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Sodium in PDB 2isp: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate, PDB code: 2isp was solved by C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.Martinek, Y.Xiang, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.36 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 20.1 / 26.1

Other elements in 2isp:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate (pdb code 2isp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate, PDB code: 2isp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2isp

Go back to Sodium Binding Sites List in 2isp
Sodium binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:8.3
occ:1.00
OD2 A:ASP190 2.0 16.7 1.0
OD2 A:ASP256 2.0 22.3 1.0
OD1 A:ASP192 2.2 19.6 1.0
O1A A:GGH338 2.6 13.4 1.0
CG A:ASP190 3.0 17.0 1.0
CG A:ASP192 3.2 16.9 1.0
CG A:ASP256 3.3 22.4 1.0
OD1 A:ASP190 3.3 14.9 1.0
C3' P:DOC10 3.3 36.4 1.0
MG A:MG339 3.5 17.1 1.0
OD2 A:ASP192 3.5 19.8 1.0
P1 A:GGH338 3.5 17.4 1.0
O5' A:GGH338 3.6 14.9 1.0
O2A A:GGH338 4.0 15.4 1.0
CB A:ASP256 4.0 20.4 1.0
C5' A:GGH338 4.1 15.8 1.0
O A:HOH501 4.2 39.4 1.0
OD1 A:ASP256 4.2 20.7 1.0
C4' P:DOC10 4.3 34.1 1.0
CB A:ASP190 4.4 15.3 1.0
C2' P:DOC10 4.4 34.0 1.0
C5' P:DOC10 4.5 33.2 1.0
O A:MET191 4.5 13.1 1.0
CB A:ASP192 4.6 17.1 1.0
OP1 P:DOC10 4.6 27.2 1.0
NH2 A:ARG254 4.6 19.2 1.0
O5' P:DOC10 4.7 30.7 1.0
O1G A:GGH338 4.8 17.8 1.0
O3A A:GGH338 4.9 16.1 1.0
O2B A:GGH338 4.9 11.7 1.0

Sodium binding site 2 out of 3 in 2isp

Go back to Sodium Binding Sites List in 2isp
Sodium binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:23.5
occ:1.00
OP1 P:DG9 2.4 24.0 1.0
O A:THR101 2.5 23.5 1.0
O P:HOH188 2.5 29.3 1.0
O A:ILE106 2.6 15.1 1.0
O A:VAL103 2.6 20.9 1.0
O A:HOH562 2.9 43.4 1.0
C A:THR101 3.4 21.8 1.0
P P:DG9 3.4 23.1 1.0
C A:ILE106 3.5 17.5 1.0
OP2 P:DG9 3.6 25.9 1.0
C A:VAL103 3.6 19.0 1.0
N A:ILE106 3.8 20.7 1.0
N A:GLY105 4.0 19.4 1.0
CA A:SER104 4.1 18.2 1.0
CA A:THR101 4.1 22.8 1.0
O A:HOH496 4.1 32.2 1.0
CA A:ILE106 4.2 18.2 1.0
N A:VAL103 4.2 18.5 1.0
N A:SER104 4.2 18.8 1.0
O3' P:DC8 4.3 24.9 1.0
N A:ARG102 4.3 20.9 1.0
C A:ARG102 4.3 18.9 1.0
C A:SER104 4.4 19.2 1.0
N A:GLY107 4.4 16.2 1.0
CB A:ILE106 4.5 20.0 1.0
CA A:ARG102 4.6 20.4 1.0
CA A:VAL103 4.6 18.5 1.0
CA A:GLY107 4.7 17.7 1.0
O5' P:DG9 4.7 24.6 1.0
C A:GLY105 4.7 22.4 1.0
CB A:THR101 4.7 20.8 1.0
O A:ARG102 4.8 18.7 1.0
O A:LEU100 4.9 21.0 1.0
CA A:GLY105 4.9 22.0 1.0

Sodium binding site 3 out of 3 in 2isp

Go back to Sodium Binding Sites List in 2isp
Sodium binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:47.1
occ:1.00
O A:LYS60 2.1 34.2 1.0
O A:VAL65 2.2 30.4 1.0
O A:LEU62 2.6 32.8 1.0
OP1 D:DC3 2.8 35.7 1.0
C A:LYS60 3.2 33.7 1.0
C A:VAL65 3.3 28.6 1.0
C A:LEU62 3.6 32.4 1.0
CA A:LYS60 3.8 32.3 1.0
N A:VAL65 3.8 28.2 1.0
P D:DC3 3.9 35.1 1.0
CG A:LYS60 3.9 35.4 1.0
CA A:VAL65 4.0 28.1 1.0
OP2 D:DC3 4.0 37.0 1.0
N A:LEU62 4.2 33.7 1.0
CB A:VAL65 4.2 25.9 1.0
N A:LYS61 4.3 35.0 1.0
C A:LYS61 4.3 35.3 1.0
N A:GLY64 4.3 30.9 1.0
N A:GLY66 4.3 28.4 1.0
CA A:PRO63 4.3 32.4 1.0
N A:PRO63 4.4 32.9 1.0
CB A:LYS60 4.4 32.5 1.0
CA A:GLY66 4.6 29.1 1.0
CA A:LEU62 4.6 32.5 1.0
CA A:LYS61 4.6 36.0 1.0
O A:LYS61 4.6 36.7 1.0
O A:ALA59 4.7 25.2 1.0
O3' D:DT2 4.7 35.2 1.0
C A:PRO63 4.8 31.7 1.0
C A:GLY64 4.9 29.4 1.0
NZ A:LYS60 5.0 40.8 1.0

Reference:

C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.K.Batra, V.Martinek, Y.Xiang, W.A.Beard, L.C.Pedersen, S.H.Wilson, C.E.Mckenna, J.Florian, A.Warshel, M.F.Goodman. Modifying the Beta,Gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of Dna Polymerase Beta. Biochemistry V. 46 461 2007.
ISSN: ISSN 0006-2960
PubMed: 17209556
DOI: 10.1021/BI061517B
Page generated: Tue Dec 15 05:51:16 2020

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