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Magnesium in PDB 3v6k: Replication of N2,3-Ethenoguanine By Dna Polymerases

Enzymatic activity of Replication of N2,3-Ethenoguanine By Dna Polymerases

All present enzymatic activity of Replication of N2,3-Ethenoguanine By Dna Polymerases:
2.7.7.7;

Protein crystallography data

The structure of Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6k was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.855, 110.953, 100.238, 90.00, 102.70, 90.00
R / Rfree (%) 22.9 / 30.3

Other elements in 3v6k:

The structure of Replication of N2,3-Ethenoguanine By Dna Polymerases also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Calcium (Ca) 7 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Replication of N2,3-Ethenoguanine By Dna Polymerases (pdb code 3v6k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3v6k

Go back to Magnesium Binding Sites List in 3v6k
Magnesium binding site 1 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:0.6
occ:1.00
OD2 A:ASP7 2.5 56.2 1.0
OD2 A:ASP105 2.7 49.7 1.0
MG A:MG402 2.8 0.6 1.0
OD1 A:ASP105 3.5 49.6 1.0
CG A:ASP105 3.5 49.3 1.0
CG A:ASP7 3.6 55.3 1.0
OE2 A:GLU106 3.9 59.1 1.0
C5' P:2DT14 4.1 0.2 1.0
OD1 A:ASP7 4.1 56.7 1.0
C4' P:2DT14 4.1 0.3 1.0
O5' P:2DT14 4.2 0.1 1.0
O A:PHE8 4.3 49.3 1.0
OP2 P:2DT14 4.3 0.1 1.0
NZ A:LYS159 4.5 62.8 1.0
CD A:GLU106 4.5 57.2 1.0
CG A:GLU106 4.5 54.6 1.0
O A:ASP105 4.5 49.2 1.0
P P:2DT14 4.5 0.6 1.0
OP1 P:2DT14 4.7 0.1 1.0
C3' P:2DT14 4.7 1.0 1.0
CB A:ASP7 4.9 53.5 1.0
CB A:ASP105 5.0 48.4 1.0

Magnesium binding site 2 out of 4 in 3v6k

Go back to Magnesium Binding Sites List in 3v6k
Magnesium binding site 2 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:0.6
occ:1.00
MG A:MG401 2.8 0.6 1.0
NZ A:LYS159 3.5 62.8 1.0
O A:PHE8 3.5 49.3 1.0
OD2 A:ASP105 3.5 49.7 1.0
N A:TYR10 3.7 52.4 1.0
NH2 A:ARG51 3.8 65.7 1.0
CA A:TYR10 3.8 52.8 1.0
OD2 A:ASP7 4.1 56.2 1.0
NH1 A:ARG51 4.2 68.0 1.0
OD1 A:ASP7 4.3 56.7 1.0
C A:ASP9 4.4 51.7 1.0
CZ A:ARG51 4.5 67.2 1.0
N A:PHE11 4.5 49.2 1.0
C3' P:2DT14 4.6 1.0 1.0
CG A:ASP7 4.6 55.3 1.0
C A:PHE8 4.6 50.0 1.0
CA A:ASP9 4.7 51.7 1.0
CG A:ASP105 4.8 49.3 1.0
C A:TYR10 4.8 51.1 1.0
CB A:TYR10 4.8 56.6 1.0
CE A:LYS159 4.9 62.1 1.0
C4' P:2DT14 4.9 0.3 1.0

Magnesium binding site 3 out of 4 in 3v6k

Go back to Magnesium Binding Sites List in 3v6k
Magnesium binding site 3 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg401

b:0.6
occ:1.00
OD1 J:ASP7 2.6 0.2 1.0
OP2 K:2DT14 2.8 0.7 1.0
MG J:MG403 3.0 0.6 1.0
OD2 J:ASP105 3.2 94.4 1.0
CG J:ASP7 3.4 0.1 1.0
OE2 J:GLU106 3.5 0.0 1.0
P K:2DT14 3.5 0.8 1.0
OD2 J:ASP7 3.5 0.1 1.0
C5' K:2DT14 3.6 0.6 1.0
O5' K:2DT14 3.7 0.3 1.0
OP1 K:2DT14 3.8 0.6 1.0
O J:HOH502 3.9 90.6 1.0
OD1 J:ASP105 3.9 92.0 1.0
CG J:ASP105 4.0 94.1 1.0
CD J:GLU106 4.3 0.7 1.0
CG J:GLU106 4.5 0.0 1.0
C4' K:2DT14 4.6 0.7 1.0
CB J:ASP7 4.8 0.7 1.0

Magnesium binding site 4 out of 4 in 3v6k

Go back to Magnesium Binding Sites List in 3v6k
Magnesium binding site 4 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg403

b:0.6
occ:1.00
OD2 J:ASP105 2.3 94.4 1.0
O J:HOH502 2.6 90.6 1.0
O J:PHE8 2.7 0.6 1.0
OD2 J:ASP7 2.8 0.1 1.0
MG J:MG401 3.0 0.6 1.0
OD1 J:ASP7 3.1 0.2 1.0
CG J:ASP7 3.3 0.1 1.0
CG J:ASP105 3.5 94.1 1.0
C J:PHE8 3.8 0.2 1.0
N J:TYR10 4.1 95.1 1.0
CA J:ASP9 4.4 99.8 1.0
OD1 J:ASP105 4.4 92.0 1.0
CB J:ASP105 4.4 93.5 1.0
N J:PHE11 4.5 87.5 1.0
C J:ASP9 4.5 97.2 1.0
N J:ASP9 4.5 0.6 1.0
N J:PHE8 4.6 0.1 1.0
CB J:ASP7 4.7 0.7 1.0
C J:ASP7 4.8 0.8 1.0
CA J:PHE8 4.8 0.3 1.0
CA J:TYR10 4.8 91.7 1.0
CB J:PHE11 4.9 82.1 1.0

Reference:

L.Zhao, P.P.Christov, I.D.Kozekov, M.G.Pence, P.S.Pallan, C.J.Rizzo, M.Egli, F.P.Guengerich. Replication of N(2) ,3-Ethenoguanine By Dna Polymerases. Angew.Chem.Int.Ed.Engl. V. 51 5466 2012.
ISSN: ISSN 1433-7851
PubMed: 22488769
DOI: 10.1002/ANIE.201109004
Page generated: Mon Dec 14 08:58:04 2020

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