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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 Oct 8 00:22:04 2024

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