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Sodium in PDB 4fs1: Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota

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

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

Protein crystallography data

The structure of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota, PDB code: 4fs1 was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.41 / 2.50
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.470, 97.470, 203.541, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 27

Other elements in 4fs1:

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

Fluorine (F) 1 atom
Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota (pdb code 4fs1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota, PDB code: 4fs1:

Sodium binding site 1 out of 1 in 4fs1

Go back to Sodium Binding Sites List in 4fs1
Sodium binding site 1 out of 1 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:58.2
occ:1.00
 O A:SER154 2.6 40.2 1.0
O A:HIS156 3.0 36.5 1.0
N A:HIS156 3.3 34.3 1.0
O A:GLN218 3.3 32.8 1.0
C A:GLY155 3.4 37.1 1.0
N A:VAL220 3.5 25.6 1.0
CA A:GLY155 3.5 31.1 1.0
CG A:GLN218 3.5 31.5 1.0
C A:THR219 3.5 30.6 1.0
C A:GLN218 3.6 31.6 1.0
CA A:THR219 3.6 30.4 1.0
C A:SER154 3.6 35.2 1.0
N A:THR219 3.7 30.1 1.0
NE2 A:GLN218 3.7 30.3 1.0
C A:HIS156 3.9 35.5 1.0
O A:GLY155 4.0 40.8 1.0
N A:GLY155 4.0 31.2 1.0
CG1 A:VAL220 4.0 25.6 1.0
CB A:VAL220 4.0 25.2 1.0
CB A:SER177 4.1 33.0 1.0
O A:THR219 4.1 29.1 1.0
CA A:HIS156 4.1 34.5 1.0
CD A:GLN218 4.1 35.7 1.0
CB A:GLN218 4.2 33.0 1.0
CA A:VAL220 4.3 26.0 1.0
CA A:GLN218 4.5 34.6 1.0
CG2 A:VAL153 4.5 30.7 1.0
OG A:SER177 4.8 35.1 1.0
CA A:SER154 4.9 36.5 1.0
CB A:HIS156 5.0 34.4 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 Oct 7 15:27:30 2024

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