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

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

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

Protein crystallography data

The structure of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog, PDB code: 4gxj 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) 21.06 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.084, 77.432, 55.125, 90.00, 114.45, 90.00
R / Rfree (%) 23.1 / 29.2

Other elements in 4gxj:

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

Fluorine (F) 2 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog (pdb code 4gxj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog, PDB code: 4gxj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 4gxj

Go back to Manganese Binding Sites List in 4gxj
Manganese binding site 1 out of 7 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp 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 Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:32.3
occ:1.00
 O3' P:DA10 2.0 28.9 1.0
OD1 A:ASP192 2.0 25.4 1.0
OD2 A:ASP190 2.1 36.9 1.0
OD2 A:ASP256 2.1 27.6 1.0
O2A A:6CF401 2.1 24.9 1.0
O A:HOH502 2.2 24.8 1.0
CG A:ASP192 3.1 30.6 1.0
CG A:ASP190 3.1 29.1 1.0
C3' P:DA10 3.3 34.5 1.0
CG A:ASP256 3.3 31.8 1.0
MN A:MN403 3.4 28.3 1.0
P1 A:6CF401 3.4 37.8 1.0
OD2 A:ASP192 3.5 29.3 1.0
OD1 A:ASP190 3.5 33.4 1.0
O1A A:6CF401 3.6 37.6 1.0
C4' P:DA10 3.9 36.3 1.0
CB A:ASP256 4.0 20.5 1.0
C5' A:6CF401 4.2 41.2 1.0
O5' A:6CF401 4.2 42.3 1.0
C5' P:DA10 4.2 30.5 1.0
OD1 A:ASP256 4.3 23.5 1.0
O5' P:DA10 4.3 32.2 1.0
CB A:ASP190 4.4 26.2 1.0
CB A:ASP192 4.4 33.0 1.0
C2' P:DA10 4.4 36.3 1.0
O2G A:6CF401 4.7 31.1 1.0
O1B A:6CF401 4.7 29.8 1.0
OP1 P:DA10 4.7 26.3 1.0
CA A:ASP192 4.9 17.0 1.0
O P:HOH201 4.9 27.8 1.0
C3A A:6CF401 5.0 35.8 1.0
O A:MET191 5.0 25.3 1.0

Manganese binding site 2 out of 7 in 4gxj

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Manganese binding site 2 out of 7 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp 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 Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:28.3
occ:1.00
 O1B A:6CF401 2.0 29.8 1.0
OD1 A:ASP190 2.0 33.4 1.0
O2A A:6CF401 2.0 24.9 1.0
OD2 A:ASP192 2.1 29.3 1.0
O A:HOH501 2.1 26.1 1.0
O2G A:6CF401 2.1 31.1 1.0
CG A:ASP190 3.0 29.1 1.0
CG A:ASP192 3.0 30.6 1.0
P2 A:6CF401 3.0 41.5 1.0
P1 A:6CF401 3.1 37.8 1.0
OD2 A:ASP190 3.2 36.9 1.0
P3 A:6CF401 3.2 42.8 1.0
OD1 A:ASP192 3.3 25.4 1.0
MN A:MN402 3.4 32.3 1.0
C3A A:6CF401 3.5 35.8 1.0
O3B A:6CF401 3.6 31.7 1.0
O3G A:6CF401 3.7 33.9 1.0
F2A A:6CF401 3.8 28.0 1.0
C5' A:6CF401 3.9 41.2 1.0
O5' A:6CF401 4.0 42.3 1.0
O A:ASP190 4.3 22.7 1.0
CB A:ASP190 4.3 26.2 1.0
O1A A:6CF401 4.4 37.6 1.0
CB A:ASP192 4.4 33.0 1.0
O2B A:6CF401 4.4 46.5 1.0
O1G A:6CF401 4.4 35.3 1.0
N A:ASP190 4.4 22.7 1.0
O A:HOH502 4.5 24.8 1.0
C A:ASP190 4.5 29.2 1.0
O3' P:DA10 4.6 28.9 1.0
CA A:GLY179 4.6 31.5 1.0
F1A A:6CF401 4.7 32.2 1.0
CA A:ASP190 4.7 24.7 1.0
N A:SER180 4.8 31.7 1.0
O A:HOH533 4.8 32.7 1.0
N A:ASP192 4.9 22.9 1.0
OG A:SER180 4.9 30.7 1.0

Manganese binding site 3 out of 7 in 4gxj

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Manganese binding site 3 out of 7 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp 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 Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:76.7
occ:1.00
 NE2 A:HIS51 2.1 49.2 1.0
CE1 A:HIS51 3.0 56.2 1.0
CD2 A:HIS51 3.0 55.7 1.0
ND1 A:HIS51 4.0 53.4 1.0
CG A:HIS51 4.0 50.4 1.0

Manganese binding site 4 out of 7 in 4gxj

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Manganese binding site 4 out of 7 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp 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 Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:79.1
occ:1.00
 O A:HOH572 2.1 69.7 1.0
OD2 A:ASP314 2.2 20.0 1.0
O A:HOH573 2.2 63.3 1.0
O A:HOH571 2.4 43.9 1.0
CG A:ASP314 2.8 20.0 1.0
OD1 A:ASP314 3.3 20.0 1.0
CB A:ASP314 3.7 20.0 1.0
O A:ASP314 4.4 55.0 1.0
C A:ASP314 4.7 53.9 1.0
CA A:ASP314 4.8 54.6 1.0

Manganese binding site 5 out of 7 in 4gxj

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Manganese binding site 5 out of 7 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:65.2
occ:1.00
 O P:HOH208 2.2 43.4 1.0
N7 P:DG4 2.3 54.5 1.0
C8 P:DG4 3.1 48.3 1.0
C5 P:DG4 3.4 45.5 1.0
N6 P:DA5 3.8 20.0 1.0
O6 P:DG4 3.8 38.7 1.0
C6 P:DG4 4.0 39.4 1.0
C2' P:DT3 4.2 48.9 1.0
N9 P:DG4 4.3 51.7 1.0
C4 P:DG4 4.5 52.7 1.0
OP2 P:DG4 4.6 58.3 1.0
O4 T:DT12 4.6 37.8 1.0
C6 P:DA5 5.0 20.0 1.0

Manganese binding site 6 out of 7 in 4gxj

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Manganese binding site 6 out of 7 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:68.6
occ:1.00
 O T:HOH204 2.1 37.6 1.0
O T:HOH214 2.2 55.2 1.0
N7 T:DG3 2.6 49.3 1.0
C8 T:DG3 3.4 51.1 1.0
C5 T:DG3 3.8 42.4 1.0
O6 T:DG3 4.2 45.5 1.0
C6 T:DG3 4.4 40.0 1.0
N9 T:DG3 4.6 46.3 1.0
C2' T:DC2 4.8 59.5 1.0
O4 D:DT2 4.8 38.0 1.0
C4 T:DG3 4.9 44.8 1.0
N6 T:DA4 4.9 41.6 1.0

Manganese binding site 7 out of 7 in 4gxj

Go back to Manganese Binding Sites List in 4gxj
Manganese binding site 7 out of 7 in the R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of R283K Dna Polymerase Beta Ternary Complex with A Templating 8OG and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn102

b:86.7
occ:1.00
 N7 T:DA14 4.2 40.5 1.0
O T:HOH210 4.2 37.6 1.0
N7 T:DG15 4.5 37.0 1.0
C8 T:DA14 4.7 40.9 1.0
O6 T:DG15 4.7 35.9 1.0
N4 T:DC16 4.8 34.9 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 19:40:13 2024

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