Atomistry » Magnesium » PDB 3v4k-3vdb » 3v6k
Atomistry »
  Magnesium »
    PDB 3v4k-3vdb »
      3v6k »

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: Thu Aug 15 12:45:21 2024

Last articles

Cl in 3KQF
Cl in 3KPY
Cl in 3KQI
Cl in 3KQ6
Cl in 3KQ0
Cl in 3KOQ
Cl in 3KOO
Cl in 3KPF
Cl in 3KMO
Cl in 3KMY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy