Atomistry » Magnesium » PDB 7r7j-7re3 » 7rbi
Atomistry »
  Magnesium »
    PDB 7r7j-7re3 »
      7rbi »

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

Go back to Magnesium Binding Sites List in 7rbi
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

Go back to Magnesium Binding Sites List in 7rbi
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

Go back to Magnesium Binding Sites List in 7rbi
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

Go back to Magnesium Binding Sites List in 7rbi
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

Go back to Magnesium Binding Sites List in 7rbi
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

Go back to Magnesium Binding Sites List in 7rbi
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

Go back to Magnesium Binding Sites List in 7rbi
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

Last articles

Cl in 3N8K
Cl in 3N9R
Cl in 3NB5
Cl in 3NA6
Cl in 3N9J
Cl in 3N9E
Cl in 3N9C
Cl in 3N9B
Cl in 3N8Y
Cl in 3N9A
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy