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Magnesium in PDB 3v6j: 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: 3v6j was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.700, 111.419, 98.807, 90.00, 102.57, 90.00
R / Rfree (%) 21 / 27.3

Other elements in 3v6j:

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

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Replication of N2,3-Ethenoguanine By Dna Polymerases (pdb code 3v6j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3v6j

Go back to Magnesium Binding Sites List in 3v6j
Magnesium binding site 1 out of 5 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:Mg402

b:19.7
occ:1.00
 OE1 A:GLU106 2.2 45.9 1.0
O2A A:DCP401 2.3 35.3 1.0
OD1 A:ASP105 2.4 29.6 1.0
OD2 A:ASP7 2.5 33.3 1.0
O A:HOH559 2.5 43.9 1.0
OD1 A:ASP7 2.9 38.3 1.0
CG A:ASP7 2.9 31.9 1.0
CG A:ASP105 3.2 27.4 1.0
OD2 A:ASP105 3.2 32.8 1.0
MG A:MG403 3.3 13.3 1.0
PA A:DCP401 3.4 37.7 1.0
CD A:GLU106 3.4 39.8 1.0
O5' A:DCP401 3.9 46.4 1.0
O1A A:DCP401 3.9 41.3 1.0
C5' A:DCP401 4.0 37.5 1.0
CB A:GLU106 4.2 34.6 1.0
CG A:GLU106 4.3 35.8 1.0
OE2 A:GLU106 4.3 42.5 1.0
CB A:ASP7 4.3 27.9 1.0
NZ A:LYS152 4.5 40.3 1.0
NZ A:LYS159 4.6 40.1 1.0
O1G A:DCP401 4.6 26.6 1.0
CB A:ASP105 4.6 27.2 1.0
O A:ASP105 4.7 31.5 1.0
O3A A:DCP401 4.7 28.3 1.0
OP2 P:DOC13 4.8 79.5 1.0
C A:ASP105 4.8 27.9 1.0
O A:HOH596 4.8 44.3 1.0
O1B A:DCP401 4.8 24.7 1.0
CA A:ASP7 4.9 24.6 1.0

Magnesium binding site 2 out of 5 in 3v6j

Go back to Magnesium Binding Sites List in 3v6j
Magnesium binding site 2 out of 5 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:Mg403

b:13.3
occ:1.00
 OD1 A:ASP7 2.0 38.3 1.0
O2A A:DCP401 2.1 35.3 1.0
OD2 A:ASP105 2.1 32.8 1.0
O A:HOH596 2.2 44.3 1.0
O A:PHE8 2.2 24.2 1.0
O1G A:DCP401 2.3 26.6 1.0
O1B A:DCP401 2.3 24.7 1.0
CG A:ASP7 3.2 31.9 1.0
MG A:MG402 3.3 19.7 1.0
CG A:ASP105 3.3 27.4 1.0
PA A:DCP401 3.3 37.7 1.0
PB A:DCP401 3.4 27.5 1.0
C A:PHE8 3.4 25.6 1.0
PG A:DCP401 3.5 33.9 1.0
O3A A:DCP401 3.5 28.3 1.0
OD1 A:ASP105 3.7 29.6 1.0
OD2 A:ASP7 3.7 33.3 1.0
O3B A:DCP401 3.8 32.2 1.0
N A:PHE8 3.9 23.7 1.0
NZ A:LYS159 4.1 40.1 1.0
C5' A:DCP401 4.1 37.5 1.0
O2G A:DCP401 4.2 27.7 1.0
C A:ASP7 4.2 23.9 1.0
O5' A:DCP401 4.2 46.4 1.0
CA A:PHE8 4.3 24.0 1.0
N A:ASP9 4.3 25.9 1.0
N A:TYR10 4.4 24.3 1.0
CB A:ASP7 4.4 27.9 1.0
CA A:ASP9 4.5 25.0 1.0
O A:ASP7 4.5 23.4 1.0
O1A A:DCP401 4.5 41.3 1.0
CB A:ASP105 4.5 27.2 1.0
C A:ASP9 4.7 23.2 1.0
O3G A:DCP401 4.7 36.1 1.0
N A:PHE11 4.7 23.0 1.0
CA A:ASP7 4.8 24.6 1.0
O2B A:DCP401 4.8 33.1 1.0
O A:ASP105 4.9 31.5 1.0

Magnesium binding site 3 out of 5 in 3v6j

Go back to Magnesium Binding Sites List in 3v6j
Magnesium binding site 3 out of 5 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:Mg402

b:43.0
occ:1.00
 OE1 J:GLU106 2.0 65.6 1.0
O2A J:DCP401 2.2 45.9 1.0
OD1 J:ASP7 2.3 59.0 1.0
OD1 J:ASP105 2.5 48.9 1.0
OD2 J:ASP105 2.5 50.0 1.0
OD2 J:ASP7 2.5 60.0 1.0
CG J:ASP7 2.7 52.2 1.0
MG J:MG403 2.8 28.0 1.0
CG J:ASP105 2.9 49.8 1.0
CD J:GLU106 3.0 60.3 1.0
CG J:GLU106 3.3 59.3 1.0
PA J:DCP401 3.4 65.1 1.0
O5' J:DCP401 3.7 74.3 1.0
OP2 K:DOC13 4.0 61.2 1.0
CB J:ASP7 4.1 51.3 1.0
O1A J:DCP401 4.1 56.2 1.0
O1G J:DCP401 4.2 51.8 1.0
OE2 J:GLU106 4.2 56.6 1.0
NZ J:LYS152 4.3 59.1 1.0
CB J:ASP105 4.4 49.5 1.0
O1B J:DCP401 4.5 50.4 1.0
O J:PHE8 4.5 42.3 1.0
CB J:GLU106 4.7 55.2 1.0
O J:ASP105 4.7 63.3 1.0
O3A J:DCP401 4.7 65.4 1.0
CA J:ASP7 4.8 48.8 1.0
OG J:SER103 4.8 43.5 1.0
C J:ASP105 4.8 55.4 1.0

Magnesium binding site 4 out of 5 in 3v6j

Go back to Magnesium Binding Sites List in 3v6j
Magnesium binding site 4 out of 5 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:28.0
occ:1.00
 O1G J:DCP401 1.9 51.8 1.0
O2A J:DCP401 2.1 45.9 1.0
OD1 J:ASP7 2.2 59.0 1.0
O J:PHE8 2.2 42.3 1.0
OD2 J:ASP105 2.2 50.0 1.0
O1B J:DCP401 2.5 50.4 1.0
MG J:MG402 2.8 43.0 1.0
CG J:ASP7 3.1 52.2 1.0
OD2 J:ASP7 3.3 60.0 1.0
PG J:DCP401 3.4 46.5 1.0
CG J:ASP105 3.4 49.8 1.0
C J:PHE8 3.4 44.1 1.0
PA J:DCP401 3.5 65.1 1.0
PB J:DCP401 3.6 62.5 1.0
O3A J:DCP401 3.9 65.4 1.0
O3B J:DCP401 4.0 56.6 1.0
OD1 J:ASP105 4.0 48.9 1.0
O3G J:DCP401 4.1 54.7 1.0
N J:PHE8 4.2 46.8 1.0
N J:ASP9 4.3 42.1 1.0
CA J:ASP9 4.3 41.3 1.0
CA J:PHE8 4.4 45.5 1.0
CB J:ASP7 4.4 51.3 1.0
N J:TYR10 4.4 41.4 1.0
O5' J:DCP401 4.4 74.3 1.0
C J:ASP7 4.4 46.7 1.0
O2G J:DCP401 4.4 52.2 1.0
CB J:ASP105 4.4 49.5 1.0
O1A J:DCP401 4.6 56.2 1.0
C J:ASP9 4.6 42.0 1.0
N J:PHE11 4.8 38.7 1.0
OE1 J:GLU106 4.8 65.6 1.0
CA J:ASP7 4.8 48.8 1.0
O J:ASP7 4.8 47.4 1.0
CB J:PHE11 5.0 41.0 1.0
O2B J:DCP401 5.0 72.1 1.0

Magnesium binding site 5 out of 5 in 3v6j

Go back to Magnesium Binding Sites List in 3v6j
Magnesium binding site 5 out of 5 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 5 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg101

b:49.6
occ:1.00
 O1A J:DCP401 2.7 56.2 1.0
OP1 K:DOC13 3.8 63.9 1.0
OP2 K:DOC13 3.9 61.2 1.0
PA J:DCP401 4.0 65.1 1.0
O5' J:DCP401 4.2 74.3 1.0
P K:DOC13 4.3 69.2 1.0
O J:HOH503 4.3 69.2 1.0
C5' J:DCP401 4.5 72.8 1.0
O J:HOH525 4.7 47.2 1.0
NZ J:LYS152 4.8 59.1 1.0
O2A J:DCP401 4.9 45.9 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: Thu Aug 15 12:45:11 2024

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