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Sodium in PDB 6p1s: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp

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

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 Amp:
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 Amp, PDB code: 6p1s 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) 31.39 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.880, 68.838, 110.562, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.6

Other elements in 6p1s:

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

Manganese (Mn) 1 atom
Chlorine (Cl) 2 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 Amp (pdb code 6p1s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 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 Amp, PDB code: 6p1s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6p1s

Go back to Sodium Binding Sites List in 6p1s
Sodium binding site 1 out of 2 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:21.7
occ:1.00
OD1 A:ASP330 2.2 18.1 1.0
O2G A:ATP501 2.2 20.6 0.5
O2G A:ATP501 2.2 21.0 0.4
OD2 A:ASP332 2.2 18.6 1.0
O A:HOH735 2.3 22.8 1.0
O2B A:ATP501 2.5 30.7 0.4
O2B A:ATP501 2.5 30.8 0.5
OP1 P:A5 2.6 25.2 1.0
CG A:ASP330 3.3 20.6 1.0
CG A:ASP332 3.3 18.8 1.0
PG A:ATP501 3.4 24.6 0.5
PG A:ATP501 3.4 24.3 0.4
MN A:MN502 3.5 19.4 1.0
PB A:ATP501 3.5 32.1 0.4
O3B A:ATP501 3.6 27.4 0.4
O3B A:ATP501 3.6 27.1 0.5
PB A:ATP501 3.6 32.3 0.5
OD1 A:ASP332 3.7 18.2 1.0
OD2 A:ASP330 3.8 21.1 1.0
P P:A5 3.8 24.9 1.0
O A:HOH608 3.9 31.8 0.4
O5' P:A5 4.0 18.4 1.0
C5' P:A5 4.0 15.9 1.0
O A:ASP330 4.2 17.9 1.0
O3G A:ATP501 4.2 25.7 0.4
ND1 A:HIS329 4.2 24.1 0.6
O3G A:ATP501 4.2 25.7 0.5
O A:HOH615 4.2 17.4 1.0
N A:GLY320 4.3 15.3 1.0
CE1 A:HIS329 4.4 24.8 0.6
O A:HOH824 4.4 29.8 1.0
C A:ASP330 4.4 17.5 1.0
O1B A:ATP501 4.5 33.1 0.5
O1B A:ATP501 4.5 33.0 0.4
CA A:GLY319 4.6 14.8 1.0
CB A:ASP332 4.6 13.7 1.0
CB A:ASP330 4.6 17.4 1.0
O1G A:ATP501 4.6 21.2 0.5
O1G A:ATP501 4.6 21.7 0.4
OP2 P:A5 4.7 24.0 1.0
O3A A:ATP501 4.7 34.7 0.4
N A:ASP330 4.8 18.7 1.0
CA A:ASP330 4.8 18.0 1.0
O3A A:ATP501 4.9 34.8 0.5
O3' P:DA4 4.9 26.8 1.0
N A:ASP332 4.9 14.2 1.0
N A:VAL331 5.0 16.1 1.0
C A:GLY319 5.0 15.6 1.0

Sodium binding site 2 out of 2 in 6p1s

Go back to Sodium Binding Sites List in 6p1s
Sodium binding site 2 out of 2 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:23.3
occ:1.00
O A:ILE243 2.3 25.4 1.0
O A:VAL246 2.4 24.8 1.0
O A:THR241 2.4 24.3 1.0
O P:HOH111 2.4 28.4 1.0
O A:HOH817 2.4 31.6 1.0
OP1 P:DT3 2.6 24.7 1.0
C A:ILE243 3.4 24.5 1.0
C A:VAL246 3.4 24.8 1.0
C A:THR241 3.4 24.1 1.0
P P:DT3 3.7 23.4 1.0
N A:VAL246 3.7 22.7 1.0
OP2 P:DT3 3.9 21.2 1.0
N A:ILE243 4.0 25.9 1.0
CA A:VAL246 4.1 25.6 1.0
C A:GLN242 4.1 26.2 1.0
CA A:THR241 4.1 23.0 1.0
N A:PHE244 4.2 22.7 1.0
N A:GLY245 4.2 21.8 1.0
CA A:PHE244 4.2 23.8 1.0
CA A:ILE243 4.3 23.0 1.0
N A:GLN242 4.4 25.5 1.0
O A:HOH831 4.4 43.1 1.0
CB A:VAL246 4.4 24.3 1.0
N A:GLY247 4.5 24.4 1.0
O A:GLN242 4.5 27.9 1.0
CA A:GLN242 4.5 25.6 1.0
C A:PHE244 4.6 26.0 1.0
O3' P:DG2 4.6 22.8 1.0
O A:PHE240 4.7 23.8 1.0
CA A:GLY247 4.8 23.9 1.0
C A:GLY245 4.8 24.4 1.0
CB A:THR241 4.8 24.3 1.0
O5' P:DT3 4.9 21.9 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 12:39:55 2024

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