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Magnesium in PDB 4tqr: Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp

Enzymatic activity of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp

All present enzymatic activity of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp, PDB code: 4tqr was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.32 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.537, 89.406, 112.390, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.2

Other elements in 4tqr:

The structure of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp (pdb code 4tqr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp, PDB code: 4tqr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4tqr

Go back to Magnesium Binding Sites List in 4tqr
Magnesium binding site 1 out of 3 in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:8.7
occ:1.00
 OD2 A:ASP105 2.3 15.7 1.0
OD1 A:ASP7 2.3 18.7 1.0
O A:PHE8 2.3 15.7 1.0
O A:HOH706 2.4 22.3 1.0
O1G T:TTP101 2.4 18.0 1.0
O2B T:TTP101 2.4 17.3 1.0
CG A:ASP7 3.4 17.4 1.0
CG A:ASP105 3.5 16.1 1.0
PG T:TTP101 3.5 16.4 1.0
PB T:TTP101 3.5 16.7 1.0
C A:PHE8 3.5 15.6 1.0
O3B T:TTP101 3.7 15.2 1.0
O2G T:TTP101 3.9 15.9 1.0
OD2 A:ASP7 3.9 20.2 1.0
O1B T:TTP101 4.0 16.7 1.0
NZ A:LYS159 4.0 18.3 1.0
N A:PHE8 4.1 14.2 1.0
O A:HOH703 4.2 18.1 1.0
N A:TYR10 4.2 14.1 1.0
CB A:ASP105 4.3 13.9 1.0
O A:HOH704 4.3 23.6 1.0
OD1 A:ASP105 4.3 16.8 1.0
CA A:PHE8 4.4 15.2 1.0
C A:ASP7 4.4 16.2 1.0
N A:ASP9 4.4 14.9 1.0
O T:HOH265 4.4 23.1 1.0
CA A:ASP9 4.4 15.6 1.0
N4 T:DC2 4.5 15.7 1.0
C A:ASP9 4.6 15.0 1.0
N A:PHE11 4.6 13.6 1.0
CB A:ASP7 4.7 15.6 1.0
O3G T:TTP101 4.7 16.0 1.0
MG A:MG403 4.7 10.1 1.0
O3A T:TTP101 4.8 19.5 1.0
O A:ASP7 4.8 15.8 1.0
CB A:PHE11 4.8 14.3 1.0
O A:ASP105 4.9 16.6 1.0
CA A:ASP7 4.9 14.6 1.0
CE A:LYS159 5.0 20.6 1.0
CA A:TYR10 5.0 14.4 1.0

Magnesium binding site 2 out of 3 in 4tqr

Go back to Magnesium Binding Sites List in 4tqr
Magnesium binding site 2 out of 3 in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:36.9
occ:1.00
 O A:HOH795 2.1 49.4 1.0
O A:HOH817 2.2 45.3 1.0
O A:ILE186 2.3 35.6 1.0
O A:HOH816 2.3 44.6 1.0
O A:ALA181 2.4 39.5 1.0
O P:HOH257 2.6 67.2 1.0
C A:ILE186 3.5 39.4 1.0
C A:ALA181 3.6 41.5 1.0
CA A:GLY187 4.1 35.6 1.0
N A:GLY187 4.3 34.8 1.0
CA A:ALA181 4.3 43.0 1.0
C A:GLY187 4.4 41.0 1.0
O A:VAL183 4.4 33.9 1.0
O A:GLY187 4.5 42.7 1.0
CA A:ILE186 4.6 34.7 1.0
N A:ASP182 4.6 40.6 1.0
CB A:ALA181 4.7 50.1 1.0
CB A:ILE186 4.7 38.4 1.0
CA A:ASP182 4.7 41.6 1.0
N A:ILE186 4.9 28.2 1.0
OP1 P:DOC101 4.9 39.4 1.0

Magnesium binding site 3 out of 3 in 4tqr

Go back to Magnesium Binding Sites List in 4tqr
Magnesium binding site 3 out of 3 in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:10.1
occ:1.00
 O1B T:TTP101 2.3 16.7 1.0
O T:HOH248 2.3 20.1 1.0
OD1 A:ASP105 2.4 16.8 1.0
O A:HOH703 2.4 18.1 1.0
OE2 A:GLU106 2.5 17.7 1.0
N3 T:DC2 2.5 14.6 1.0
O2 T:DC2 2.6 15.4 1.0
C2 T:DC2 2.9 14.4 1.0
CG A:ASP105 3.2 16.1 1.0
OD2 A:ASP105 3.3 15.7 1.0
CD A:GLU106 3.3 21.0 1.0
PB T:TTP101 3.6 16.7 1.0
C4 T:DC2 3.7 15.1 1.0
CG A:GLU106 3.8 17.6 1.0
OG A:SER103 3.8 18.3 1.0
O2B T:TTP101 3.9 17.3 1.0
N4 T:DC2 4.1 15.7 1.0
O1A T:TTP101 4.1 24.6 0.7
OE1 A:GLU106 4.2 23.8 1.0
O T:HOH267 4.3 44.2 1.0
N1 T:DC2 4.3 15.8 1.0
C5M T:TTP101 4.3 18.4 1.0
O3A T:TTP101 4.5 19.5 1.0
O A:HOH840 4.6 39.8 1.0
CB A:ASP105 4.6 13.9 1.0
O3B T:TTP101 4.6 15.2 1.0
CB A:SER103 4.7 18.2 1.0
MG A:MG401 4.7 8.7 1.0
N1 T:DA3 4.8 20.3 1.0
C5 T:DC2 4.9 15.7 1.0
PA T:TTP101 5.0 31.3 1.0

Reference:

W.Xu, A.M.Ouellette, Z.Wawrzak, S.J.Shriver, S.M.Anderson, L.Zhao. Kinetic and Structural Mechanisms of (5'S)-8,5'-Cyclo-2'-Deoxyguanosine-Induced Dna Replication Stalling. Biochemistry V. 54 639 2015.
ISSN: ISSN 0006-2960
PubMed: 25569151
DOI: 10.1021/BI5014936
Page generated: Tue Aug 20 04:13:33 2024

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