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Manganese in PDB 4rq2: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 Dctp 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 Dctp 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 Dctp Soaked with MNCL2 For 35 S, PDB code: 4rq2 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) 46.64 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.850, 82.290, 54.680, 90.00, 110.68, 90.00
R / Rfree (%) 19.4 / 26.9

Other elements in 4rq2:

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

Sodium (Na) 7 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 Dctp Soaked with MNCL2 For 35 S (pdb code 4rq2). 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 Dctp Soaked with MNCL2 For 35 S, PDB code: 4rq2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4rq2

Go back to Manganese Binding Sites List in 4rq2
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 Dctp 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:23.6
occ:1.00
 OD1 A:ASP190 2.0 26.2 1.0
OP1 P:DC11 2.1 20.7 1.0
O A:HOH587 2.1 22.2 1.0
O21 A:PPV401 2.2 29.1 1.0
OD2 A:ASP192 2.2 21.1 1.0
O22 A:PPV401 2.3 34.3 1.0
P1 A:PPV401 3.1 31.1 1.0
CG A:ASP192 3.2 21.4 1.0
CG A:ASP190 3.2 25.7 1.0
O31 A:PPV401 3.3 35.3 1.0
MN A:MN403 3.3 26.3 1.0
P P:DC11 3.5 24.6 1.0
OD1 A:ASP192 3.5 21.6 1.0
P2 A:PPV401 3.5 38.2 1.0
OPP A:PPV401 3.7 34.8 1.0
OD2 A:ASP190 3.9 25.5 1.0
C5' P:DC11 4.1 21.3 1.0
O5' P:DC11 4.1 22.3 1.0
O32 A:PPV401 4.2 31.8 1.0
N A:ASP190 4.3 25.2 1.0
O A:ASP190 4.3 22.8 1.0
OP2 P:DC11 4.3 25.4 1.0
C A:ASP190 4.4 23.7 1.0
CB A:ASP190 4.4 23.9 1.0
O11 A:PPV401 4.5 31.0 1.0
O A:HOH501 4.5 16.5 1.0
O3' P:DC10 4.5 24.0 1.0
O P:HOH207 4.6 38.9 1.0
O A:HOH588 4.6 5.6 0.5
CB A:ASP192 4.6 22.0 1.0
CA A:ASP190 4.6 24.3 1.0
MN P:MN101 4.6 35.4 0.8
CA A:GLY179 4.7 26.0 1.0
O12 A:PPV401 4.8 36.4 1.0
OG A:SER180 4.8 31.8 1.0
N A:SER180 4.9 27.6 1.0
N A:ASP192 5.0 21.7 1.0
N A:MET191 5.0 24.2 1.0

Manganese binding site 2 out of 6 in 4rq2

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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 Dctp 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:26.3
occ:1.00
 OD1 A:ASP192 2.0 21.6 1.0
OD2 A:ASP190 2.0 25.5 1.0
OD2 A:ASP256 2.1 26.3 1.0
OP1 P:DC11 2.2 20.7 1.0
O A:HOH588 2.4 5.6 0.5
O3' P:DC10 2.6 24.0 1.0
CG A:ASP190 2.7 25.7 1.0
OD1 A:ASP190 2.8 26.2 1.0
P P:DC11 2.9 24.6 1.0
CG A:ASP192 3.0 21.4 1.0
CG A:ASP256 3.2 25.1 1.0
OD2 A:ASP192 3.3 21.1 1.0
MN A:MN402 3.3 23.6 1.0
CB A:ASP256 3.8 22.7 1.0
C3' P:DC10 3.9 22.0 1.0
OP2 P:DC11 3.9 25.4 1.0
CB A:ASP190 4.2 23.9 1.0
O5' P:DC11 4.2 22.3 1.0
OD1 A:ASP256 4.2 27.6 1.0
C4' P:DC10 4.3 22.6 1.0
CB A:ASP192 4.3 22.0 1.0
C5' P:DC11 4.4 21.3 1.0
C5' P:DC10 4.5 23.0 1.0
O P:HOH207 4.8 38.9 1.0
O A:MET191 4.8 23.1 1.0
O22 A:PPV401 4.9 34.3 1.0
CA A:ASP192 4.9 21.2 1.0
NH2 A:ARG254 4.9 26.0 1.0
N A:ASP256 4.9 22.7 1.0
C A:MET191 4.9 22.2 1.0
N A:ASP192 4.9 21.7 1.0
OP1 P:DC10 5.0 23.8 1.0
C2' P:DC10 5.0 21.1 1.0

