7 1.0

Manganese binding site 3 out of 4 in 4gxk

Go back to Manganese Binding Sites List in 4gxk
Manganese binding site 3 out of 4 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG 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 R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:30.0
occ:1.00
 O A:HOH640 2.1 30.0 1.0
O A:HOH642 2.1 30.0 1.0
O A:HOH641 2.1 30.0 1.0
O A:HOH607 2.2 42.1 1.0
OD1 A:ASP124 2.3 29.9 1.0
O A:HOH596 2.3 40.6 1.0
CG A:ASP124 3.1 37.5 1.0
OD2 A:ASP124 3.3 29.6 1.0
OG1 A:THR121 4.0 34.4 1.0
CB A:ASP124 4.5 33.4 1.0
OE1 A:GLU123 4.9 47.8 1.0
N A:ASP124 4.9 29.8 1.0
CA A:ASP124 5.0 31.5 1.0

Manganese binding site 4 out of 4 in 4gxk

Go back to Manganese Binding Sites List in 4gxk
Manganese binding site 4 out of 4 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG 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 R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:30.0
occ:1.00
 O P:HOH216 2.1 30.0 1.0
O T:HOH122 2.3 30.0 1.0
N7 P:DG4 2.7 20.0 1.0
C8 P:DG4 3.5 20.0 1.0
O P:HOH214 3.7 40.4 1.0
C5 P:DG4 3.8 20.0 1.0
O6 P:DG4 4.0 20.0 1.0
N6 P:DA5 4.1 27.6 1.0
O T:HOH118 4.1 40.0 1.0
C2' P:DT3 4.2 39.4 1.0
C6 P:DG4 4.3 20.0 1.0
OP2 P:DG4 4.4 43.7 1.0
N9 P:DG4 4.7 20.0 1.0
O3' P:DT3 4.8 43.6 1.0
C3' P:DT3 4.8 38.2 1.0
C4 P:DG4 4.8 20.0 1.0

Reference:

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Dna Polymerase Minor Groove Interactions Modulate Mutagenic Bypass of A Templating 8-Oxoguanine Lesion. Nucleic Acids Res. V. 41 1848 2013.
ISSN: ISSN 0305-1048
PubMed: 23267011
DOI: 10.1093/NAR/GKS1276
Page generated: Sat Oct 5 19:40:14 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy