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Magnesium in PDB 2w9a: Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dgtp

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

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

Protein crystallography data

The structure of Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dgtp, PDB code: 2w9a 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) 19.94 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.670, 103.757, 52.750, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.6

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 Dgtp (pdb code 2w9a). 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 DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dgtp, PDB code: 2w9a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2w9a

Go back to Magnesium Binding Sites List in 2w9a
Magnesium binding site 1 out of 4 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dgtp


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 Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:14.6
occ:1.00
 OD1 A:ASP7 2.1 38.9 1.0
O A:HOH2040 2.2 20.2 1.0
OD1 A:ASP105 2.3 32.5 1.0
O2A A:DGT594 2.3 32.1 1.0
O P:HOH2009 2.6 53.0 1.0
OE1 A:GLU106 2.6 37.0 1.0
CG A:ASP105 3.2 29.2 1.0
CG A:ASP7 3.3 37.7 1.0
OD2 A:ASP105 3.5 30.1 1.0
CD A:GLU106 3.6 37.0 1.0
PA A:DGT594 3.6 31.8 1.0
CG A:GLU106 3.8 33.0 1.0
CB A:GLU106 3.9 31.4 1.0
O A:HOH2018 3.9 37.3 1.0
OD2 A:ASP7 3.9 41.0 1.0
O A:HOH2017 3.9 46.5 1.0
MG A:MG1001 3.9 11.6 1.0
OG A:SER103 4.1 34.9 1.0
C5' A:DGT594 4.2 31.4 1.0
O5' A:DGT594 4.2 33.3 1.0
O1A A:DGT594 4.3 35.4 1.0
O5' P:DOC14 4.4 48.7 1.0
CB A:ASP7 4.4 35.4 1.0
O A:ASP105 4.6 27.4 1.0
C A:ASP105 4.6 28.0 1.0
CB A:ASP105 4.6 29.2 1.0
OE2 A:GLU106 4.7 37.5 1.0
N A:GLU106 4.7 29.5 1.0
C4' P:DOC14 4.9 56.8 1.0
OP2 P:DOC14 4.9 45.5 1.0
O3A A:DGT594 4.9 35.2 1.0
CA A:GLU106 4.9 30.9 1.0
O A:HOH2019 5.0 27.9 1.0

Magnesium binding site 2 out of 4 in 2w9a

Go back to Magnesium Binding Sites List in 2w9a
Magnesium binding site 2 out of 4 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dgtp


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 Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:11.6
occ:1.00
 O1B A:DGT594 1.8 40.5 1.0
OD2 A:ASP7 2.1 41.0 1.0
O A:PHE8 2.3 26.7 1.0
OD2 A:ASP105 2.3 30.1 1.0
O3G A:DGT594 2.4 35.2 1.0
O2A A:DGT594 2.8 32.1 1.0
CG A:ASP7 2.9 37.7 1.0
PB A:DGT594 3.0 37.7 1.0
OD1 A:ASP7 3.1 38.9 1.0
O3A A:DGT594 3.3 35.2 1.0
CG A:ASP105 3.5 29.2 1.0
C A:PHE8 3.5 26.9 1.0
PA A:DGT594 3.5 31.8 1.0
PG A:DGT594 3.5 36.7 1.0
O3B A:DGT594 3.7 37.6 1.0
MG A:MG1000 3.9 14.6 1.0
OD1 A:ASP105 4.0 32.5 1.0
N A:PHE8 4.1 31.1 1.0
C5' A:DGT594 4.1 31.4 1.0
C A:ASP7 4.2 34.3 1.0
CB A:ASP7 4.2 35.4 1.0
O5' A:DGT594 4.3 33.3 1.0
O2B A:DGT594 4.3 35.0 1.0
O1G A:DGT594 4.3 40.2 1.0
CA A:PHE8 4.4 27.9 1.0
N A:ASP9 4.4 26.9 1.0
N A:TYR10 4.4 26.1 1.0
O A:HOH2040 4.4 20.2 1.0
CA A:ASP9 4.5 27.1 1.0
O A:ASP7 4.5 36.5 1.0
CB A:ASP105 4.6 29.2 1.0
C A:ASP9 4.7 26.9 1.0
CA A:ASP7 4.7 34.7 1.0
N A:PHE11 4.7 27.1 1.0
O2G A:DGT594 4.8 37.4 1.0
O A:ASP105 4.9 27.4 1.0
O1A A:DGT594 4.9 35.4 1.0
CB A:PHE11 4.9 25.9 1.0
CE A:LYS159 5.0 63.6 1.0

Magnesium binding site 3 out of 4 in 2w9a

Go back to Magnesium Binding Sites List in 2w9a
Magnesium binding site 3 out of 4 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dgtp


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 Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:33.0
occ:1.00
 O A:HOH2020 2.2 42.5 1.0
O A:HOH2023 2.2 37.1 1.0
O A:ALA181 2.4 42.1 1.0
O P:HOH2006 2.4 40.5 1.0
O A:ILE186 2.5 29.3 1.0
C A:ALA181 3.6 41.8 1.0
C A:ILE186 3.6 30.7 1.0
OP2 P:DC13 4.0 31.1 1.0
O P:HOH2010 4.1 60.8 1.0
CA A:ALA181 4.3 42.8 1.0
OP1 P:DC13 4.3 31.3 1.0
CA A:GLY187 4.4 33.9 1.0
CB A:ALA181 4.4 42.8 1.0
N A:GLY187 4.4 32.0 1.0
O A:VAL183 4.6 32.2 1.0
N A:ASP182 4.6 41.6 1.0
CA A:ILE186 4.7 29.6 1.0
P P:DC13 4.7 31.9 1.0
CA A:ASP182 4.8 41.1 1.0
CB A:ILE186 4.8 29.8 1.0
N A:ILE186 4.9 29.7 1.0
C A:GLY187 5.0 36.2 1.0

Magnesium binding site 4 out of 4 in 2w9a

Go back to Magnesium Binding Sites List in 2w9a
Magnesium binding site 4 out of 4 in the Ternary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna with Incoming Dgtp


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 Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:25.5
occ:1.00
 O1A A:DGT594 2.1 35.4 1.0
O A:HOH2042 2.2 40.3 1.0
O A:HOH2039 2.4 27.6 1.0
OP2 P:DOC14 2.5 45.5 1.0
O A:HOH2041 2.7 44.2 1.0
O3' P:DC13 3.4 42.0 1.0
P P:DOC14 3.6 44.7 1.0
O P:HOH2009 3.6 53.0 1.0
PA A:DGT594 3.7 31.8 1.0
O A:HOH2038 4.3 27.4 1.0
O A:HOH2040 4.3 20.2 1.0
O5' A:DGT594 4.3 33.3 1.0
O3A A:DGT594 4.4 35.2 1.0
O5' P:DOC14 4.4 48.7 1.0
O2A A:DGT594 4.4 32.1 1.0
C3' P:DC13 4.6 39.6 1.0
C8 A:DGT594 4.6 34.2 1.0
OP1 P:DOC14 4.7 46.1 1.0
C2' P:DC13 4.9 39.7 1.0
N7 A:DGT594 4.9 36.8 1.0

Reference:

H.Zhang, R.L.Eoff, I.D.Kozekov, 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 06:00:11 2024

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