Atomistry » Sodium » PDB 5txq-5u4u » 5u2s
Atomistry »
  Sodium »
    PDB 5txq-5u4u »
      5u2s »

Sodium in PDB 5u2s: Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+.

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+.

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and CA2+., PDB code: 5u2s 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) 44.03 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.630, 79.450, 55.170, 90.00, 106.66, 90.00
R / Rfree (%) 23 / 28.4

Other elements in 5u2s:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+. also contains other interesting chemical elements:

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 (-)3TC-Tp and CA2+. (pdb code 5u2s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+., PDB code: 5u2s:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5u2s

Go back to Sodium Binding Sites List in 5u2s
Sodium binding site 1 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:38.8
occ:1.00
 O D:HOH102 2.2 19.4 1.0
O A:VAL65 2.4 22.2 1.0
O A:LYS60 2.4 35.1 1.0
OP1 D:DC3 2.7 27.9 1.0
O A:LEU62 2.9 28.3 1.0
C A:LYS60 3.5 34.5 1.0
C A:VAL65 3.6 22.8 1.0
OP2 D:DC3 3.6 23.9 1.0
P D:DC3 3.6 24.9 1.0
C A:LEU62 3.9 29.0 1.0
CG A:LYS60 4.2 33.9 1.0
N A:VAL65 4.3 24.5 1.0
CA A:LYS60 4.3 32.9 1.0
C A:LYS61 4.3 33.9 1.0
CA A:VAL65 4.4 22.7 1.0
CA A:PRO63 4.5 30.8 1.0
N A:LEU62 4.5 31.1 1.0
N A:LYS61 4.5 35.5 1.0
N A:GLY66 4.5 22.3 1.0
O A:LYS61 4.6 36.8 1.0
N A:GLY64 4.6 28.4 1.0
CA A:LYS61 4.6 34.6 1.0
O3' D:DT2 4.6 25.0 1.0
N A:PRO63 4.7 29.3 1.0
CA A:GLY66 4.7 23.2 1.0
CB A:VAL65 4.7 23.2 1.0
O5' D:DC3 4.8 25.5 1.0
CB A:LYS60 4.8 33.8 1.0
CA A:LEU62 4.9 29.9 1.0

Sodium binding site 2 out of 4 in 5u2s

Go back to Sodium Binding Sites List in 5u2s
Sodium binding site 2 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:16.5
occ:1.00
 O A:ILE106 2.3 16.6 1.0
O A:THR101 2.3 21.2 1.0
OXT A:ACT406 2.3 30.1 1.0
OP1 P:DG9 2.3 20.1 1.0
O P:HOH104 2.4 22.5 1.0
O A:VAL103 2.5 19.5 1.0
C A:ACT406 3.1 34.5 1.0
O A:ACT406 3.3 40.9 1.0
C A:THR101 3.3 20.9 1.0
C A:VAL103 3.3 19.6 1.0
C A:ILE106 3.3 15.7 1.0
P P:DG9 3.5 22.9 1.0
N A:ILE106 3.7 16.6 1.0
OP2 P:DG9 3.8 21.6 1.0
CA A:THR101 3.8 19.4 1.0
N A:SER104 3.9 18.3 1.0
CA A:SER104 3.9 16.7 1.0
CA A:ILE106 4.1 15.6 1.0
N A:GLY105 4.1 16.2 1.0
N A:VAL103 4.2 20.5 1.0
CB A:THR101 4.3 19.9 1.0
N A:GLY107 4.3 15.1 1.0
CA A:VAL103 4.3 21.5 1.0
C A:ARG102 4.4 21.1 1.0
N A:ARG102 4.4 20.9 1.0
C A:SER104 4.4 16.1 1.0
CH3 A:ACT406 4.4 33.7 1.0
CB A:ILE106 4.5 15.9 1.0
O3' P:DC8 4.5 20.9 1.0
CA A:GLY107 4.6 15.6 1.0
O5' P:DG9 4.6 24.6 1.0
C A:GLY105 4.6 16.5 1.0
CA A:ARG102 4.7 20.2 1.0
O A:ARG102 4.8 21.4 1.0
O A:LEU100 4.9 20.6 1.0
CA A:GLY105 5.0 16.6 1.0

Sodium binding site 3 out of 4 in 5u2s

Go back to Sodium Binding Sites List in 5u2s
Sodium binding site 3 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:48.4
occ:1.00
 O A:HOH568 2.2 25.8 1.0
OD1 A:ASN24 2.6 22.9 1.0
O A:HOH521 2.9 25.3 1.0
NZ A:LYS27 3.2 37.1 1.0
CG A:ASN24 3.3 24.2 1.0
ND2 A:ASN28 3.3 18.7 1.0
CE A:LYS27 3.3 34.5 1.0
CB A:ASN24 3.9 22.4 1.0
ND2 A:ASN24 4.1 26.8 1.0
CG A:ASN28 4.2 19.1 1.0
OD1 A:ASN28 4.2 21.4 1.0
CA A:ASN24 4.4 20.6 1.0
CD A:LYS27 4.9 29.4 1.0
OG1 A:THR101 5.0 19.0 1.0

Sodium binding site 4 out of 4 in 5u2s

Go back to Sodium Binding Sites List in 5u2s
Sodium binding site 4 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:37.6
occ:1.00
 O A:HOH507 2.6 42.6 1.0
O1A A:1RZ401 2.8 67.6 1.0
O3' P:DC10 2.8 51.9 1.0
O2A A:1RZ401 2.8 68.9 1.0
PA A:1RZ401 3.1 68.1 1.0
C4' P:DC10 3.3 40.4 1.0
O P:HOH101 3.3 41.7 1.0
C3' P:DC10 3.3 42.3 1.0
C2' P:DC10 3.4 42.6 1.0
O5' A:1RZ401 3.9 73.8 1.0
C1' P:DC10 4.1 42.1 1.0
O4' P:DC10 4.1 43.0 1.0
S3' A:1RZ401 4.1 82.9 1.0
C5' P:DC10 4.3 36.2 1.0
OD1 A:ASP192 4.4 35.0 1.0
CA A:CA402 4.6 64.0 1.0
O3A A:1RZ401 4.6 62.6 1.0
O5' P:DC10 4.7 30.3 1.0
C5' A:1RZ401 4.9 75.8 1.0
OD2 A:ASP190 4.9 29.6 1.0
CG A:ASP192 4.9 38.3 1.0
OD2 A:ASP192 5.0 45.6 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 Dec 15 11:40:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy