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Magnesium in PDB 4fs2: Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota

Enzymatic activity of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota

All present enzymatic activity of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota:
2.7.7.7;

Protein crystallography data

The structure of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota, PDB code: 4fs2 was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.26 / 2.05
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.298, 97.298, 202.906, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 26.1

Other elements in 4fs2:

The structure of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota also contains other interesting chemical elements:

Fluorine (F) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota (pdb code 4fs2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota, PDB code: 4fs2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4fs2

Go back to Magnesium Binding Sites List in 4fs2
Magnesium binding site 1 out of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:15.1
occ:0.50
OD2 A:ASP126 2.0 42.2 1.0
O1G A:DCP503 2.1 38.8 1.0
O1A A:DCP503 2.1 39.0 1.0
OD1 A:ASP34 2.2 35.3 1.0
O2B A:DCP503 2.3 29.8 1.0
O A:LEU35 2.3 39.0 1.0
CG A:ASP126 3.1 38.8 1.0
MG A:MG505 3.2 30.0 1.0
PB A:DCP503 3.3 41.8 1.0
PG A:DCP503 3.4 40.2 1.0
PA A:DCP503 3.4 38.7 1.0
C A:LEU35 3.5 32.4 1.0
CG A:ASP34 3.5 33.6 1.0
OD1 A:ASP126 3.5 36.7 1.0
O3A A:DCP503 3.7 42.5 1.0
O3B A:DCP503 3.8 44.4 1.0
O A:HOH664 3.8 39.8 1.0
N A:LEU35 3.9 32.8 1.0
O2G A:DCP503 4.0 37.5 1.0
OD2 A:ASP34 4.1 39.4 1.0
C A:ASP34 4.1 33.7 1.0
C5' A:DCP503 4.2 41.4 1.0
CA A:LEU35 4.2 32.8 1.0
O5' A:DCP503 4.3 41.7 1.0
CB A:ASP126 4.4 33.7 1.0
O A:ASP34 4.5 31.4 1.0
N A:CYS37 4.5 31.1 1.0
N A:ASP36 4.5 33.5 1.0
O2A A:DCP503 4.6 42.4 1.0
O3G A:DCP503 4.6 41.8 1.0
CB A:ASP34 4.6 32.8 1.0
CA A:ASP34 4.7 29.5 1.0
O1B A:DCP503 4.7 37.7 1.0
CA A:ASP36 4.7 34.5 1.0
CB A:LEU35 4.8 33.5 1.0
C A:ASP36 4.8 34.3 1.0
N A:PHE38 4.8 35.5 1.0
O A:ASP126 4.8 31.5 1.0
CB A:PHE38 5.0 30.3 1.0

Magnesium binding site 2 out of 3 in 4fs2

Go back to Magnesium Binding Sites List in 4fs2
Magnesium binding site 2 out of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:41.1
occ:1.00
O A:HOH601 2.7 33.1 1.0
O A:GLY124 2.7 33.0 1.0
O A:GLU127 2.9 30.0 1.0
NH2 A:ARG122 3.2 31.0 1.0
C A:PHE125 3.5 34.0 1.0
CZ A:ARG122 3.5 31.2 1.0
O A:PHE125 3.5 31.7 1.0
CG A:ARG122 3.6 30.9 1.0
ND2 A:ASN128 3.6 26.4 1.0
CB A:ARG122 3.6 30.0 1.0
OG A:SER106 3.7 31.5 1.0
N A:ASP126 3.7 32.2 1.0
N A:GLU127 3.7 27.4 1.0
C A:GLY124 3.8 30.6 1.0
C A:GLU127 3.8 29.1 1.0
OD1 A:ASN128 3.9 32.1 1.0
CA A:PHE125 3.9 31.4 1.0
NH1 A:ARG122 4.0 28.7 1.0
OG1 A:THR110 4.0 29.2 1.0
CA A:ARG122 4.0 29.1 1.0
CG A:ASN128 4.0 29.6 1.0
NE A:ARG122 4.1 30.5 1.0
N A:LEU123 4.1 27.9 1.0
CA A:ASP126 4.2 31.1 1.0
C A:ASP126 4.3 30.9 1.0
N A:PHE125 4.3 29.8 1.0
CD A:ARG122 4.4 29.0 1.0
O A:LEU123 4.4 31.2 1.0
CA A:GLU127 4.5 27.2 1.0
C A:ARG122 4.5 29.4 1.0
C A:LEU123 4.7 33.0 1.0
N A:ASN128 4.8 29.0 1.0
O A:SER106 4.8 32.6 1.0

Magnesium binding site 3 out of 3 in 4fs2

Go back to Magnesium Binding Sites List in 4fs2
Magnesium binding site 3 out of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:30.0
occ:1.00
O1A A:DCP503 2.1 39.0 1.0
OE2 A:GLU127 2.2 38.0 1.0
OD1 A:ASP34 2.9 35.3 1.0
OD1 A:ASP126 2.9 36.7 1.0
OD2 A:ASP34 3.0 39.4 1.0
CD A:GLU127 3.1 32.4 1.0
PA A:DCP503 3.2 38.7 1.0
CG A:ASP34 3.2 33.6 1.0
MG A:MG501 3.2 15.1 0.5
CG A:GLU127 3.3 28.1 1.0
O2A A:DCP503 3.6 42.4 1.0
C3' B:DOC13 3.6 47.4 1.0
CG A:ASP126 3.7 38.8 1.0
OD2 A:ASP126 3.7 42.2 1.0
O5' A:DCP503 4.0 41.7 1.0
O1G A:DCP503 4.0 38.8 1.0
O A:HOH635 4.1 31.3 1.0
C4' B:DOC13 4.3 48.0 1.0
OE1 A:GLU127 4.3 33.8 1.0
CB A:ASP34 4.5 32.8 1.0
O3A A:DCP503 4.5 42.5 1.0
C5' A:DCP503 4.5 41.4 1.0
C5' B:DOC13 4.7 48.5 1.0
C2' B:DOC13 4.7 46.9 1.0
O2B A:DCP503 4.7 29.8 1.0
CB A:GLU127 4.8 27.4 1.0
O A:ASP126 5.0 31.5 1.0

Reference:

L.Zhao, M.G.Pence, P.P.Christov, Z.Wawrzak, J.Y.Choi, C.J.Rizzo, M.Egli, F.P.Guengerich. Basis of Miscoding of the Dna Adduct N2,3-Ethenoguanine By Human Y-Family Dna Polymerases. J.Biol.Chem. V. 287 35516 2012.
ISSN: ISSN 0021-9258
PubMed: 22910910
DOI: 10.1074/JBC.M112.403253
Page generated: Mon Dec 14 15:42:18 2020

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