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Sodium in PDB 2ofi: Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA

Protein crystallography data

The structure of Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA, PDB code: 2ofi was solved by A.H.Metz, T.Hollis, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.85
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 101.963, 101.963, 55.461, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 19.8

Other elements in 2ofi:

The structure of Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA (pdb code 2ofi). 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 Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA, PDB code: 2ofi:

Sodium binding site 1 out of 1 in 2ofi

Go back to Sodium Binding Sites List in 2ofi
Sodium binding site 1 out of 1 in the Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:39.8
occ:1.00
O A:HOH418 2.1 43.2 1.0
O A:VAL120 2.2 36.7 1.0
O A:TRP117 2.3 31.7 1.0
O A:HOH419 2.6 49.2 1.0
O A:HOH417 2.8 56.3 1.0
C A:VAL120 3.4 36.6 1.0
C A:TRP117 3.4 30.2 1.0
N A:VAL120 4.1 34.7 1.0
CA A:VAL120 4.1 36.4 1.0
CG2 A:VAL120 4.1 39.5 1.0
CA A:SER118 4.2 30.5 1.0
N A:SER118 4.2 29.7 1.0
N A:GLY122 4.3 37.8 1.0
N A:ASP121 4.3 38.1 1.0
CA A:TRP117 4.4 29.2 1.0
C A:SER118 4.4 30.6 1.0
CB A:TRP117 4.5 28.9 1.0
CB A:VAL120 4.5 37.3 1.0
CA A:ASP121 4.5 38.3 1.0
O A:SER118 4.7 30.7 1.0
O A:GLY122 4.7 38.5 1.0
O A:HOH416 4.7 39.2 1.0
CE3 A:TRP117 4.8 28.1 1.0
CG1 A:VAL120 4.8 38.1 1.0
C A:ASP121 4.9 38.3 1.0
N A:PHE119 5.0 30.3 1.0

Reference:

A.H.Metz, T.Hollis, B.F.Eichman. Dna Damage Recognition and Repair By 3-Methyladenine Dna Glycosylase I (Tag). Embo J. V. 26 2411 2007.
ISSN: ISSN 0261-4189
PubMed: 17410210
DOI: 10.1038/SJ.EMBOJ.7601649
Page generated: Tue Dec 15 05:52:22 2020

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