Atomistry » Sodium » PDB 2htx-2isp » 2isp
Atomistry »
  Sodium »
    PDB 2htx-2isp »
      2isp »

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: Mon Oct 7 02:54:30 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy