Atomistry » Manganese » PDB 6tzp-6vf4 » 6u6b
Atomistry »
  Manganese »
    PDB 6tzp-6vf4 »
      6u6b »

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: Sun Oct 6 07:15:34 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy