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

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

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

Resolution Low / High (Å) 28.41 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.120, 184.242, 52.124, 90.00, 110.09, 90.00
R / Rfree (%) 22.8 / 29

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 Dctp (pdb code 4tqs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 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 Dctp, PDB code: 4tqs:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4tqs

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


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:0.6
occ:1.00
 O3G A:DCP401 2.2 20.4 1.0
O A:PHE8 2.3 9.8 1.0
OD2 A:ASP105 2.4 10.6 1.0
O2B A:DCP401 2.5 12.1 1.0
OD2 A:ASP7 2.5 11.4 1.0
OD1 A:ASP7 2.7 13.9 1.0
CG A:ASP7 2.9 9.9 1.0
O2A A:DCP401 3.0 32.6 1.0
PG A:DCP401 3.3 19.3 1.0
C A:PHE8 3.4 10.0 1.0
PB A:DCP401 3.6 31.0 1.0
MG A:MG403 3.6 1.8 1.0
O2G A:DCP401 3.6 27.2 1.0
CG A:ASP105 3.6 9.4 1.0
O3B A:DCP401 3.8 5.8 1.0
N A:PHE8 3.9 10.1 1.0
O A:HOH557 4.0 11.2 1.0
PA A:DCP401 4.1 37.1 1.0
CA A:PHE8 4.2 10.1 1.0
O3A A:DCP401 4.2 0.2 1.0
N A:TYR10 4.3 10.1 1.0
N A:ASP9 4.3 10.2 1.0
CB A:ASP7 4.4 10.2 1.0
CB A:ASP105 4.4 9.6 1.0
OD1 A:ASP105 4.5 11.3 1.0
O P:HOH204 4.5 11.2 1.0
CA A:ASP9 4.5 12.5 1.0
C A:ASP7 4.5 10.3 1.0
C A:ASP9 4.6 10.8 1.0
O1G A:DCP401 4.6 15.8 1.0
N A:PHE11 4.6 10.0 1.0
O A:HOH657 4.7 23.5 1.0
CB A:PHE8 4.8 10.1 1.0
O A:HOH534 4.8 21.6 1.0
O1B A:DCP401 4.8 38.3 1.0
O A:ASP105 4.9 9.8 1.0
CB A:PHE11 4.9 10.0 1.0
CA A:ASP7 5.0 10.3 1.0
CA A:TYR10 5.0 10.1 1.0

Magnesium binding site 2 out of 4 in 4tqs

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


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:1.8
occ:1.00
 OP2 P:DOC101 2.2 31.2 1.0
OE1 A:GLU106 2.3 9.6 1.0
OD1 A:ASP7 2.4 13.9 1.0
O P:HOH204 2.4 11.2 1.0
OD1 A:ASP105 2.5 11.3 1.0
OD2 A:ASP105 2.6 10.6 1.0
O2A A:DCP401 2.8 32.6 1.0
CG A:ASP105 2.9 9.4 1.0
P P:DOC101 3.4 38.6 1.0
CG A:ASP7 3.5 9.9 1.0
CD A:GLU106 3.5 9.8 1.0
MG A:MG402 3.6 0.6 1.0
OP1 P:DOC101 3.6 18.9 1.0
PA A:DCP401 4.1 37.1 1.0
OD2 A:ASP7 4.1 11.4 1.0
CB A:GLU106 4.2 9.8 1.0
O5' P:DOC101 4.2 24.1 1.0
CG A:GLU106 4.2 9.7 1.0
O A:HOH657 4.2 23.5 1.0
C5' A:DCP401 4.4 34.2 1.0
CB A:ASP105 4.4 9.6 1.0
CB A:ASP7 4.5 10.2 1.0
OE2 A:GLU106 4.5 12.8 1.0
O5' A:DCP401 4.5 37.2 1.0
O A:ASP105 4.6 9.8 1.0
O3' P:DT12 4.6 26.5 1.0
O A:HOH628 4.7 14.8 1.0
C A:ASP105 4.7 10.1 1.0
O1A A:DCP401 4.8 41.5 1.0
OG A:SER103 4.8 9.5 1.0
NZ A:LYS152 4.8 12.2 1.0
C5' P:DOC101 4.8 20.8 1.0
O2B A:DCP401 4.9 12.1 1.0

Magnesium binding site 3 out of 4 in 4tqs

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


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:0.0
occ:1.00
 OD1 B:ASP7 2.2 14.2 1.0
O C:HOH211 2.3 4.7 1.0
OP2 C:DOC101 2.3 16.6 1.0
OE1 B:GLU106 2.4 16.7 1.0
OD1 B:ASP105 2.6 10.8 1.0
OD2 B:ASP105 2.6 20.2 1.0
O2A B:DCP401 2.7 16.7 1.0
CG B:ASP105 2.9 13.9 1.0
CG B:ASP7 3.4 16.9 1.0
MG B:MG403 3.4 0.6 1.0
P C:DOC101 3.5 26.1 1.0
CD B:GLU106 3.6 19.6 1.0
OP1 C:DOC101 3.8 15.5 1.0
O B:HOH607 3.8 16.0 1.0
PA B:DCP401 4.0 34.3 1.0
OD2 B:ASP7 4.0 11.1 1.0
CB B:GLU106 4.2 11.3 1.0
CG B:GLU106 4.3 11.0 1.0
O5' C:DOC101 4.3 18.9 1.0
O5' B:DCP401 4.4 29.7 1.0
CB B:ASP105 4.4 11.1 1.0
O B:ASP105 4.4 11.6 1.0
CB B:ASP7 4.5 11.5 1.0
C5' B:DCP401 4.5 33.8 1.0
OE2 B:GLU106 4.6 10.8 1.0
NZ B:LYS152 4.6 10.4 1.0
C B:ASP105 4.6 17.4 1.0
O2B B:DCP401 4.7 53.6 1.0
O2G B:DCP401 4.7 29.5 1.0
O1A B:DCP401 4.7 20.2 1.0
O3' C:DT12 4.7 19.6 1.0
OG B:SER103 4.9 10.8 1.0
C5' C:DOC101 5.0 17.4 1.0

Magnesium binding site 4 out of 4 in 4tqs

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:0.6
occ:1.00
 O2B B:DCP401 2.2 53.6 1.0
O3G B:DCP401 2.3 17.6 1.0
OD2 B:ASP105 2.4 20.2 1.0
OD2 B:ASP7 2.4 11.1 1.0
O B:PHE8 2.4 11.5 1.0
O2A B:DCP401 2.7 16.7 1.0
OD1 B:ASP7 2.8 14.2 1.0
CG B:ASP7 2.9 16.9 1.0
PG B:DCP401 3.3 13.7 1.0
O2G B:DCP401 3.4 29.5 1.0
PB B:DCP401 3.4 62.5 1.0
MG B:MG402 3.4 0.0 1.0
CG B:ASP105 3.5 13.9 1.0
C B:PHE8 3.6 11.9 1.0
O3B B:DCP401 3.7 10.4 1.0
PA B:DCP401 4.0 34.3 1.0
O3A B:DCP401 4.1 0.5 1.0
N B:PHE8 4.2 12.0 1.0
N B:TYR10 4.2 11.6 1.0
O B:HOH548 4.3 10.3 1.0
CB B:ASP105 4.4 11.1 1.0
OD1 B:ASP105 4.4 10.8 1.0
CB B:ASP7 4.4 11.5 1.0
CA B:PHE8 4.5 12.3 1.0
N B:ASP9 4.5 12.2 1.0
CA B:ASP9 4.5 12.0 1.0
O C:HOH211 4.5 4.7 1.0
C B:ASP7 4.6 12.1 1.0
O1B B:DCP401 4.6 71.2 1.0
C B:ASP9 4.6 12.9 1.0
O1G B:DCP401 4.6 9.1 1.0
N B:PHE11 4.7 11.7 1.0
O B:ASP105 4.7 11.6 1.0
O1A B:DCP401 4.8 20.2 1.0
CA B:ASP7 4.9 11.9 1.0
CA B:TYR10 4.9 11.5 1.0
CB B:PHE11 5.0 11.8 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 12 00:11:30 2025

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