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Sodium in PDB 5u2t: Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+., PDB code: 5u2t was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.78 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.615, 79.395, 54.795, 90.00, 107.60, 90.00
R / Rfree (%) 20 / 24.7

Other elements in 5u2t:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. (pdb code 5u2t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+., PDB code: 5u2t:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5u2t

Go back to Sodium Binding Sites List in 5u2t
Sodium binding site 1 out of 5 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.8
occ:1.00
 O A:THR101 2.3 23.4 1.0
OP1 P:DG9 2.3 25.4 1.0
O A:ILE106 2.3 24.8 1.0
O A:HOH641 2.4 29.0 1.0
O P:HOH209 2.4 27.3 1.0
O A:VAL103 2.5 24.6 1.0
C A:THR101 3.3 25.0 1.0
C A:ILE106 3.4 22.8 1.0
O A:HOH551 3.4 35.9 1.0
P P:DG9 3.4 25.6 1.0
C A:VAL103 3.5 27.7 1.0
OP2 P:DG9 3.7 27.6 1.0
N A:ILE106 3.8 22.1 1.0
CA A:THR101 3.9 24.2 1.0
N A:GLY105 4.0 24.6 1.0
CA A:SER104 4.1 25.5 1.0
CA A:ILE106 4.1 21.4 1.0
N A:SER104 4.1 25.7 1.0
N A:VAL103 4.2 25.4 1.0
N A:GLY107 4.3 22.3 1.0
CB A:THR101 4.3 25.4 1.0
C A:ARG102 4.3 27.4 1.0
N A:ARG102 4.4 26.8 1.0
C A:SER104 4.4 26.8 1.0
O3' P:DC8 4.4 24.7 1.0
CA A:VAL103 4.5 27.2 1.0
CA A:GLY107 4.5 20.6 1.0
CB A:ILE106 4.5 22.2 1.0
O5' P:DG9 4.6 26.3 1.0
C A:GLY105 4.6 23.0 1.0
CA A:ARG102 4.7 26.0 1.0
O A:ARG102 4.7 26.8 1.0
O P:HOH229 4.8 51.9 1.0
O A:HOH506 4.9 38.6 1.0
CA A:GLY105 4.9 23.8 1.0
O A:LEU100 4.9 26.0 1.0

Sodium binding site 2 out of 5 in 5u2t

Go back to Sodium Binding Sites List in 5u2t
Sodium binding site 2 out of 5 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:35.9
occ:1.00
 O A:SER30 2.3 26.7 1.0
O A:HOH591 2.4 41.6 1.0
O A:HOH656 2.6 42.6 1.0
C A:SER30 3.5 26.6 1.0
O A:HOH627 4.1 47.7 1.0
CA A:SER30 4.2 25.9 1.0
O A:GLN31 4.3 27.1 1.0
CB A:SER30 4.4 29.6 1.0
C A:GLN31 4.5 25.7 1.0
N A:GLN31 4.6 26.5 1.0
CB A:GLN31 4.7 28.0 1.0
CA A:GLN31 4.9 25.9 1.0

Sodium binding site 3 out of 5 in 5u2t

Go back to Sodium Binding Sites List in 5u2t
Sodium binding site 3 out of 5 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:41.4
occ:1.00
 O A:VAL65 2.3 37.3 1.0
O D:HOH109 2.3 39.0 1.0
O A:HOH642 2.3 46.7 1.0
O A:LYS60 2.4 38.7 1.0
O A:LEU62 2.5 33.5 1.0
OP1 D:DC3 2.8 37.1 1.0
C A:VAL65 3.4 36.2 1.0
C A:LYS60 3.5 38.3 1.0
C A:LEU62 3.5 34.5 1.0
P D:DC3 3.7 37.5 1.0
OP2 D:DC3 3.8 29.6 1.0
N A:VAL65 3.9 33.9 1.0
N A:LEU62 4.1 35.3 1.0
CA A:VAL65 4.1 32.6 1.0
C A:LYS61 4.2 37.4 1.0
N A:GLY64 4.2 33.4 1.0
CA A:PRO63 4.2 38.2 1.0
CA A:LYS60 4.3 37.3 1.0
N A:PRO63 4.3 37.0 1.0
CG A:LYS60 4.3 44.8 1.0
CB A:VAL65 4.4 32.5 1.0
O A:LYS61 4.5 39.7 1.0
N A:LYS61 4.5 38.5 1.0
CA A:LEU62 4.5 37.5 1.0
N A:GLY66 4.5 35.3 1.0
C A:PRO63 4.6 36.2 1.0
CA A:LYS61 4.6 36.7 1.0
O3' D:DT2 4.6 31.5 1.0
CA A:GLY66 4.8 36.3 1.0
C A:GLY64 4.9 33.9 1.0
O A:ALA59 4.9 34.6 1.0
CB A:LYS60 4.9 40.4 1.0

Sodium binding site 4 out of 5 in 5u2t

Go back to Sodium Binding Sites List in 5u2t
Sodium binding site 4 out of 5 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:46.6
occ:1.00
 O A:HOH508 2.2 44.1 1.0
O3' P:DC10 2.2 41.4 1.0
O A:HOH564 2.4 52.7 1.0
OAD A:1RY401 2.5 49.3 1.0
OD1 A:ASP192 2.5 42.5 1.0
O A:HOH654 2.5 51.0 1.0
C3' P:DC10 3.3 39.1 1.0
CG A:ASP192 3.5 41.0 1.0
PBA A:1RY401 3.5 46.8 1.0
CA A:CA402 3.5 40.4 1.0
OAH A:1RY401 3.7 48.1 1.0
C4' P:DC10 3.8 39.6 1.0
OD2 A:ASP192 3.8 41.9 1.0
OD2 A:ASP190 4.0 41.1 1.0
OAO A:1RY401 4.2 57.0 1.0
OD1 A:ASP190 4.4 34.0 1.0
C5' P:DC10 4.4 38.2 1.0
OD2 A:ASP256 4.5 43.0 1.0
C2' P:DC10 4.6 40.9 1.0
SAS A:1RY401 4.6 55.0 1.0
CG A:ASP190 4.7 36.7 1.0
CB A:ASP192 4.7 34.7 1.0
OAR A:1RY401 4.8 46.5 1.0

Sodium binding site 5 out of 5 in 5u2t

Go back to Sodium Binding Sites List in 5u2t
Sodium binding site 5 out of 5 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na102

b:48.1
occ:1.00
 O P:HOH226 2.2 43.4 1.0
O T:HOH123 2.3 41.5 1.0
O P:HOH230 2.4 44.5 0.5
O P:HOH219 2.6 22.6 0.5
O2 P:DT3 2.6 38.2 1.0
O4' P:DG4 3.1 40.0 1.0
C4' P:DG4 3.7 41.4 1.0
C2 P:DT3 3.8 38.0 1.0
C1' P:DG4 3.9 39.3 1.0
C2 T:DA14 4.2 37.0 1.0
N2 T:DG15 4.3 32.9 1.0
N9 P:DG4 4.4 36.5 1.0
O T:HOH111 4.4 47.9 1.0
C1' P:DT3 4.4 44.5 1.0
N3 P:DG4 4.4 35.8 1.0
C5' P:DG4 4.4 39.5 1.0
C4 P:DG4 4.6 34.6 1.0
N1 P:DT3 4.6 37.5 1.0
N3 T:DG15 4.7 36.0 1.0
N3 P:DT3 4.8 36.6 1.0
C2 T:DG15 4.8 31.9 1.0
N1 T:DA14 4.9 36.0 1.0
N3 T:DA14 5.0 37.3 1.0
C3' P:DG4 5.0 39.4 1.0

Reference:

R.Vyas, A.J.Reed, A.T.Raper, W.J.Zahurancik, P.C.Wallenmeyer, Z.Suo. Structural Basis For the D-Stereoselectivity of Human Dna Polymerase Beta. Nucleic Acids Res. V. 45 6228 2017.
ISSN: ESSN 1362-4962
PubMed: 28402499
DOI: 10.1093/NAR/GKX252
Page generated: Tue Oct 8 00:22:36 2024

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