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Magnesium in PDB 7rbi: Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange

Enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange, PDB code: 7rbi was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.12 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.019, 79.297, 55.125, 90, 105.86, 90
R / Rfree (%) 18.6 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange (pdb code 7rbi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange, PDB code: 7rbi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7rbi

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Magnesium binding site 1 out of 7 in the Human Dna Polymerase Beta Crosslinked Complex, 20 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, 20 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:15.9
occ:1.00
 O2A P:DCP401 2.0 19.8 0.7
OD1 A:ASP190 2.1 27.4 1.0
O2G P:DCP401 2.2 24.5 0.7
OD2 A:ASP192 2.2 22.8 1.0
O A:HOH514 2.2 29.3 1.0
O2B P:DCP401 2.2 21.2 0.7
O32 A:PPV402 2.4 21.0 0.3
OP1 P:DC11 2.6 23.5 0.3
O11 A:PPV402 2.7 23.3 0.3
O12 A:PPV402 3.2 22.3 0.3
CG A:ASP192 3.2 21.1 1.0
PB P:DCP401 3.3 24.0 0.7
P2 A:PPV402 3.3 22.9 0.3
PG P:DCP401 3.3 26.2 0.7
PA P:DCP401 3.4 23.5 0.7
CG A:ASP190 3.4 27.4 1.0
O A:ASP190 3.5 26.4 1.0
O3A P:DCP401 3.5 23.4 0.7
OD1 A:ASP192 3.6 20.6 1.0
O3B P:DCP401 3.6 24.0 0.7
MG P:MG402 3.7 14.6 1.0
P P:DC11 3.8 24.1 0.3
O1G P:DCP401 3.9 24.8 0.7
P1 A:PPV402 3.9 25.2 0.3
C A:ASP190 4.0 24.9 1.0
OPP A:PPV402 4.0 23.1 0.3
N A:ASP190 4.1 24.4 1.0
O5' P:DC11 4.1 26.6 0.3
OD2 A:ASP190 4.1 32.5 1.0
C5' P:DCP401 4.2 19.3 0.7
O A:HOH577 4.2 25.0 1.0
O5' P:DCP401 4.3 18.8 0.7
CA A:ASP190 4.3 24.5 1.0
CB A:ASP190 4.4 23.3 1.0
O1A P:DCP401 4.5 20.4 0.7
OG A:SER180 4.5 27.1 1.0
OP2 P:DC11 4.5 23.7 0.3
CB A:ASP192 4.6 21.6 1.0
O3G P:DCP401 4.6 25.7 0.7
N A:SER180 4.6 26.4 1.0
CA A:GLY179 4.6 26.2 1.0
O22 A:PPV402 4.7 22.8 0.3
O1B P:DCP401 4.7 25.8 0.7
O P:HOH502 4.7 30.6 1.0
O31 A:PPV402 4.7 22.2 0.3
N A:MET191 4.8 24.1 1.0
N A:ASP192 4.8 21.7 1.0
C5' P:DC11 5.0 26.5 0.3

Magnesium binding site 2 out of 7 in 7rbi

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Magnesium binding site 2 out of 7 in the Human Dna Polymerase Beta Crosslinked Complex, 20 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, 20 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:16.3
occ:1.00
 O A:HOH607 2.0 33.3 1.0
O A:HOH505 2.3 41.7 1.0
O A:THR101 2.3 20.5 1.0
OP1 P:DG9 2.4 26.1 1.0
O P:HOH504 2.4 23.5 1.0
O A:ILE106 2.5 22.1 1.0
O A:VAL103 2.5 20.5 1.0
C A:THR101 3.4 22.8 1.0
P P:DG9 3.4 26.9 1.0
C A:VAL103 3.5 20.9 1.0
C A:ILE106 3.5 21.3 1.0
OP2 P:DG9 3.6 25.4 1.0
N A:ILE106 3.9 18.6 1.0
CA A:THR101 4.1 20.5 1.0
N A:SER104 4.1 20.4 1.0
N A:VAL103 4.1 21.4 1.0
CA A:SER104 4.1 19.9 1.0
N A:GLY105 4.1 17.6 1.0
C A:ARG102 4.2 22.6 1.0
CA A:ILE106 4.3 19.8 1.0
N A:ARG102 4.4 20.7 1.0
CA A:VAL103 4.5 21.5 1.0
N A:GLY107 4.5 18.2 1.0
O A:ARG102 4.5 24.8 1.0
C A:SER104 4.5 18.2 1.0
O3' P:DC8 4.5 27.4 1.0
O5' P:DG9 4.6 29.3 1.0
CA A:ARG102 4.6 24.9 1.0
CB A:THR101 4.7 21.2 1.0
CA A:GLY107 4.7 18.0 1.0
CB A:ILE106 4.8 19.3 1.0
C A:GLY105 4.8 19.1 1.0
O A:LEU100 4.9 20.5 1.0

Magnesium binding site 3 out of 7 in 7rbi

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Magnesium binding site 3 out of 7 in the Human Dna Polymerase Beta Crosslinked Complex, 20 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, 20 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:24.5
occ:1.00
 O A:HOH619 3.0 34.4 1.0
NH2 A:ARG299 3.2 39.6 1.0
OG1 A:THR297 3.3 35.2 1.0
ND2 A:ASN294 3.4 26.4 1.0
NE A:ARG299 3.5 38.6 1.0
CZ A:ARG299 3.8 42.9 1.0
CB A:TYR296 4.0 26.2 1.0
OD1 A:ASN294 4.0 25.5 1.0
CG2 A:THR297 4.0 27.5 1.0
CD2 A:TYR296 4.1 26.5 1.0
CG A:ASN294 4.1 24.3 1.0
O T:HOH113 4.2 43.8 1.0
CB A:THR297 4.3 29.3 1.0
CG A:TYR296 4.5 26.3 1.0
CD A:ARG299 4.7 36.6 1.0
N A:THR297 4.8 26.2 1.0
O A:HOH598 4.9 33.2 1.0

Magnesium binding site 4 out of 7 in 7rbi

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Magnesium binding site 4 out of 7 in the Human Dna Polymerase Beta Crosslinked Complex, 20 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, 20 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:35.1
occ:1.00
 O A:ASN28 2.7 27.4 1.0
O A:PRO108 2.7 23.2 1.0
NH2 A:ARG112 2.8 21.1 0.5
NE2 A:GLN31 3.0 19.2 0.5
NE A:ARG112 3.1 30.4 0.5
CZ A:ARG112 3.4 25.5 0.5
C A:PRO108 3.4 22.0 1.0
CB A:ARG112 3.5 20.2 0.5
OE1 A:GLN31 3.6 31.3 0.5
O A:VAL29 3.6 24.5 1.0
CB A:ARG112 3.6 25.1 0.5
CG2 A:ILE97 3.6 27.6 1.0
CG A:GLN31 3.7 28.7 0.5
CD A:GLN31 3.7 32.2 0.5
CA A:PRO108 3.7 21.9 1.0
CB A:PRO108 3.8 21.7 1.0
C A:ASN28 3.8 24.4 1.0
CG A:GLN31 3.8 21.0 0.5
CD A:GLN31 3.9 21.1 0.5
CA A:VAL29 4.1 24.3 1.0
C A:VAL29 4.2 25.4 1.0
CG A:ARG112 4.3 18.9 0.5
N A:ARG112 4.3 21.2 1.0
CD A:ARG112 4.3 28.4 0.5
N A:VAL29 4.4 22.6 1.0
CA A:ARG112 4.4 20.6 0.5
CA A:ARG112 4.4 22.6 0.5
N A:SER109 4.5 20.8 1.0
NE2 A:GLN31 4.6 35.3 0.5
CG A:ARG112 4.7 26.0 0.5
NH1 A:ARG112 4.7 26.4 0.5
CD A:ARG112 4.9 18.8 0.5
CD1 A:ILE97 4.9 32.6 1.0
CB A:ILE97 4.9 28.5 1.0
CA A:ASN28 5.0 23.1 1.0
CA A:SER109 5.0 22.5 1.0

Magnesium binding site 5 out of 7 in 7rbi

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Magnesium binding site 5 out of 7 in the Human Dna Polymerase Beta Crosslinked Complex, 20 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, 20 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:34.0
occ:1.00
 N A:HIS34 3.2 27.1 1.0
CA A:ALA32 3.3 25.9 1.0
C A:ALA32 3.4 27.8 1.0
CB A:ALA32 3.5 24.5 1.0
CB A:HIS34 3.5 28.8 1.0
N A:ILE33 3.7 25.2 1.0
N A:LYS35 3.7 24.9 1.0
CA A:HIS34 3.8 28.5 1.0
O A:ALA32 3.9 28.4 1.0
CD2 A:HIS34 4.1 28.1 1.0
CG A:HIS34 4.1 30.6 1.0
C A:HIS34 4.2 24.2 1.0
C A:ILE33 4.3 29.0 1.0
CG A:LYS35 4.4 26.4 1.0
O A:HOH524 4.5 32.8 1.0
CA A:ILE33 4.6 27.9 1.0
O6 D:DG1 4.7 29.2 1.0
N A:ALA32 4.8 27.3 1.0
CB A:LYS35 4.8 24.4 1.0
CA A:LYS35 4.9 23.3 1.0

Magnesium binding site 6 out of 7 in 7rbi

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Magnesium binding site 6 out of 7 in the Human Dna Polymerase Beta Crosslinked Complex, 20 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 6 of Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:34.5
occ:1.00
 O D:HOH203 2.2 35.6 1.0
O A:HOH507 2.3 43.0 1.0
O A:VAL65 2.5 32.6 1.0
O A:LYS60 2.6 33.5 1.0
O A:HOH626 2.6 48.6 1.0
O A:LEU62 2.7 30.6 1.0
OP1 D:DC3 2.7 38.5 1.0
P D:DC3 3.6 31.2 1.0
OP2 D:DC3 3.6 34.9 1.0
C A:LEU62 3.6 29.3 1.0
C A:VAL65 3.7 26.8 1.0
C A:LYS60 3.7 32.1 1.0
N A:VAL65 4.0 23.8 1.0
N A:GLY64 4.2 28.2 1.0
CA A:PRO63 4.2 32.2 1.0
N A:LEU62 4.2 29.9 1.0
C A:LYS61 4.3 37.8 1.0
N A:PRO63 4.3 30.0 1.0
CA A:VAL65 4.3 27.1 1.0
CA A:LYS60 4.5 32.7 1.0
N A:LYS61 4.6 32.4 1.0
O A:LYS61 4.6 39.5 1.0
O3' D:DT2 4.6 31.0 1.0
C A:PRO63 4.6 29.9 1.0
CA A:LEU62 4.6 30.6 1.0
CB A:VAL65 4.7 25.0 1.0
CA A:LYS61 4.7 36.4 1.0
N A:GLY66 4.7 26.8 1.0
CG A:LYS60 4.7 45.0 1.0
O5' D:DC3 4.8 32.4 1.0
CA A:GLY66 4.9 25.1 1.0
C A:GLY64 5.0 24.9 1.0

Magnesium binding site 7 out of 7 in 7rbi

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Magnesium binding site 7 out of 7 in the Human Dna Polymerase Beta Crosslinked Complex, 20 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 7 of Human Dna Polymerase Beta Crosslinked Complex, 20 S Ca to Mg Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg402

b:14.6
occ:1.00
 OP1 P:DC11 1.6 23.5 0.3
OD2 A:ASP256 2.1 19.6 1.0
OD2 A:ASP190 2.1 32.5 1.0
OD1 A:ASP192 2.2 20.6 1.0
O P:HOH502 2.3 30.6 1.0
O3' P:DC10 2.5 26.2 0.3
O3' P:DC10 2.5 27.1 0.7
P P:DC11 2.5 24.1 0.3
O2A P:DCP401 2.8 19.8 0.7
CG A:ASP190 2.8 27.4 1.0
OD1 A:ASP190 2.8 27.4 1.0
CG A:ASP192 3.2 21.1 1.0
CG A:ASP256 3.3 20.7 1.0
OP2 P:DC11 3.5 23.7 0.3
OD2 A:ASP192 3.5 22.8 1.0
MG A:MG403 3.7 15.9 1.0
PA P:DCP401 3.7 23.5 0.7
C3' P:DC10 3.7 24.8 0.3
O5' P:DC11 3.7 26.6 0.3
C3' P:DC10 3.7 22.9 0.7
CB A:ASP256 3.9 19.7 1.0
O5' P:DCP401 4.0 18.8 0.7
C5' P:DC10 4.1 24.9 0.3
C4' P:DC10 4.2 25.1 0.3
C5' P:DC10 4.2 22.0 0.7
C4' P:DC10 4.2 23.5 0.7
CB A:ASP190 4.2 23.3 1.0
C5' P:DCP401 4.3 19.3 0.7
OD1 A:ASP256 4.3 20.8 1.0
O1A P:DCP401 4.3 20.4 0.7
CB A:ASP192 4.5 21.6 1.0
O A:MET191 4.5 21.7 1.0
OP1 P:DC10 4.6 22.2 0.7
O5' P:DC10 4.7 24.7 0.3
OP1 P:DC10 4.8 24.4 0.3
O2G P:DCP401 4.8 24.5 0.7
NH2 A:ARG254 4.8 22.1 1.0
O5' P:DC10 4.9 23.1 0.7
C2' P:DC10 4.9 24.9 0.3
C A:MET191 4.9 23.3 1.0
C2' P:DC10 4.9 22.9 0.7
N A:ASP256 5.0 18.6 1.0
CA A:ASP192 5.0 20.3 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: Thu Oct 3 07:45:10 2024

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