Manganese binding site 3 out of 6 in 4rq2

Go back to Manganese Binding Sites List in 4rq2
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 Dctp 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:52.4
occ:1.00
 O A:HOH599 2.0 30.2 1.0
NE2 A:HIS337 2.3 34.7 1.0
NE2 A:HIS339 2.6 53.5 1.0
O A:HOH600 2.6 37.6 1.0
O A:HOH510 2.7 30.5 1.0
CD2 A:HIS337 3.2 35.4 1.0
CD2 A:HIS339 3.3 50.6 1.0
CE1 A:HIS337 3.4 34.7 1.0
CE1 A:HIS339 3.6 57.5 1.0
CG A:HIS337 4.4 32.9 1.0
ND1 A:HIS337 4.4 34.0 1.0
CG A:HIS339 4.4 50.7 1.0
ND1 A:HIS339 4.6 56.1 1.0
CG A:GLU9 4.8 53.7 1.0
CD A:GLU9 5.0 56.9 1.0

Manganese binding site 4 out of 6 in 4rq2

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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 Dctp 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:30.9
occ:1.00
 O A:LYS48 2.0 28.1 1.0
O A:HOH594 2.1 24.8 1.0
NE2 A:HIS336 2.3 31.5 1.0
NE2 A:HIS338 2.4 34.2 1.0
C A:LYS48 3.0 32.9 1.0
CE1 A:HIS336 3.2 33.9 1.0
CE1 A:HIS338 3.2 33.9 1.0
CD2 A:HIS336 3.4 31.4 1.0
CD2 A:HIS338 3.5 32.1 1.0
CA A:LYS48 3.5 32.9 1.0
CB A:LYS48 3.8 36.2 1.0
N A:TYR49 4.2 34.0 1.0
ND1 A:HIS336 4.4 34.2 1.0
ND1 A:HIS338 4.4 32.3 1.0
CG A:HIS336 4.5 33.7 1.0
CG A:HIS338 4.5 32.2 1.0
CG A:LYS48 4.6 39.3 1.0
C A:TYR49 4.7 36.1 1.0
CA A:TYR49 4.8 35.2 1.0
N A:PRO50 4.8 40.2 1.0
N A:LYS48 4.9 31.0 1.0

Manganese binding site 5 out of 6 in 4rq2

Go back to Manganese Binding Sites List in 4rq2
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 Dctp 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:48.7
occ:1.00
 O A:HOH511 2.3 25.4 1.0
NE2 A:HIS341 2.4 61.3 1.0
O A:HOH612 2.4 9.9 0.5
CE1 A:HIS341 2.9 59.8 1.0
CD2 A:HIS341 3.7 56.8 1.0
ND1 A:HIS341 4.2 59.2 1.0
CG A:HIS341 4.6 59.0 1.0

Manganese binding site 6 out of 6 in 4rq2

Go back to Manganese Binding Sites List in 4rq2
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 Dctp 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 Dctp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:35.4
occ:0.80
 O A:HOH590 1.9 42.1 1.0
O P:HOH208 2.2 39.9 1.0
OP2 P:DC11 2.2 25.4 1.0
O A:HOH589 2.2 24.1 1.0
O31 A:PPV401 2.2 35.3 1.0
O P:HOH207 2.3 38.9 1.0
P P:DC11 3.2 24.6 1.0
O5' P:DC11 3.7 22.3 1.0
P1 A:PPV401 3.7 31.1 1.0
OP1 P:DC11 3.7 20.7 1.0
O22 A:PPV401 3.9 34.3 1.0
O12 A:PPV401 4.1 36.4 1.0
OPP A:PPV401 4.1 34.8 1.0
P2 A:PPV401 4.3 38.2 1.0
O A:HOH591 4.5 26.4 1.0
O11 A:PPV401 4.5 31.0 1.0
O21 A:PPV401 4.6 29.1 1.0
MN A:MN402 4.6 23.6 1.0
O3' P:DC10 4.6 24.0 1.0
O A:HOH588 4.8 5.6 0.5
C5' P:DC11 4.9 21.3 1.0
C6 P:DC11 4.9 21.0 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 21:11:38 2024

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