Atomistry » Sodium » PDB 6fmq-6g3o » 6g2q
Atomistry »
  Sodium »
    PDB 6fmq-6g3o »
      6g2q »

Sodium in PDB 6g2q: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue, PDB code: 6g2q was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.63 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.397, 76.851, 54.544, 90.00, 103.81, 90.00
R / Rfree (%) 19.6 / 26

Other elements in 6g2q:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue (pdb code 6g2q). 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 Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue, PDB code: 6g2q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6g2q

Go back to Sodium Binding Sites List in 6g2q
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:36.7
occ:1.00
O A:THR101 2.5 29.6 1.0
OP1 P:DG9 2.5 27.6 1.0
O A:HOH593 2.6 42.6 1.0
O A:VAL103 2.6 25.3 1.0
O A:HOH604 3.2 34.3 1.0
C A:VAL103 3.4 28.1 1.0
O A:ILE106 3.4 25.1 1.0
P P:DG9 3.6 28.0 1.0
C A:THR101 3.6 26.6 1.0
CA A:SER104 3.7 26.9 1.0
OP2 P:DG9 3.7 25.2 1.0
N A:SER104 3.9 28.8 1.0
N A:GLY105 4.0 24.4 1.0
C A:ARG102 4.0 28.6 1.0
N A:VAL103 4.1 30.8 1.0
O A:ARG102 4.1 27.9 1.0
C A:SER104 4.3 26.3 1.0
N A:ILE106 4.3 21.0 1.0
CA A:VAL103 4.4 27.9 1.0
C A:ILE106 4.4 25.8 1.0
CA A:ARG102 4.4 29.3 1.0
CA A:THR101 4.5 27.3 1.0
N A:ARG102 4.5 27.7 1.0
O3' P:DC8 4.6 26.6 1.0
O5' P:DG9 4.8 27.3 1.0
CA A:ILE106 4.9 24.5 1.0
CB A:SER104 4.9 28.6 1.0

Sodium binding site 2 out of 3 in 6g2q

Go back to Sodium Binding Sites List in 6g2q
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:55.4
occ:1.00
O A:LYS60 2.6 40.3 1.0
O A:VAL65 2.8 44.4 1.0
O A:LEU62 3.6 45.8 1.0
OP2 D:DC3 3.6 43.4 1.0
OP1 D:DC3 3.7 51.5 1.0
C A:LYS60 3.8 44.5 1.0
C A:VAL65 4.0 41.8 1.0
P D:DC3 4.2 44.8 1.0
CG A:LYS60 4.2 42.4 1.0
CA A:LYS60 4.5 39.8 1.0
C A:LEU62 4.6 41.4 1.0
N A:VAL65 4.7 39.7 1.0
C A:LYS61 4.7 43.0 1.0
N A:LYS61 4.8 40.3 1.0
N A:GLY66 4.9 37.6 1.0
CA A:VAL65 4.9 38.6 1.0
CA A:LYS61 4.9 40.1 1.0
CA A:GLY66 4.9 36.6 1.0
N A:LEU62 4.9 43.4 1.0
CB A:LYS60 4.9 40.9 1.0

Sodium binding site 3 out of 3 in 6g2q

Go back to Sodium Binding Sites List in 6g2q
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:51.8
occ:1.00
OD2 A:ASP190 2.2 37.4 1.0
OD1 A:ASP192 2.4 32.0 1.0
C3' P:DOC10 2.7 34.9 1.0
O1A A:EJH401 2.8 33.3 1.0
C4' P:DOC10 3.2 34.6 1.0
C5' P:DOC10 3.2 35.2 1.0
CG A:ASP190 3.3 34.6 1.0
CG A:ASP192 3.5 36.5 1.0
PA A:EJH401 3.7 29.7 1.0
O5' A:EJH401 3.7 29.5 1.0
OD1 A:ASP190 3.7 32.8 1.0
OD2 A:ASP192 3.9 30.7 1.0
O5' P:DOC10 3.9 31.6 1.0
CB A:ASP256 4.0 31.6 1.0
MG A:MG402 4.0 35.7 1.0
C5' A:EJH401 4.1 30.4 1.0
O2A A:EJH401 4.1 34.1 1.0
C2' P:DOC10 4.1 31.2 1.0
OD2 A:ASP256 4.2 30.1 1.0
O A:HOH541 4.4 34.9 1.0
OP1 P:DOC10 4.4 39.2 1.0
CB A:ASP190 4.6 30.0 1.0
O4' P:DOC10 4.6 30.6 1.0
CG A:ASP256 4.6 32.8 1.0
NH1 A:ARG254 4.7 40.9 1.0
P P:DOC10 4.7 34.9 1.0
CB A:ASP192 4.8 29.1 1.0
CE1 A:PHE272 5.0 29.6 1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418
Page generated: Tue Oct 8 08:53:33 2024

Last articles

F in 5DU8
F in 5DUC
F in 5DXI
F in 5DY7
F in 5DWR
F in 5DX6
F in 5DUF
F in 5DWJ
F in 5DU6
F in 5DU4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy