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Sodium in PDB 131d: The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove

Protein crystallography data

The structure of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove, PDB code: 131d was solved by D.Bancroft, L.D.Williams, A.Rich, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 1.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 18.265, 30.690, 42.460, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove (pdb code 131d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove, PDB code: 131d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 131d

Go back to Sodium Binding Sites List in 131d
Sodium binding site 1 out of 2 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na15

b:22.8
occ:1.00
OP1 A:DC5 2.7 14.2 1.0
O A:HOH18 2.8 30.1 1.0
O A:HOH21 2.9 26.7 1.0
O A:HOH17 2.9 12.1 1.0
O A:HOH20 3.0 18.6 1.0
O A:HOH19 3.0 12.7 1.0
O A:HOH72 3.3 37.2 1.0
P A:DC5 4.1 11.4 1.0
NA A:NA16 4.3 28.3 1.0
O3' A:DG4 4.5 10.6 1.0
OP2 A:DC5 5.0 15.1 1.0

Sodium binding site 2 out of 2 in 131d

Go back to Sodium Binding Sites List in 131d
Sodium binding site 2 out of 2 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na16

b:28.3
occ:1.00
O A:HOH23 2.6 31.3 1.0
O A:HOH24 2.7 33.6 1.0
O A:HOH18 2.8 30.1 1.0
OP2 A:DC5 2.8 15.1 1.0
O A:HOH22 2.8 21.8 1.0
O3' A:DG4 2.8 10.6 1.0
P A:DC5 2.9 11.4 1.0
OP1 A:DC5 3.0 14.2 1.0
O A:HOH17 3.9 12.1 1.0
C4' A:DG4 4.0 7.5 1.0
C3' A:DG4 4.0 8.4 1.0
C5' A:DG4 4.1 8.1 1.0
NA A:NA15 4.3 22.8 1.0
O5' A:DC5 4.6 8.3 1.0
O A:HOH66 4.6 23.3 1.0
O A:HOH72 4.7 37.2 1.0
O5' A:DG4 4.8 9.3 1.0
O A:HOH21 4.9 26.7 1.0

Reference:

D.Bancroft, L.D.Williams, A.Rich, M.Egli. The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove. Biochemistry V. 33 1073 1994.
ISSN: ISSN 0006-2960
PubMed: 8110738
DOI: 10.1021/BI00171A005
Page generated: Tue Dec 15 05:21:32 2020

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