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Sodium in PDB 231d: Structure of A Dna-Porphyrin Complex

Protein crystallography data

The structure of Structure of A Dna-Porphyrin Complex, PDB code: 231d was solved by L.A.Lipscomb, F.X.Zhou, S.R.Presnell, R.J.Woo, M.E.Peek, R.R.Plaskon, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 39.490, 39.490, 56.150, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / n/a

Other elements in 231d:

The structure of Structure of A Dna-Porphyrin Complex also contains other interesting chemical elements:

Copper (Cu) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Dna-Porphyrin Complex (pdb code 231d). 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 Structure of A Dna-Porphyrin Complex, PDB code: 231d:

Sodium binding site 1 out of 1 in 231d

Go back to Sodium Binding Sites List in 231d
Sodium binding site 1 out of 1 in the Structure of A Dna-Porphyrin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Dna-Porphyrin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na8

b:23.1
occ:0.50
O2 A:DT4 2.4 28.3 1.0
O A:HOH13 3.1 13.5 1.0
C2 A:DT4 3.6 29.6 1.0
C1' A:DT4 4.3 34.5 1.0
C2 A:DA3 4.3 27.3 1.0
O4' A:DC5 4.5 18.1 1.0
N1 A:DT4 4.5 31.4 1.0
N3 A:DT4 4.5 24.4 1.0
N1 A:DA3 4.8 23.1 1.0
N3 A:DA3 4.8 22.8 1.0
O4' A:DT4 4.9 36.5 1.0

Reference:

L.A.Lipscomb, F.X.Zhou, S.R.Presnell, R.J.Woo, M.E.Peek, R.R.Plaskon, L.D.Williams. Structure of Dna-Porphyrin Complex. Biochemistry V. 35 2818 1996.
ISSN: ISSN 0006-2960
PubMed: 8608116
DOI: 10.1021/BI952443Z
Page generated: Tue Dec 15 05:44:51 2020

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