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Manganese in PDB 4rq8: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S

Enzymatic activity of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S

All present enzymatic activity of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S, PDB code: 4rq8 was solved by R.Vyas, A.J.Reed, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.79 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.220, 82.540, 54.740, 90.00, 110.89, 90.00
R / Rfree (%) 20.7 / 27

Other elements in 4rq8:

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 9 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S (pdb code 4rq8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S, PDB code: 4rq8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4rq8

Go back to Manganese Binding Sites List in 4rq8
Manganese binding site 1 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


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 with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:18.4
occ:1.00
 OD2 A:ASP190 1.9 18.4 1.0
OD2 A:ASP256 2.0 18.2 1.0
OD1 A:ASP192 2.1 19.1 1.0
OP1 P:DA11 2.2 17.9 1.0
O A:HOH501 2.3 19.0 1.0
O3' P:DC10 2.6 18.6 1.0
CG A:ASP190 2.9 18.0 1.0
P P:DA11 2.9 18.2 1.0
CG A:ASP192 3.1 19.1 1.0
CG A:ASP256 3.1 18.2 1.0
OD1 A:ASP190 3.1 17.1 1.0
OD2 A:ASP192 3.4 19.5 1.0
MN A:MN404 3.5 17.9 1.0
CB A:ASP256 3.8 18.6 1.0
C3' P:DC10 3.8 18.7 1.0
OP2 P:DA11 3.9 18.5 1.0
OD1 A:ASP256 4.1 18.9 1.0
C4' P:DC10 4.1 19.5 1.0
O5' P:DA11 4.2 17.1 1.0
CB A:ASP190 4.2 18.9 1.0
C5' P:DC10 4.2 20.2 1.0
O P:HOH501 4.3 30.2 1.0
C5' P:DA11 4.4 16.1 1.0
CB A:ASP192 4.4 19.0 1.0
NH2 A:ARG254 4.7 19.4 1.0
N A:ASP256 4.8 18.7 1.0
O A:MET191 4.8 18.2 1.0
CA A:ASP192 4.9 19.0 1.0
O5' P:DC10 4.9 22.3 1.0
CA A:ASP256 4.9 19.0 1.0
C2' P:DC10 4.9 18.9 1.0
OP1 P:DC10 4.9 22.8 1.0
O12 A:PPV401 4.9 24.0 1.0

Manganese binding site 2 out of 6 in 4rq8

Go back to Manganese Binding Sites List in 4rq8
Manganese binding site 2 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


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 with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:35.9
occ:1.00
 O A:HOH522 1.9 30.5 1.0
NE2 A:HIS337 2.2 31.0 1.0
O A:HOH519 2.2 31.4 1.0
NE2 A:HIS339 2.3 36.4 1.0
O A:HOH520 2.4 31.2 1.0
O A:HOH521 2.4 29.9 1.0
CD2 A:HIS337 3.0 30.4 1.0
CD2 A:HIS339 3.2 34.6 1.0
CE1 A:HIS339 3.3 36.3 1.0
CE1 A:HIS337 3.3 32.0 1.0
OE1 A:GLU9 3.6 43.1 1.0
CG A:HIS337 4.2 29.3 1.0
ND1 A:HIS337 4.3 31.4 1.0
CG A:HIS339 4.4 33.3 1.0
ND1 A:HIS339 4.4 35.5 1.0
CD A:GLU9 4.5 43.3 1.0
OE2 A:GLU9 4.8 41.1 1.0
OG1 A:THR10 4.8 24.2 1.0

Manganese binding site 3 out of 6 in 4rq8

Go back to Manganese Binding Sites List in 4rq8
Manganese binding site 3 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:17.9
occ:1.00
 OD2 A:ASP192 2.1 19.5 1.0
O21 A:PPV401 2.1 21.3 1.0
OP1 P:DA11 2.1 17.9 1.0
OD1 A:ASP190 2.1 17.1 1.0
O A:HOH502 2.2 16.4 1.0
O12 A:PPV401 2.2 24.0 1.0
CG A:ASP192 3.1 19.1 1.0
P1 A:PPV401 3.2 21.0 1.0
CG A:ASP190 3.2 18.0 1.0
O11 A:PPV401 3.4 23.7 1.0
P2 A:PPV401 3.5 27.6 1.0
P P:DA11 3.5 18.2 1.0
OD1 A:ASP192 3.5 19.1 1.0
MN A:MN402 3.5 18.4 1.0
OPP A:PPV401 3.7 23.7 1.0
O P:HOH501 3.7 30.2 1.0
OD2 A:ASP190 3.7 18.4 1.0
C5' P:DA11 4.0 16.1 1.0
O5' P:DA11 4.1 17.1 1.0
O A:ASP190 4.1 17.9 1.0
O22 A:PPV401 4.1 25.7 1.0
N A:ASP190 4.4 20.1 1.0
OP2 P:DA11 4.4 18.5 1.0
CB A:ASP192 4.4 19.0 1.0
C A:ASP190 4.4 19.8 1.0
CB A:ASP190 4.5 18.9 1.0
O31 A:PPV401 4.5 21.3 1.0
O A:HOH501 4.5 19.0 1.0
O3' P:DC10 4.6 18.6 1.0
CA A:GLY179 4.6 20.8 1.0
O32 A:PPV401 4.7 25.2 1.0
O A:HOH503 4.7 21.1 1.0
CA A:ASP190 4.7 19.4 1.0
MN P:MN101 4.8 38.7 1.0
N A:SER180 4.8 20.6 1.0
OG A:SER180 5.0 20.7 1.0

