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Sodium in PDB 6p1u: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp

Enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp, PDB code: 6p1u was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.98 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.864, 68.825, 110.594, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.3

Other elements in 6p1u:

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp (pdb code 6p1u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp, PDB code: 6p1u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6p1u

Go back to Sodium Binding Sites List in 6p1u
Sodium binding site 1 out of 3 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:16.8
occ:1.00
 O2A A:CTP509 1.9 9.5 0.2
O2B A:CTP509 2.1 20.2 0.2
OD2 A:ASP332 2.2 19.2 1.0
OD1 A:ASP330 2.2 19.1 1.0
O A:HOH730 2.3 20.4 1.0
O11 A:PPV508 2.3 20.0 0.8
O32 A:PPV508 2.3 17.2 0.3
O2G A:CTP509 2.3 18.3 0.2
OP1 P:C5 2.7 22.6 0.8
PB A:CTP509 3.0 18.7 0.2
PA A:CTP509 3.1 9.7 0.2
CG A:ASP332 3.2 18.2 1.0
CG A:ASP330 3.3 22.3 1.0
O3A A:CTP509 3.3 16.7 0.2
P2 A:PPV508 3.4 29.1 0.3
PG A:CTP509 3.4 23.4 0.2
MN A:MN501 3.5 22.0 1.0
O3B A:CTP509 3.5 21.8 0.2
P1 A:PPV508 3.6 22.1 0.8
OD1 A:ASP332 3.6 20.6 1.0
OPP A:PPV508 3.7 25.1 0.8
OD2 A:ASP330 3.7 22.0 1.0
O12 A:PPV508 3.7 26.6 0.3
P P:C5 3.9 24.0 0.8
O3G A:CTP509 4.0 21.9 0.2
O5' P:C5 4.0 22.8 0.8
C5' A:CTP509 4.0 6.7 0.2
C5' P:C5 4.0 21.8 0.8
O5' A:CTP509 4.1 7.4 0.2
O A:ASP330 4.2 18.9 1.0
O1A A:CTP509 4.2 10.8 0.2
O A:HOH614 4.2 19.0 1.0
N A:GLY320 4.3 16.0 1.0
O A:HOH740 4.3 29.4 1.0
O1B A:CTP509 4.4 19.2 0.2
O21 A:PPV508 4.4 24.3 0.8
C A:ASP330 4.4 18.6 1.0
CB A:ASP332 4.5 15.0 1.0
CA A:GLY319 4.5 17.1 1.0
CB A:ASP330 4.6 19.3 1.0
O P:HOH201 4.6 15.4 0.2
O22 A:PPV508 4.7 29.4 0.3
O1G A:CTP509 4.7 28.4 0.2
O31 A:PPV508 4.7 20.8 0.8
N A:ASP330 4.8 19.7 1.0
OP2 P:C5 4.8 24.4 0.8
CA A:ASP330 4.8 19.5 1.0
N A:ASP332 4.9 16.0 1.0
N A:VAL331 5.0 19.4 1.0

Sodium binding site 2 out of 3 in 6p1u

Go back to Sodium Binding Sites List in 6p1u
Sodium binding site 2 out of 3 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:24.7
occ:1.00
 O A:VAL246 2.3 25.4 1.0
O A:ILE243 2.3 27.7 1.0
O A:THR241 2.4 27.2 1.0
O P:HOH213 2.4 31.9 1.0
O A:HOH800 2.4 34.0 1.0
OP1 P:DT3 2.7 24.8 1.0
C A:VAL246 3.4 25.8 1.0
C A:ILE243 3.4 27.3 1.0
C A:THR241 3.4 25.6 1.0
P P:DT3 3.7 24.3 1.0
N A:VAL246 3.7 26.4 1.0
OP2 P:DT3 3.8 21.4 1.0
O A:HOH726 3.9 42.8 0.8
N A:ILE243 4.0 25.3 1.0
CA A:VAL246 4.0 25.8 1.0
CA A:THR241 4.1 25.1 1.0
N A:PHE244 4.2 24.3 1.0
C A:GLN242 4.2 27.0 1.0
N A:GLY245 4.2 24.9 1.0
CA A:PHE244 4.3 24.7 1.0
CA A:ILE243 4.3 24.1 1.0
CB A:VAL246 4.4 26.1 1.0
N A:GLY247 4.4 25.8 1.0
N A:GLN242 4.4 26.2 1.0
O A:HOH813 4.5 38.3 0.8
CA A:GLN242 4.6 29.1 1.0
O A:GLN242 4.6 30.0 1.0
O3' P:DG2 4.6 23.1 1.0
C A:PHE244 4.6 26.6 1.0
O A:PHE240 4.7 25.5 1.0
CA A:GLY247 4.7 25.3 1.0
C A:GLY245 4.8 24.6 1.0
CB A:THR241 4.9 26.8 1.0
O5' P:DT3 4.9 22.5 1.0

Sodium binding site 3 out of 3 in 6p1u

Go back to Sodium Binding Sites List in 6p1u
Sodium binding site 3 out of 3 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:26.5
occ:1.00
 O T:HOH227 2.2 45.5 0.9
OP1 T:8OG5 2.3 24.3 1.0
O8 T:8OG5 2.4 21.9 1.0
O T:HOH221 2.4 24.3 0.4
O T:HOH226 2.5 52.9 1.0
C8 T:8OG5 3.5 23.1 1.0
P T:8OG5 3.6 23.4 1.0
O5' T:8OG5 3.7 24.3 1.0
NH2 A:ARG442 3.9 28.2 1.0
N7 T:8OG5 4.1 25.1 1.0
C2' T:DC4 4.2 23.0 1.0
O T:HOH221 4.2 20.7 0.6
C3' T:DC4 4.3 22.8 1.0
C7 T:DT6 4.4 28.4 1.0
O3' T:DC4 4.5 24.0 1.0
C2' T:8OG5 4.6 24.6 1.0
N9 T:8OG5 4.6 21.3 1.0
OP2 T:8OG5 4.7 22.4 1.0
O T:HOH222 4.7 39.1 1.0
CZ A:ARG442 4.9 28.6 1.0

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Unexpected Behavior of Dna Polymerase Mu Opposite Template 8-Oxo-7,8-Dihydro-2'-Guanosine. Nucleic Acids Res. V. 47 9410 2019.
ISSN: ESSN 1362-4962
PubMed: 31435651
DOI: 10.1093/NAR/GKZ680
Page generated: Tue Oct 8 12:40:04 2024

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