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Manganese in PDB 6u6b: Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site, PDB code: 6u6b was solved by H.Ouzon-Shubeita, C.K.Vilas, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.14 / 3.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.430, 78.216, 53.965, 90.00, 110.57, 90.00
R / Rfree (%) 22.2 / 26.8

Other elements in 6u6b:

The structure of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site (pdb code 6u6b). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site, PDB code: 6u6b:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6u6b

Go back to Manganese Binding Sites List in 6u6b
Manganese binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:73.6
occ:1.00
OD2 A:ASP190 1.8 43.0 1.0
O3' P:DC10 1.9 63.5 1.0
OD1 A:ASP192 2.0 61.5 1.0
OD2 A:ASP256 2.0 41.5 1.0
O1A A:DZ4405 2.5 61.7 1.0
CG A:ASP190 2.9 43.9 1.0
C3' P:DC10 3.0 72.4 1.0
CG A:ASP192 3.1 54.0 1.0
CG A:ASP256 3.2 31.4 1.0
H3' P:DC10 3.3 86.9 1.0
H4' P:DC10 3.3 84.1 1.0
OD1 A:ASP190 3.4 44.3 1.0
OD2 A:ASP192 3.5 55.2 1.0
H5'' P:DC10 3.5 73.9 1.0
HB2 A:ASP256 3.6 36.3 1.0
C4' P:DC10 3.6 70.1 1.0
PA A:DZ4405 3.6 47.3 1.0
H5' A:DZ4405 3.8 65.2 1.0
O5' A:DZ4405 3.9 49.4 1.0
CB A:ASP256 4.0 30.2 1.0
MN A:MN402 4.0 54.8 1.0
C5' P:DC10 4.0 61.5 1.0
O2A A:DZ4405 4.1 43.3 1.0
H5'A A:DZ4405 4.1 65.2 1.0
C5' A:DZ4405 4.2 54.4 1.0
CB A:ASP190 4.2 34.7 1.0
OD1 A:ASP256 4.2 34.6 1.0
HB2 A:ASP190 4.3 41.6 1.0
H2'' P:DC10 4.3 78.3 1.0
C2' P:DC10 4.3 65.2 1.0
HB3 A:ASP256 4.4 36.3 1.0
CB A:ASP192 4.4 47.1 1.0
HB3 A:ASP190 4.4 41.6 1.0
HA A:ASP192 4.4 55.9 1.0
HB3 A:ASP192 4.6 56.6 1.0
O5' P:DC10 4.6 60.5 1.0
H A:ASP256 4.8 45.5 1.0
H5' P:DC10 4.9 73.9 1.0
CA A:ASP192 4.9 46.5 1.0
H2' P:DC10 4.9 78.3 1.0
O4' P:DC10 4.9 61.9 1.0

Manganese binding site 2 out of 2 in 6u6b

Go back to Manganese Binding Sites List in 6u6b
Manganese binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:54.8
occ:1.00
OD2 A:ASP192 1.8 55.2 1.0
OD1 A:ASP190 1.9 44.3 1.0
O2B A:DZ4405 2.0 61.7 1.0
O3G A:DZ4405 2.1 57.7 1.0
O1A A:DZ4405 2.5 61.7 1.0
CG A:ASP192 3.0 54.0 1.0
PB A:DZ4405 3.0 39.8 1.0
CG A:ASP190 3.1 43.9 1.0
PA A:DZ4405 3.1 47.3 1.0
N3A A:DZ4405 3.2 65.8 1.0
O5' A:DZ4405 3.3 49.4 1.0
PG A:DZ4405 3.4 46.7 1.0
H A:SER180 3.4 47.6 1.0
H A:ASP190 3.4 47.4 1.0
O A:ASP190 3.5 45.7 1.0
OD1 A:ASP192 3.5 61.5 1.0
O3B A:DZ4405 3.6 46.6 1.0
HA3 A:GLY179 3.6 39.3 1.0
OD2 A:ASP190 3.6 43.0 1.0
HN3A A:DZ4405 3.9 79.0 1.0
MN A:MN401 4.0 73.6 1.0
C A:ASP190 4.0 39.3 1.0
HG A:SER180 4.1 46.1 1.0
HB2 A:ASP192 4.1 56.6 1.0
CB A:ASP192 4.2 47.1 1.0
N A:ASP190 4.2 39.5 1.0
N A:SER180 4.2 39.7 1.0
OG A:SER180 4.2 38.4 1.0
H A:ASP192 4.3 53.9 1.0
O1G A:DZ4405 4.3 55.3 1.0
CB A:ASP190 4.3 34.7 1.0
O1B A:DZ4405 4.3 32.1 1.0
O2G A:DZ4405 4.4 41.1 1.0
CA A:ASP190 4.4 31.4 1.0
CA A:GLY179 4.4 32.7 1.0
HA2 A:GLY179 4.5 39.3 1.0
C5' A:DZ4405 4.5 54.4 1.0
O2A A:DZ4405 4.6 43.3 1.0
N A:ASP192 4.6 44.9 1.0
H5' A:DZ4405 4.6 65.2 1.0
HB3 A:SER180 4.6 47.8 1.0
H A:GLY189 4.7 45.4 1.0
HB3 A:ASP190 4.7 41.6 1.0
HB3 A:ASP192 4.9 56.6 1.0
N A:MET191 4.9 40.9 1.0
C A:GLY179 4.9 33.1 1.0
HA A:MET191 4.9 43.2 1.0
CB A:SER180 4.9 39.8 1.0
O3' P:DC10 4.9 63.5 1.0
CA A:ASP192 5.0 46.5 1.0
HB2 A:ASP190 5.0 41.6 1.0

Reference:

H.Ouzon-Shubeita, C.K.Vilas, S.Lee. Structures of the Mutagenic Bypass of the Major Cisplatin-Dna Lesion By Human Dna Polymerase Beta Reveal Insights Into Cisplatin-Induced Mutagenesis To Be Published.
Page generated: Tue Dec 15 05:02:31 2020

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