Manganese binding site 4 out of 6 in 4rq8

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Manganese binding site 4 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:31.7
occ:1.00
 O A:HOH669 2.1 17.6 0.5
O A:HOH660 2.3 34.4 1.0
O A:HOH639 2.4 27.9 1.0
OD2 A:ASP321 2.5 21.8 0.5
CG A:ASP321 3.4 22.6 0.5
CB A:ASP321 3.7 22.6 0.5
CB A:ASP321 3.7 24.0 0.5
OD2 A:ASP321 4.2 25.0 0.5
OD1 A:ASP318 4.4 22.1 1.0
CG A:ASP321 4.5 24.6 0.5
OD1 A:ASP321 4.5 21.8 0.5
O A:ASP318 4.6 20.7 1.0
CA A:ASP318 4.9 20.9 1.0
C A:ASP321 4.9 23.5 0.5
CA A:ASP321 4.9 23.6 0.5
CG A:ASP318 4.9 21.8 1.0
N A:TYR322 5.0 24.1 1.0
CE1 A:TYR322 5.0 25.1 1.0
CA A:ASP321 5.0 22.7 0.5
C A:ASP321 5.0 23.0 0.5

Manganese binding site 5 out of 6 in 4rq8

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Manganese binding site 5 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:21.9
occ:1.00
 O A:HOH659 1.9 26.8 1.0
O A:LYS48 2.1 20.3 1.0
NE2 A:HIS338 2.2 26.7 1.0
NE2 A:HIS336 2.3 21.8 1.0
CE1 A:HIS338 2.9 25.4 1.0
C A:LYS48 3.1 21.7 1.0
CE1 A:HIS336 3.1 22.8 1.0
CD2 A:HIS336 3.4 23.1 1.0
CD2 A:HIS338 3.4 24.3 1.0
CA A:LYS48 3.5 22.7 1.0
CB A:LYS48 3.8 25.2 1.0
ND1 A:HIS338 4.1 24.1 1.0
N A:TYR49 4.3 21.3 1.0
ND1 A:HIS336 4.3 22.8 1.0
CG A:HIS338 4.4 24.5 1.0
CG A:HIS336 4.5 23.9 1.0
N A:PRO50 4.7 21.0 1.0
CG A:LYS48 4.7 26.7 1.0
CD A:PRO50 4.8 21.8 1.0
C A:TYR49 4.8 21.1 1.0
CA A:TYR49 4.8 21.9 1.0
CB A:PRO50 4.9 21.9 1.0
N A:LYS48 5.0 20.7 1.0

Manganese binding site 6 out of 6 in 4rq8

Go back to Manganese Binding Sites List in 4rq8
Manganese binding site 6 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:38.7
occ:1.00
 O P:HOH509 1.8 31.2 1.0
O A:HOH575 2.2 31.4 1.0
OP2 P:DA11 2.2 18.5 1.0
O11 A:PPV401 2.5 23.7 1.0
O P:HOH501 2.5 30.2 1.0
P P:DA11 3.3 18.2 1.0
O P:HOH515 3.4 20.7 0.5
O5' P:DA11 3.7 17.1 1.0
OP1 P:DA11 3.8 17.9 1.0
P1 A:PPV401 3.9 21.0 1.0
O12 A:PPV401 4.1 24.0 1.0
O A:HOH512 4.2 24.6 1.0
O32 A:PPV401 4.3 25.2 1.0
OPP A:PPV401 4.4 23.7 1.0
P2 A:PPV401 4.5 27.6 1.0
O3' P:DC10 4.6 18.6 1.0
O21 A:PPV401 4.8 21.3 1.0
MN A:MN404 4.8 17.9 1.0
O A:HOH501 4.8 19.0 1.0
O31 A:PPV401 4.8 21.3 1.0
C8 P:DA11 4.8 14.1 1.0
C5' P:DA11 4.9 16.1 1.0
C3' P:DC10 5.0 18.7 1.0

Reference:

R.Vyas, A.J.Reed, E.J.Tokarsky, Z.Suo. Viewing Human Dna Polymerase Beta Faithfully and Unfaithfully Bypass An Oxidative Lesion By Time-Dependent Crystallography. J.Am.Chem.Soc. V. 137 5225 2015.
ISSN: ISSN 0002-7863
PubMed: 25825995
DOI: 10.1021/JACS.5B02109
Page generated: Sat Oct 5 21:11:45 2024

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