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Magnesium in PDB 7rbk: Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange

Enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange, PDB code: 7rbk was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.18 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.558, 80.398, 55.419, 90, 107.64, 90
R / Rfree (%) 19.8 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange (pdb code 7rbk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange, PDB code: 7rbk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7rbk

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Magnesium binding site 1 out of 5 in the Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:41.9
occ:1.00
 O A:HOH566 1.9 39.3 1.0
O A:HOH515 2.2 28.8 1.0
O A:THR101 2.2 25.3 1.0
O A:HOH502 2.3 17.8 1.0
C A:THR101 3.4 25.3 1.0
O A:HOH525 4.0 26.8 1.0
CA A:ARG102 4.1 25.7 1.0
N A:ARG102 4.2 25.4 1.0
OP1 P:DG9 4.2 26.2 1.0
OP2 P:DG9 4.4 26.7 1.0
CA A:THR101 4.4 26.4 1.0
O A:ILE106 4.4 22.4 1.0
C A:ARG102 4.5 24.6 1.0
CB A:THR101 4.5 26.8 1.0
O A:VAL103 4.6 22.4 1.0
O A:ARG102 4.8 23.9 1.0
P P:DG9 4.8 25.6 1.0

Magnesium binding site 2 out of 5 in 7rbk

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Magnesium binding site 2 out of 5 in the Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:13.2
occ:1.00
 O2B P:DCP102 1.9 21.8 0.3
O2A P:DCP102 1.9 20.9 0.3
OD1 A:ASP190 2.1 26.7 1.0
O P:HOH202 2.1 18.7 1.0
O11 A:PPV407 2.2 22.3 0.7
O32 A:PPV407 2.3 22.8 0.7
OP1 P:DC11 2.3 19.3 0.7
OD2 A:ASP192 2.3 21.2 1.0
O12 A:PPV407 3.0 24.2 0.7
P2 A:PPV407 3.1 23.2 0.7
PB P:DCP102 3.1 21.9 0.3
PA P:DCP102 3.1 21.2 0.3
CG A:ASP190 3.2 25.2 1.0
CG A:ASP192 3.2 20.9 1.0
O3A P:DCP102 3.4 21.8 0.3
P1 A:PPV407 3.5 23.2 0.7
O2G P:DCP102 3.5 22.2 0.3
OD1 A:ASP192 3.5 21.5 1.0
OPP A:PPV407 3.5 23.2 0.7
MG A:MG405 3.6 15.2 1.0
P P:DC11 3.7 20.2 0.7
OD2 A:ASP190 3.8 27.1 1.0
O3B P:DCP102 3.8 22.1 0.3
O P:HOH208 3.9 41.9 1.0
O A:ASP190 4.0 24.7 1.0
O1A P:DCP102 4.1 21.4 0.3
O5' P:DC11 4.2 19.5 0.7
PG P:DCP102 4.2 22.2 0.3
N A:ASP190 4.2 22.9 1.0
O5' P:DCP102 4.2 21.2 0.3
O21 A:PPV407 4.2 22.6 0.7
C5' P:DCP102 4.3 20.8 0.3
C5' P:DC11 4.3 18.8 0.7
C A:ASP190 4.3 23.6 1.0
O A:HOH536 4.3 24.4 1.0
O1B P:DCP102 4.3 22.2 0.3
CB A:ASP190 4.4 24.5 1.0
O3G P:DCP102 4.4 22.4 0.3
O22 A:PPV407 4.5 23.1 0.7
OP2 P:DC11 4.5 19.7 0.7
O A:HOH509 4.5 23.5 1.0
CA A:ASP190 4.6 23.6 1.0
CA A:GLY179 4.6 23.2 1.0
MG P:MG101 4.6 49.9 0.7
O31 A:PPV407 4.6 23.4 0.7
CB A:ASP192 4.6 21.5 1.0
N A:SER180 4.7 22.9 1.0
O3' P:DC10 4.7 20.7 0.7
OG A:SER180 4.8 21.7 1.0

Magnesium binding site 3 out of 5 in 7rbk

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Magnesium binding site 3 out of 5 in the Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:15.2
occ:1.00
 OD2 A:ASP256 2.0 21.2 1.0
OD2 A:ASP190 2.0 27.1 1.0
O A:HOH509 2.1 23.5 1.0
OP1 P:DC11 2.1 19.3 0.7
OD1 A:ASP192 2.2 21.5 1.0
O3' P:DC10 2.5 20.7 0.7
O3' P:DC10 2.6 25.4 0.3
O2A P:DCP102 2.8 20.9 0.3
P P:DC11 2.8 20.2 0.7
CG A:ASP190 2.8 25.2 1.0
OD1 A:ASP190 3.1 26.7 1.0
CG A:ASP256 3.2 20.6 1.0
CG A:ASP192 3.3 20.9 1.0
MG A:MG404 3.6 13.2 1.0
C3' P:DC10 3.6 25.4 0.3
OD2 A:ASP192 3.7 21.2 1.0
C3' P:DC10 3.7 21.5 0.7
OP2 P:DC11 3.7 19.7 0.7
PA P:DCP102 3.8 21.2 0.3
CB A:ASP256 4.0 20.2 1.0
C4' P:DC10 4.0 21.9 0.7
C5' P:DC10 4.0 25.3 0.3
O5' P:DC11 4.1 19.5 0.7
C5' P:DC10 4.1 22.8 0.7
OD1 A:ASP256 4.1 20.3 1.0
C5' P:DCP102 4.1 20.8 0.3
C4' P:DC10 4.1 25.4 0.3
O5' P:DCP102 4.2 21.2 0.3
O1A P:DCP102 4.2 21.4 0.3
CB A:ASP190 4.2 24.5 1.0
O P:HOH208 4.3 41.9 1.0
C5' P:DC11 4.4 18.8 0.7
OP1 P:DC10 4.5 25.6 0.3
CB A:ASP192 4.5 21.5 1.0
OP1 P:DC10 4.7 25.9 0.7
O5' P:DC10 4.7 24.0 0.7
NH2 A:ARG254 4.8 22.0 1.0
O5' P:DC10 4.8 25.4 0.3
C2' P:DC10 4.8 21.4 0.7
O A:MET191 4.9 21.8 1.0
N A:ASP256 4.9 19.9 1.0
C2' P:DC10 5.0 25.3 0.3

Magnesium binding site 4 out of 5 in 7rbk

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Magnesium binding site 4 out of 5 in the Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:39.8
occ:1.00
 O A:LYS60 2.4 42.6 1.0
OP1 D:DC3 2.5 41.1 1.0
O A:LEU62 2.6 38.3 1.0
O A:VAL65 2.6 31.2 1.0
O D:HOH103 2.8 46.5 1.0
C A:LYS60 3.6 42.0 1.0
C A:LEU62 3.6 39.0 1.0
P D:DC3 3.6 40.2 1.0
C A:VAL65 3.7 31.8 1.0
OP2 D:DC3 3.9 39.8 1.0
C A:LYS61 4.1 42.6 1.0
N A:LEU62 4.1 41.0 1.0
N A:VAL65 4.2 32.6 1.0
CA A:PRO63 4.3 37.5 1.0
N A:PRO63 4.3 38.2 1.0
O A:LYS61 4.3 43.3 1.0
N A:LYS61 4.4 43.3 1.0
CA A:VAL65 4.5 32.0 1.0
CA A:LYS60 4.5 41.0 1.0
CA A:LYS61 4.5 44.3 1.0
N A:GLY64 4.5 35.0 1.0
CA A:LEU62 4.5 39.2 1.0
O5' D:DC3 4.6 42.0 1.0
N A:GLY66 4.7 32.1 1.0
C A:PRO63 4.8 36.4 1.0
CB A:VAL65 4.8 32.2 1.0
O3' D:DT2 4.8 37.8 1.0
CG A:LYS60 4.8 45.2 1.0
CA A:GLY66 4.9 32.7 1.0

Magnesium binding site 5 out of 5 in 7rbk

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Magnesium binding site 5 out of 5 in the Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Dna Polymerase Beta Crosslinked Complex, 40 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:49.9
occ:0.70
 O1A P:DCP102 1.3 21.4 0.3
O P:HOH203 2.0 56.1 1.0
O A:HOH512 2.0 62.3 1.0
O12 A:PPV407 2.4 24.2 0.7
OP2 P:DC11 2.4 19.7 0.7
PA P:DCP102 2.4 21.2 0.3
O P:HOH207 2.4 28.2 1.0
O P:HOH208 2.7 41.9 1.0
O3A P:DCP102 2.7 21.8 0.3
P P:DC11 3.4 20.2 0.7
O2A P:DCP102 3.5 20.9 0.3
O5' P:DCP102 3.6 21.2 0.3
O31 A:PPV407 3.6 23.4 0.7
O3B P:DCP102 3.7 22.1 0.3
O3G P:DCP102 3.7 22.4 0.3
OP1 P:DC11 3.7 19.3 0.7
P2 A:PPV407 3.8 23.2 0.7
O11 A:PPV407 3.8 22.3 0.7
PB P:DCP102 3.9 21.9 0.3
O5' P:DC11 3.9 19.5 0.7
P1 A:PPV407 4.1 23.2 0.7
OPP A:PPV407 4.1 23.2 0.7
O A:HOH501 4.3 22.3 1.0
PG P:DCP102 4.4 22.2 0.3
O A:HOH509 4.5 23.5 1.0
O22 A:PPV407 4.5 23.1 0.7
O P:HOH209 4.5 34.8 1.0
O2B P:DCP102 4.5 21.8 0.3
MG A:MG404 4.6 13.2 1.0
O3' P:DC10 4.8 20.7 0.7
O32 A:PPV407 4.8 22.8 0.7
C5' P:DCP102 4.9 20.8 0.3

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: Thu Apr 6 21:51:55 2023

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