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Magnesium in PDB 2w9c: Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp

Enzymatic activity of Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp

All present enzymatic activity of Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp, PDB code: 2w9c was solved by R.L.Eoff, H.Zhang, I.D.Kosekov, C.J.Rizzo, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.33 / 2.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.707, 101.622, 96.753, 90.00, 92.29, 90.00
R / Rfree (%) 25.2 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp (pdb code 2w9c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp, PDB code: 2w9c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2w9c

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Magnesium binding site 1 out of 6 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming 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 DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1342

b:68.0
occ:1.00
 O A:HOH2021 1.9 51.2 1.0
OD2 A:ASP105 2.4 41.5 1.0
O1A A:TTP1345 2.5 65.4 1.0
OD1 A:ASP105 3.0 39.8 1.0
CG A:ASP105 3.0 41.0 1.0
OE2 A:GLU106 3.2 57.0 1.0
O3B A:TTP1345 3.3 59.2 1.0
O5' A:TTP1345 3.4 61.4 1.0
O A:HOH2022 3.6 43.6 1.0
PA A:TTP1345 3.6 65.0 1.0
MG A:MG1343 3.7 25.3 1.0
C5' A:TTP1345 3.8 58.3 1.0
O1B A:TTP1345 3.9 62.1 1.0
PB A:TTP1345 4.2 59.1 1.0
O3G A:TTP1345 4.3 61.5 1.0
PG A:TTP1345 4.3 63.9 1.0
CD A:GLU106 4.4 55.6 1.0
C4' A:TTP1345 4.4 58.5 1.0
CB A:ASP105 4.5 42.7 1.0
O3A A:TTP1345 4.5 61.5 1.0
OD2 A:ASP7 4.6 45.4 1.0
OG A:SER103 4.6 43.5 1.0
O1G A:TTP1345 4.7 65.9 1.0
O2A A:TTP1345 4.7 63.9 1.0
CB A:SER103 5.0 44.1 1.0

Magnesium binding site 2 out of 6 in 2w9c

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Magnesium binding site 2 out of 6 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming 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 DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1343

b:25.3
occ:1.00
 O1G A:TTP1345 2.0 65.9 1.0
OD2 A:ASP105 2.1 41.5 1.0
O A:PHE8 2.2 42.9 1.0
O1B A:TTP1345 2.4 62.1 1.0
OD1 A:ASP7 2.8 40.5 1.0
CG A:ASP105 2.9 41.0 1.0
O3B A:TTP1345 2.9 59.2 1.0
PG A:TTP1345 3.0 63.9 1.0
CB A:ASP105 3.1 42.7 1.0
PB A:TTP1345 3.1 59.1 1.0
CG A:ASP7 3.3 44.5 1.0
OD2 A:ASP7 3.3 45.4 1.0
C A:PHE8 3.5 41.6 1.0
O2B A:TTP1345 3.7 57.6 1.0
MG A:MG1342 3.7 68.0 1.0
O3G A:TTP1345 3.8 61.5 1.0
O A:HOH2043 3.9 58.4 1.0
OD1 A:ASP105 3.9 39.8 1.0
N A:PHE8 4.0 42.8 1.0
O1A A:TTP1345 4.2 65.4 1.0
O2G A:TTP1345 4.2 59.3 1.0
CA A:PHE8 4.3 42.8 1.0
O A:ASP105 4.3 47.1 1.0
O A:HOH2021 4.4 51.2 1.0
N A:ASP9 4.4 40.4 1.0
CA A:ASP9 4.4 41.1 1.0
NZ A:LYS159 4.5 53.2 1.0
N A:TYR10 4.5 35.3 1.0
C A:ASP7 4.5 41.0 1.0
CA A:ASP105 4.5 45.4 1.0
O3A A:TTP1345 4.5 61.5 1.0
CB A:PHE8 4.6 43.3 1.0
CB A:ASP7 4.6 43.7 1.0
C A:ASP9 4.6 38.5 1.0
N A:PHE11 4.7 27.2 1.0
CB A:PHE11 4.7 26.0 1.0
C A:ASP105 4.8 47.4 1.0
O A:HOH2022 4.8 43.6 1.0
CA A:ASP7 4.8 43.0 1.0
PA A:TTP1345 4.9 65.0 1.0

Magnesium binding site 3 out of 6 in 2w9c

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Magnesium binding site 3 out of 6 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming 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 DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1344

b:76.5
occ:1.00
 O A:ILE186 1.7 53.2 1.0
O A:HOH2029 2.2 32.0 1.0
O A:ALA181 2.4 49.7 1.0
O A:HOH2030 2.4 61.1 1.0
C A:ILE186 2.9 51.8 1.0
O A:HOH2031 3.4 44.2 1.0
OP2 C:DOC13 3.5 52.7 1.0
C A:ALA181 3.6 51.0 1.0
CA A:ILE186 3.8 50.6 1.0
N A:GLY187 3.8 52.2 1.0
CB A:ILE186 3.9 51.2 1.0
CA A:GLY187 4.0 50.5 1.0
N A:ILE186 4.1 48.9 1.0
O A:VAL183 4.1 48.7 1.0
O A:HOH2025 4.2 71.8 1.0
CG2 A:ILE186 4.3 50.4 1.0
CA A:ALA181 4.4 51.4 1.0
P C:DOC13 4.5 51.1 1.0
N A:ASP182 4.6 51.6 1.0
OP1 C:DOC13 4.6 51.5 1.0
N A:VAL183 4.6 48.8 1.0
CA A:ASP182 4.7 50.7 1.0
C A:VAL183 4.7 47.3 1.0
C A:ASP182 4.8 49.6 1.0
C A:GLY187 4.8 48.5 1.0
CB A:ALA181 4.9 51.6 1.0

Magnesium binding site 4 out of 6 in 2w9c

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Magnesium binding site 4 out of 6 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp


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 DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1342

b:68.0
occ:1.00
 OE1 B:GLU106 1.9 44.0 1.0
OD2 B:ASP105 2.0 43.6 1.0
OG B:SER103 2.4 44.8 1.0
O B:HOH2015 2.5 28.8 1.0
CG B:ASP105 2.8 42.5 1.0
CD B:GLU106 2.9 40.9 1.0
OD1 B:ASP105 2.9 44.1 1.0
O B:HOH2039 2.9 51.8 1.0
CB B:SER103 3.0 45.6 1.0
OE2 B:GLU106 3.7 40.0 1.0
CG B:GLU106 3.7 40.3 1.0
CB B:ASP105 4.2 43.7 1.0
N B:ASP105 4.2 40.1 1.0
O B:HOH2036 4.4 49.2 1.0
CA B:SER103 4.4 44.6 1.0
CB B:GLU106 4.4 39.8 1.0
O1G B:TTP1345 4.5 82.0 1.0
C B:SER103 4.6 42.5 1.0
N B:GLU106 4.6 40.4 1.0
C B:ASP105 4.6 41.4 1.0
CA B:ASP105 4.6 41.7 1.0
N B:ILE104 4.7 40.1 1.0
O B:HOH2038 4.7 67.0 1.0

Magnesium binding site 5 out of 6 in 2w9c

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Magnesium binding site 5 out of 6 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1343

b:44.2
occ:1.00
 O B:HOH2036 2.0 49.2 1.0
O1B B:TTP1345 2.1 78.1 1.0
O1G B:TTP1345 2.2 82.0 1.0
O B:HOH2001 2.2 10.9 1.0
O B:HOH2037 2.2 42.5 1.0
O B:HOH2038 2.3 67.0 1.0
O2G B:TTP1345 2.5 86.0 1.0
OD2 B:ASP7 2.5 50.2 1.0
PG B:TTP1345 2.8 79.7 1.0
CG B:ASP7 3.1 46.1 1.0
PB B:TTP1345 3.2 78.4 1.0
OD1 B:ASP7 3.3 48.1 1.0
O3B B:TTP1345 3.5 79.9 1.0
OD1 B:ASP105 3.7 44.1 1.0
O2B B:TTP1345 3.8 80.2 1.0
NZ B:LYS159 3.8 42.4 1.0
CG B:ASP105 4.0 42.5 1.0
O1A B:TTP1345 4.1 78.3 1.0
O B:HOH2039 4.1 51.8 1.0
O3G B:TTP1345 4.1 83.1 1.0
CB B:ASP105 4.2 43.7 1.0
O B:ASP105 4.2 40.8 1.0
O B:PHE8 4.3 41.0 1.0
CB B:ASP7 4.3 45.6 1.0
C B:ASP7 4.4 43.4 1.0
CG B:GLU106 4.5 40.3 1.0
N B:PHE8 4.5 40.9 1.0
C B:PHE8 4.5 40.9 1.0
OE2 B:GLU106 4.5 40.0 1.0
O3A B:TTP1345 4.6 77.8 1.0
CA B:ASP7 4.6 45.2 1.0
CD B:GLU106 4.6 40.9 1.0
O5' B:TTP1345 4.6 72.1 1.0
OD2 B:ASP105 4.6 43.6 1.0
CE B:LYS159 4.7 45.0 1.0
O B:ASP7 4.7 46.0 1.0
PA B:TTP1345 4.8 75.8 1.0
C B:ASP105 5.0 41.4 1.0

Magnesium binding site 6 out of 6 in 2w9c

Go back to Magnesium Binding Sites List in 2w9c
Magnesium binding site 6 out of 6 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1344

b:56.9
occ:1.00
 O B:HOH2025 2.1 63.5 1.0
O B:HOH2024 3.1 42.0 1.0
O B:ASP182 3.4 47.2 1.0
O B:ALA181 3.6 46.4 1.0
C B:ASP182 3.9 46.6 1.0
CA B:ASP182 3.9 46.9 1.0
OP2 D:DOC13 4.2 52.0 1.0
OP1 D:DOC13 4.4 53.9 1.0
C B:ALA181 4.5 47.6 1.0
O B:ILE186 4.5 44.2 1.0
N B:ASP182 4.7 47.7 1.0
O B:VAL183 4.8 42.4 1.0
P D:DOC13 4.8 51.4 1.0
OD1 B:ASP182 4.9 53.4 1.0
C B:VAL183 4.9 42.0 1.0
N B:VAL183 4.9 45.4 1.0
CB B:ASP182 4.9 48.5 1.0

Reference:

H.Zhang, R.L.Eoff, I.D.Kosekov, C.J.Rizzo, M.Egli, F.P.Guengerich. Structure-Function Relationships in Miscoding By Sulfolobus Solfataricus Dna Polymerase DPO4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem. V. 284 17687 2009.
ISSN: ISSN 0021-9258
PubMed: 19542237
DOI: 10.1074/JBC.M109014274
Page generated: Wed Aug 14 06:00:43 2024

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