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Sodium in PDB 3uxp: Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp

Enzymatic activity of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp

All present enzymatic activity of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp:
2.7.7.7;

Protein crystallography data

The structure of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp, PDB code: 3uxp was solved by C.L.Gridley, J.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.20 / 2.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.321, 56.607, 93.144, 90.00, 102.04, 90.00
R / Rfree (%) 21.8 / 29.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp (pdb code 3uxp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp, PDB code: 3uxp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3uxp

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Sodium binding site 1 out of 7 in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na337

b:81.1
occ:1.00
 OD1 A:ASP192 3.3 75.9 1.0
OD2 A:ASP190 3.3 86.9 1.0
O3' P:DG7 3.4 98.3 0.0
OD1 A:ASP190 3.4 69.5 1.0
O1A A:D3T336 3.5 48.4 1.0
CG A:ASP190 3.6 84.1 1.0
OD2 A:ASP192 3.6 83.8 1.0
C5' P:DG7 3.6 97.2 1.0
OD1 A:ASP256 3.7 87.1 1.0
CG A:ASP256 3.8 75.2 1.0
OD2 A:ASP256 3.8 68.7 1.0
CG A:ASP192 3.8 78.8 1.0
C3' P:DG7 3.9 96.3 1.0
O5' P:DG7 4.1 96.1 1.0
OP1 P:DG7 4.1 52.7 1.0
C4' P:DG7 4.1 99.8 1.0
C5' A:D3T336 4.2 70.2 1.0
NA A:NA338 4.3 80.0 1.0
PA A:D3T336 4.4 67.7 1.0
O2A A:D3T336 4.4 55.9 1.0
CB A:ASP256 4.6 66.0 1.0
O5' A:D3T336 4.7 85.4 1.0
P P:DG7 4.8 64.6 1.0
NH2 A:ARG254 4.9 53.9 1.0
CB A:ASP190 4.9 83.5 1.0

Sodium binding site 2 out of 7 in 3uxp

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Sodium binding site 2 out of 7 in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na338

b:80.0
occ:1.00
 O1B A:D3T336 2.0 68.4 1.0
OD2 A:ASP192 2.0 83.8 1.0
O1A A:D3T336 2.2 48.4 1.0
OD1 A:ASP190 2.3 69.5 1.0
O A:ASP190 2.6 97.3 1.0
O3G A:D3T336 3.2 91.2 1.0
CG A:ASP192 3.3 78.8 1.0
PB A:D3T336 3.4 70.2 1.0
PA A:D3T336 3.5 67.7 1.0
CG A:ASP190 3.5 84.1 1.0
C A:ASP190 3.7 93.9 1.0
N A:ASP190 3.9 73.3 1.0
O3A A:D3T336 4.0 44.7 1.0
PG A:D3T336 4.1 92.0 1.0
OD1 A:ASP192 4.2 75.9 1.0
CA A:ASP190 4.2 80.3 1.0
O3B A:D3T336 4.2 57.7 1.0
CB A:ASP192 4.2 67.9 1.0
NA A:NA337 4.3 81.1 1.0
OD2 A:ASP190 4.4 86.9 1.0
O5' A:D3T336 4.4 85.4 1.0
C5' A:D3T336 4.4 70.2 1.0
O1G A:D3T336 4.4 88.3 1.0
CB A:ASP190 4.5 83.5 1.0
O2B A:D3T336 4.5 57.9 1.0
O2A A:D3T336 4.6 55.9 1.0
N A:MET191 4.8 87.4 1.0
CA A:GLY179 4.8 74.4 1.0
N A:SER180 4.9 78.7 1.0
C A:MET191 4.9 75.8 1.0
N A:ASP192 4.9 74.6 1.0

Sodium binding site 3 out of 7 in 3uxp

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Sodium binding site 3 out of 7 in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na339

b:81.8
occ:1.00
 OP2 P:DA6 2.2 66.5 1.0
O A:VAL103 2.3 65.5 1.0
O A:THR101 2.3 44.4 1.0
O A:ILE106 2.4 52.1 1.0
C A:VAL103 3.1 68.8 1.0
C A:THR101 3.4 42.8 1.0
C A:ILE106 3.5 48.4 1.0
P P:DA6 3.6 58.3 1.0
CA A:THR104 3.6 53.6 1.0
N A:THR104 3.7 55.0 1.0
N A:VAL103 4.0 56.8 1.0
N A:ILE106 4.0 51.4 1.0
N A:GLY105 4.1 51.5 1.0
C A:ARG102 4.1 64.6 1.0
CA A:VAL103 4.2 68.4 1.0
C A:THR104 4.2 56.6 1.0
OP1 P:DA6 4.3 84.2 1.0
CA A:ILE106 4.3 46.0 1.0
N A:ARG102 4.3 44.5 1.0
CA A:THR101 4.3 48.1 1.0
CA A:ARG102 4.4 48.0 1.0
N A:GLY107 4.5 41.1 1.0
O3' P:DG5 4.6 56.5 1.0
O5' P:DA6 4.6 42.8 1.0
O A:ARG102 4.6 76.5 1.0
CB A:ILE106 4.7 48.7 1.0
CA A:GLY107 4.7 49.1 1.0
O A:LEU100 4.8 48.0 1.0
CB A:THR104 4.9 57.5 1.0
C A:GLY105 4.9 47.7 1.0

Sodium binding site 4 out of 7 in 3uxp

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Sodium binding site 4 out of 7 in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:86.8
occ:1.00
 O A:ARG283 3.2 96.5 1.0
O3' T:DA3 3.3 59.1 1.0
OP1 T:DC4 3.3 89.2 1.0
N A:ILE293 3.4 83.9 1.0
CA A:THR292 3.6 90.8 1.0
CB A:ARG283 3.7 78.6 1.0
O A:ILE293 3.7 94.4 1.0
C A:THR292 3.8 92.1 1.0
C A:ARG283 3.8 89.8 1.0
P T:DC4 3.8 76.9 1.0
O A:PHE291 3.8 0.2 1.0
CA A:ARG283 3.8 80.2 1.0
CG A:LEU287 3.8 79.1 1.0
CG A:ARG283 3.8 76.7 1.0
CD1 A:LEU287 3.9 74.3 1.0
CG2 A:THR292 4.1 69.5 1.0
C5' T:DC4 4.1 76.7 1.0
CA A:ILE293 4.2 86.7 1.0
O5' T:DC4 4.2 81.0 1.0
CB A:ILE293 4.3 73.3 1.0
C A:ILE293 4.4 90.7 1.0
CD2 A:LEU287 4.4 80.4 1.0
CB A:THR292 4.5 88.0 1.0
C3' T:DA3 4.5 75.9 1.0
N A:THR292 4.6 0.8 1.0
C A:PHE291 4.6 0.4 1.0
CD A:ARG283 4.6 60.9 1.0
C4' T:DA3 4.6 79.7 1.0
CB A:ALA286 4.7 79.6 1.0
O A:THR292 4.7 0.7 1.0
CG1 A:ILE293 4.8 87.5 1.0
N A:ALA284 4.9 90.9 1.0

Sodium binding site 5 out of 7 in 3uxp

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Sodium binding site 5 out of 7 in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na337

b:84.6
occ:1.00
 O1A B:D3T336 2.5 76.7 1.0
OD2 B:ASP192 2.7 98.2 1.0
O1B B:D3T336 3.0 82.4 1.0
O3B B:D3T336 3.1 71.3 1.0
CB B:ASP190 3.3 60.5 1.0
O3G B:D3T336 3.6 60.9 1.0
CG B:ASP192 3.6 97.5 1.0
PB B:D3T336 3.7 77.3 1.0
OD1 B:ASP190 3.7 81.7 1.0
CG B:ASP190 3.8 83.3 1.0
O B:ASP190 3.8 95.9 1.0
C B:ASP190 3.9 84.7 1.0
PA B:D3T336 4.0 62.0 1.0
PG B:D3T336 4.0 77.4 1.0
CA B:ASP190 4.1 63.4 1.0
OD1 B:ASP192 4.2 0.4 1.0
N B:ASP190 4.4 69.5 1.0
O3A B:D3T336 4.4 80.9 1.0
CA B:GLY179 4.4 67.1 1.0
N B:SER180 4.5 66.7 1.0
N B:MET191 4.5 78.3 1.0
CB B:ASP192 4.6 88.1 1.0
OG B:SER180 4.7 63.1 1.0
O2A B:D3T336 4.7 51.9 1.0
OD2 B:ASP190 4.8 97.0 1.0
C5' B:D3T336 4.8 62.7 1.0
OG B:SER188 4.8 75.3 1.0
CA B:MET191 4.8 65.9 1.0
O2G B:D3T336 4.8 74.4 1.0
N B:ASP192 4.9 56.6 1.0
C B:MET191 4.9 62.3 1.0
N B:GLY189 4.9 64.1 1.0
C B:GLY179 4.9 74.9 1.0
CB B:SER188 4.9 82.7 1.0
C B:GLY189 4.9 76.0 1.0
O2B B:D3T336 4.9 86.0 1.0

Sodium binding site 6 out of 7 in 3uxp

Go back to Sodium Binding Sites List in 3uxp
Sodium binding site 6 out of 7 in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na338

b:89.7
occ:1.00
 O B:THR101 2.1 62.5 1.0
OP2 D:DA6 2.4 56.1 1.0
O B:VAL103 2.6 60.9 1.0
O B:ILE106 2.9 58.1 1.0
C B:THR101 3.3 63.9 1.0
C B:VAL103 3.4 63.3 1.0
P D:DA6 3.8 76.9 1.0
N B:VAL103 3.9 80.5 1.0
N B:THR104 4.0 62.0 1.0
CA B:THR104 4.1 52.9 1.0
C B:ILE106 4.1 65.0 1.0
CA B:THR101 4.2 58.2 1.0
C B:ARG102 4.2 91.0 1.0
CA B:VAL103 4.3 61.6 1.0
N B:ARG102 4.3 71.3 1.0
CA B:ARG102 4.5 79.4 1.0
OP1 D:DA6 4.5 81.0 1.0
O3' D:DG5 4.7 78.3 1.0
CG2 B:THR101 4.7 65.4 1.0
N B:GLY105 4.7 59.0 1.0
C B:THR104 4.8 59.5 1.0
O5' D:DA6 4.8 57.1 1.0
O B:ARG102 4.8 0.5 1.0
O B:LEU100 4.9 58.9 1.0
N B:ILE106 4.9 61.3 1.0
CA B:ILE106 4.9 53.4 1.0
CB B:THR101 5.0 65.2 1.0

Sodium binding site 7 out of 7 in 3uxp

Go back to Sodium Binding Sites List in 3uxp
Sodium binding site 7 out of 7 in the Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Co-Crystal Structure of Rat Dna Polymerase Beta Mutator I260Q: Enzyme- Dna-Ddttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na339

b:80.7
occ:1.00
 O B:ARG283 3.3 0.8 1.0
OP1 E:DC4 3.3 0.3 1.0
N B:ILE293 3.3 0.6 1.0
O B:PHE291 3.5 0.7 1.0
CB B:ARG283 3.7 0.1 1.0
CA B:THR292 3.7 1.0 1.0
O3' E:DA3 3.7 93.3 1.0
CA B:ARG283 3.8 0.2 1.0
CB B:ALA286 3.8 96.9 1.0
CG B:ARG283 3.9 85.9 1.0
CD2 B:LEU287 3.9 0.1 1.0
C B:ARG283 4.0 0.7 1.0
CG B:LEU287 4.0 0.6 1.0
P E:DC4 4.0 0.2 1.0
C B:THR292 4.0 0.7 1.0
O B:ILE293 4.1 94.6 1.0
OG1 B:THR292 4.2 0.6 1.0
CA B:ILE293 4.2 0.1 1.0
CG1 B:ILE293 4.3 93.5 1.0
CB B:ILE293 4.3 93.9 1.0
O5' E:DC4 4.3 87.2 1.0
CB B:THR292 4.4 0.6 1.0
C B:PHE291 4.4 0.0 1.0
C B:ILE293 4.5 0.6 1.0
N B:THR292 4.6 0.1 1.0
CD B:ARG283 4.7 83.5 1.0
CD1 B:LEU287 4.7 0.1 1.0
C B:ALA286 4.8 0.5 1.0
N B:LEU287 4.8 0.5 1.0
CA B:ALA286 4.9 0.3 1.0
CD1 B:ILE293 5.0 83.9 1.0

Reference:

C.L.Gridley, S.Rangarajan, S.Firbank, S.Dalal, J.B.Sweasy, J.Jaeger. Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator Dna Polymerase Beta. Biochemistry V. 52 4422 2013.
ISSN: ISSN 0006-2960
PubMed: 23651085
DOI: 10.1021/BI301368F
Page generated: Mon Oct 7 13:36:03 2024

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