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Manganese in PDB 7rbm: Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange

Enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange, PDB code: 7rbm was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.97 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.726, 82.115, 54.203, 90, 110.18, 90
R / Rfree (%) 20.5 / 24.7

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Manganese atom in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange (pdb code 7rbm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange, PDB code: 7rbm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in 7rbm

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Manganese binding site 1 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


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 Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:33.7
occ:1.00
 OD2 A:ASP190 1.9 38.3 1.0
OD2 A:ASP256 2.0 32.2 1.0
OD1 A:ASP192 2.0 30.4 1.0
OP1 P:DC11 2.2 30.2 1.0
O3' P:DC10 2.6 31.4 1.0
O P:HOH202 2.6 35.1 1.0
CG A:ASP190 2.9 39.8 1.0
P P:DC11 2.9 31.3 1.0
CG A:ASP192 3.1 32.7 1.0
CG A:ASP256 3.1 32.6 1.0
OD1 A:ASP190 3.1 41.4 1.0
OD2 A:ASP192 3.5 32.2 1.0
MN A:MN404 3.5 35.4 1.0
CB A:ASP256 3.7 32.2 1.0
OP2 P:DC11 3.9 32.6 1.0
C3' P:DC10 3.9 32.2 1.0
OD1 A:ASP256 4.1 31.8 1.0
O5' P:DC11 4.2 30.9 1.0
C4' P:DC10 4.2 32.6 1.0
CB A:ASP190 4.2 39.4 1.0
C5' P:DC10 4.3 33.7 1.0
CB A:ASP192 4.4 33.9 1.0
C5' P:DC11 4.4 30.9 1.0
O A:HOH508 4.4 48.1 1.0
O A:MET191 4.7 37.9 1.0
N A:ASP256 4.8 34.1 1.0
NH2 A:ARG254 4.9 32.1 1.0
CA A:ASP256 4.9 33.3 1.0
OP1 P:DC10 4.9 35.4 1.0
CA A:ASP192 4.9 35.0 1.0
C2' P:DC10 5.0 32.0 1.0

Manganese binding site 2 out of 11 in 7rbm

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Manganese binding site 2 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


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 Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:35.4
occ:1.00
 OD2 A:ASP192 2.1 32.2 1.0
OD1 A:ASP190 2.1 41.4 1.0
O21 A:PPV402 2.1 41.6 1.0
OP1 P:DC11 2.2 30.2 1.0
O A:HOH535 2.2 35.5 1.0
O12 A:PPV402 2.5 44.5 1.0
CG A:ASP192 3.1 32.7 1.0
P1 A:PPV402 3.1 41.9 1.0
CG A:ASP190 3.2 39.8 1.0
O11 A:PPV402 3.3 44.4 1.0
OD1 A:ASP192 3.5 30.4 1.0
MN A:MN403 3.5 33.7 1.0
P P:DC11 3.5 31.3 1.0
OPP A:PPV402 3.6 45.6 1.0
P2 A:PPV402 3.6 46.9 1.0
O A:HOH508 3.7 48.1 1.0
OD2 A:ASP190 3.7 38.3 1.0
O5' P:DC11 4.0 30.9 1.0
C5' P:DC11 4.1 30.9 1.0
O A:ASP190 4.2 36.6 1.0
O32 A:PPV402 4.3 45.2 1.0
OP2 P:DC11 4.4 32.6 1.0
CB A:ASP192 4.5 33.9 1.0
N A:ASP190 4.5 39.3 1.0
O A:HOH510 4.5 32.8 1.0
CB A:ASP190 4.5 39.4 1.0
O31 A:PPV402 4.5 42.4 1.0
CA A:GLY179 4.5 36.4 1.0
C A:ASP190 4.5 38.1 1.0
O P:HOH202 4.6 35.1 1.0
O3' P:DC10 4.6 31.4 1.0
MN P:MN101 4.7 55.2 1.0
CA A:ASP190 4.7 38.9 1.0
N A:SER180 4.8 37.0 1.0
O22 A:PPV402 4.8 44.4 1.0

Manganese binding site 3 out of 11 in 7rbm

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Manganese binding site 3 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


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 Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:84.3
occ:1.00
 O A:HOH538 2.1 64.2 1.0
O A:HOH512 2.1 57.5 1.0
O A:HOH571 2.7 50.5 1.0
O A:LYS60 2.7 64.5 1.0
C A:LYS60 3.9 65.0 1.0
OP2 D:DC3 4.0 52.6 1.0
O A:VAL65 4.1 55.2 1.0
OP1 D:DC3 4.2 54.1 1.0
CG A:LYS60 4.3 70.7 1.0
O A:LEU62 4.4 57.6 1.0
P D:DC3 4.6 54.8 1.0
N A:LYS61 4.7 65.0 1.0
CA A:LYS61 4.8 65.0 1.0
C A:LYS61 4.8 64.4 1.0
CA A:LYS60 4.8 65.8 1.0
O A:LYS61 4.8 64.7 1.0

Manganese binding site 4 out of 11 in 7rbm

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Manganese binding site 4 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


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 Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:80.8
occ:1.00
 ND1 A:HIS285 2.3 54.2 1.0
OE1 A:GLU288 2.3 64.6 1.0
CE1 A:HIS285 3.1 56.5 1.0
CD A:GLU288 3.4 63.0 1.0
CG A:HIS285 3.4 52.6 1.0
OE2 A:GLU288 3.7 64.0 1.0
CB A:HIS285 3.9 49.5 1.0
CA A:HIS285 4.2 47.6 1.0
NE2 A:HIS285 4.3 55.8 1.0
CD2 A:HIS285 4.5 54.7 1.0
CG A:GLU288 4.7 60.4 1.0
NE1 A:TRP325 5.0 51.7 1.0

Manganese binding site 5 out of 11 in 7rbm

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Manganese binding site 5 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


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 Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:42.9
occ:1.00
 O A:THR101 2.1 38.0 1.0
OP1 P:DG9 2.3 42.5 1.0
O A:ILE106 2.3 34.6 1.0
O A:VAL103 2.3 34.2 1.0
O A:HOH555 2.3 43.7 1.0
O P:HOH201 2.3 35.0 1.0
C A:THR101 3.2 35.0 1.0
C A:VAL103 3.3 35.4 1.0
P P:DG9 3.4 39.3 1.0
C A:ILE106 3.4 33.1 1.0
OP2 P:DG9 3.6 41.6 1.0
CA A:THR101 3.9 34.9 1.0
N A:ILE106 3.9 33.4 1.0
N A:SER104 4.0 34.3 1.0
CA A:SER104 4.0 34.5 1.0
N A:VAL103 4.0 35.9 1.0
N A:GLY105 4.1 33.6 1.0
N A:ARG102 4.2 35.2 1.0
CA A:ILE106 4.2 33.4 1.0
C A:ARG102 4.2 35.5 1.0
N A:GLY107 4.3 33.8 1.0
CA A:VAL103 4.3 35.9 1.0
O3' P:DC8 4.3 40.0 1.0
C A:SER104 4.4 34.2 1.0
CA A:ARG102 4.5 36.2 1.0
CB A:THR101 4.5 34.7 1.0
CA A:GLY107 4.5 33.9 1.0
O5' P:DG9 4.6 40.1 1.0
CB A:ILE106 4.6 33.4 1.0
O A:ARG102 4.7 35.7 1.0
C A:GLY105 4.8 33.9 1.0
O A:LEU100 4.8 33.7 1.0

Manganese binding site 6 out of 11 in 7rbm

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Manganese binding site 6 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


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 Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn408

b:57.8
occ:1.00
 O A:GLU117 2.6 46.3 1.0
C A:GLU117 3.3 45.9 1.0
CA A:GLU117 3.9 46.2 1.0
N A:GLY118 4.3 46.1 1.0
CB A:GLU117 4.3 47.9 1.0
CA A:GLY118 4.6 45.3 1.0

Manganese binding site 7 out of 11 in 7rbm

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Manganese binding site 7 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:50.4
occ:1.00
 O A:LYS48 2.1 41.5 1.0
NE2 A:HIS338 2.1 54.0 1.0
NE2 A:HIS336 2.3 44.8 1.0
CE1 A:HIS338 3.1 53.5 1.0
CD2 A:HIS338 3.1 53.2 1.0
C A:LYS48 3.2 43.5 1.0
CE1 A:HIS336 3.2 45.0 1.0
CD2 A:HIS336 3.3 44.8 1.0
CA A:LYS48 3.6 44.2 1.0
CB A:LYS48 3.8 45.1 1.0
ND1 A:HIS338 4.2 52.1 1.0
CG A:HIS338 4.2 51.9 1.0
ND1 A:HIS336 4.3 46.2 1.0
N A:TYR49 4.4 45.8 1.0
CG A:HIS336 4.4 46.5 1.0
CG A:LYS48 4.6 46.5 1.0
N A:PRO50 4.8 48.2 1.0
C A:TYR49 4.9 46.8 1.0
CD A:PRO50 4.9 48.5 1.0
CA A:TYR49 4.9 46.8 1.0
CB A:PRO50 5.0 49.2 1.0
N A:LYS48 5.0 42.4 1.0

Manganese binding site 8 out of 11 in 7rbm

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Manganese binding site 8 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn410

b:68.8
occ:1.00
 O A:HOH553 2.1 43.8 1.0
NE2 A:HIS337 2.4 52.5 1.0
O A:HOH569 2.8 45.8 1.0
CD2 A:HIS337 3.0 51.8 1.0
CE1 A:HIS337 3.5 52.0 1.0
CG A:HIS337 4.3 50.4 1.0
ND1 A:HIS337 4.5 51.7 1.0
CG2 A:THR10 4.6 51.8 1.0

Manganese binding site 9 out of 11 in 7rbm

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Manganese binding site 9 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn411

b:68.7
occ:1.00
 OD1 A:ASP130 2.5 64.6 1.0
OD2 A:ASP130 2.6 63.6 1.0
CG A:ASP130 2.9 64.0 1.0
OD1 A:ASN128 4.3 52.9 1.0
CB A:ASP130 4.4 62.2 1.0
CA A:ASN128 4.7 55.0 1.0
O A:LYS127 4.8 50.8 1.0
CG A:ASN128 4.9 52.4 1.0
NZ A:LYS131 5.0 69.3 1.0

Manganese binding site 10 out of 11 in 7rbm

Go back to Manganese Binding Sites List in 7rbm
Manganese binding site 10 out of 11 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mn Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:55.2
occ:1.00
 O A:HOH539 2.1 30.0 1.0
O11 A:PPV402 2.4 44.4 1.0
OP2 P:DC11 2.4 32.6 1.0
O A:HOH507 2.5 40.7 1.0
O A:HOH508 2.5 48.1 1.0
P P:DC11 3.4 31.3 1.0
O5' P:DC11 3.8 30.9 1.0
P1 A:PPV402 3.8 41.9 1.0
O12 A:PPV402 3.8 44.5 1.0
O22 A:PPV402 3.8 44.4 1.0
OP1 P:DC11 3.8 30.2 1.0
O A:HOH514 4.2 31.1 1.0
P2 A:PPV402 4.2 46.9 1.0
OPP A:PPV402 4.2 45.6 1.0
O P:HOH202 4.5 35.1 1.0
MN A:MN404 4.7 35.4 1.0
O21 A:PPV402 4.7 41.6 1.0
O31 A:PPV402 4.7 42.4 1.0
O3' P:DC10 4.8 31.4 1.0

Reference:

A.Kumar, A.J.Reed, W.J.Zahurancik, S.M.Daskalova, S.M.Hecht, Z.Suo. Interlocking Activities of Dna Polymerase Beta in the Base Excision Repair Pathway. Proc.Natl.Acad.Sci.Usa V. 119 40119 2022.
ISSN: ESSN 1091-6490
PubMed: 35238634
DOI: 10.1073/PNAS.2118940119
Page generated: Sun Oct 6 10:27:41 2024

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