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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

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