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Sodium in PDB 4o5z: O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine

Protein crystallography data

The structure of O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine, PDB code: 4o5z was solved by F.Zhang, M.Tsunoda, K.Suzuki, Y.Kikuchi, O.Wilkinson, C.L.Millington, G.P.Margison, D.M.Williams, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.07 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.873, 41.764, 64.608, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.3

Other elements in 4o5z:

The structure of O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine also contains other interesting chemical elements:

Barium (Ba) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine (pdb code 4o5z). 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 O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine, PDB code: 4o5z:

Sodium binding site 1 out of 1 in 4o5z

Go back to Sodium Binding Sites List in 4o5z
Sodium binding site 1 out of 1 in the O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:38.2
occ:1.00
O A:HOH229 2.3 47.9 1.0
O A:HOH203 2.5 40.9 1.0
O B:HOH235 2.8 51.5 1.0
O4 A:DT9 2.9 40.6 1.0
O B:HOH218 3.5 49.4 1.0
C4 A:DT9 4.1 36.7 1.0
O A:HOH225 4.1 52.6 1.0
O A:HOH218 4.3 52.8 1.0
O B:HOH234 4.3 46.5 1.0
O B:HOH214 4.5 45.5 1.0
O7 B:C6G16 4.9 31.2 1.0
O A:HOH208 4.9 47.5 1.0
N3 A:DT9 4.9 35.0 1.0
C7 A:DT9 4.9 42.9 1.0
C5 A:DT9 5.0 38.7 1.0

Reference:

F.Zhang, M.Tsunoda, Y.Kikuchi, O.Wilkinson, C.L.Millington, G.P.Margison, D.M.Williams, A.Takenaka. O(6)-Carboxymethylguanine in Dna Forms A Sequence Context-Dependent Wobble Base-Pair Structure with Thymine Acta Crystallogr.,Sect.D V. 70 1669 2014.
ISSN: ISSN 0907-4449
PubMed: 24914978
DOI: 10.1107/S1399004714006178
Page generated: Tue Dec 15 06:56:34 2020

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