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Manganese in PDB 4tus: Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site.

Enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site.

All present enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site.:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site., PDB code: 4tus was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.878, 78.417, 54.803, 90.00, 112.80, 90.00
R / Rfree (%) 20 / 24.3

Other elements in 4tus:

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) 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 Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site. (pdb code 4tus). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site., PDB code: 4tus:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4tus

Go back to Manganese Binding Sites List in 4tus
Manganese binding site 1 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) 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 Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:31.9
occ:1.00
OD2 A:ASP190 2.1 29.8 1.0
OD1 A:ASP192 2.2 30.2 1.0
O1A A:0KX405 2.2 23.1 1.0
OD2 A:ASP256 2.3 33.7 1.0
O3' P:DC10 2.4 34.6 1.0
O A:HOH526 2.4 28.6 1.0
CG A:ASP190 3.0 30.2 1.0
CG A:ASP192 3.1 31.3 1.0
OD1 A:ASP190 3.3 28.6 1.0
OD2 A:ASP192 3.4 28.7 1.0
PA A:0KX405 3.4 26.0 1.0
CG A:ASP256 3.4 29.5 1.0
C3' P:DC10 3.5 40.3 1.0
MN A:MN402 3.7 36.3 1.0
O2A A:0KX405 3.9 23.8 1.0
CB A:ASP256 4.0 23.7 1.0
O5' A:0KX405 4.1 24.3 1.0
C4' P:DC10 4.1 32.9 1.0
C5' A:0KX405 4.2 27.7 1.0
O P:HOH111 4.2 36.2 1.0
C5' P:DC10 4.2 33.9 1.0
CB A:ASP190 4.4 28.4 1.0
OD1 A:ASP256 4.4 27.2 1.0
CB A:ASP192 4.5 34.3 1.0
O5' P:DC10 4.7 30.3 1.0
O1G A:0KX405 4.8 25.8 1.0
C2' P:DC10 4.8 34.7 1.0
O P:HOH108 4.9 39.9 1.0
N3A A:0KX405 4.9 26.8 1.0
OP1 P:DC10 4.9 33.5 1.0
O A:MET191 5.0 30.7 1.0

Manganese binding site 2 out of 2 in 4tus

Go back to Manganese Binding Sites List in 4tus
Manganese binding site 2 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) 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 Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) with Manganese in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:36.3
occ:1.00
O2B A:0KX405 2.0 28.1 1.0
OD1 A:ASP190 2.0 28.6 1.0
OD2 A:ASP192 2.1 28.7 1.0
O1G A:0KX405 2.1 25.8 1.0
O1A A:0KX405 2.3 23.1 1.0
O A:HOH517 2.5 29.5 1.0
PB A:0KX405 3.0 27.4 1.0
CG A:ASP190 3.2 30.2 1.0
CG A:ASP192 3.2 31.3 1.0
PA A:0KX405 3.2 26.0 1.0
N3A A:0KX405 3.3 26.8 1.0
PG A:0KX405 3.4 28.6 1.0
O3B A:0KX405 3.6 26.5 1.0
OD2 A:ASP190 3.7 29.8 1.0
MN A:MN401 3.7 31.9 1.0
OD1 A:ASP192 3.7 30.2 1.0
O3G A:0KX405 4.0 29.5 1.0
O A:ASP190 4.1 31.8 1.0
OG A:SER180 4.1 36.1 1.0
C5' A:0KX405 4.3 27.7 1.0
O5' A:0KX405 4.3 24.3 1.0
N A:ASP190 4.3 30.9 1.0
C A:ASP190 4.4 35.3 1.0
O A:HOH559 4.4 28.9 1.0
CB A:ASP190 4.4 28.4 1.0
N A:SER180 4.4 33.7 1.0
O1B A:0KX405 4.4 28.9 1.0
CB A:ASP192 4.4 34.3 1.0
O2A A:0KX405 4.5 23.8 1.0
CA A:GLY179 4.5 31.8 1.0
O2G A:0KX405 4.6 30.1 1.0
CA A:ASP190 4.6 30.9 1.0
O A:HOH526 4.8 28.6 1.0
N A:ASP192 4.9 28.4 1.0
N A:MET191 5.0 31.1 1.0

Reference:

M.C.Koag, L.Lai, S.Lee. Structural Basis For the Inefficient Nucleotide Incorporation Opposite Cisplatin-Dna Lesion By Human Dna Polymerase Beta J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25237188
DOI: 10.1074/JBC.M114.605451
Page generated: Tue Dec 15 04:29:12 2020

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