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Sodium in PDB 1l4j: Holliday Junction Tcggtaccga with Na and Ca Binding Sites.

Protein crystallography data

The structure of Holliday Junction Tcggtaccga with Na and Ca Binding Sites., PDB code: 1l4j was solved by J.H.Thorpe, B.C.Gale, S.C.M.Teixeira, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 66.067, 23.775, 73.816, 90.00, 110.58, 90.00
R / Rfree (%) 22.8 / 29.7

Other elements in 1l4j:

The structure of Holliday Junction Tcggtaccga with Na and Ca Binding Sites. also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites. (pdb code 1l4j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites., PDB code: 1l4j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1l4j

Go back to Sodium Binding Sites List in 1l4j
Sodium binding site 1 out of 2 in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Holliday Junction Tcggtaccga with Na and Ca Binding Sites. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na105

b:23.8
occ:1.00
O C:HOH610 2.1 25.2 1.0
O D:HOH611 2.2 23.0 1.0
O D:HOH613 2.6 38.5 1.0
O C:HOH612 2.6 26.7 1.0
O D:HOH614 3.0 34.7 1.0
O D:HOH506 4.2 22.7 1.0
O2 C:DC27 4.3 23.3 1.0
O D:HOH516 4.4 27.2 1.0
O C:HOH599 4.4 26.1 1.0
O C:HOH568 4.5 21.5 1.0
O2 D:DT35 4.6 23.0 1.0
O4' D:DA36 4.6 25.6 1.0
O D:HOH560 4.7 33.2 1.0
C4' D:DA36 4.8 22.6 1.0
O D:HOH600 4.9 20.9 1.0
C5' C:DC28 5.0 19.3 1.0

Sodium binding site 2 out of 2 in 1l4j

Go back to Sodium Binding Sites List in 1l4j
Sodium binding site 2 out of 2 in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Holliday Junction Tcggtaccga with Na and Ca Binding Sites. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na106

b:30.4
occ:1.00
O B:HOH659 2.3 26.8 1.0
O D:HOH651 2.4 27.8 1.0
O D:HOH660 2.5 42.2 1.0
O A:HOH627 2.6 25.3 1.0
O D:HOH628 2.7 30.3 1.0
N4 D:DC37 4.3 21.8 1.0
OP1 D:DA36 4.3 22.2 1.0
OP2 D:DA36 4.5 25.7 1.0
O6 A:DG4 4.6 22.7 1.0
N7 A:DG3 4.7 20.2 1.0
N6 B:DA16 4.9 22.0 1.0
C8 A:DG3 4.9 17.5 1.0
P D:DA36 4.9 23.1 1.0

Reference:

J.H.Thorpe, B.C.Gale, S.C.M.Teixeira, C.J.Cardin. Conformational and Hydration Effects of Site-Selective Sodium, Calcium and Strontium Ion Binding to the Dna Holliday Junction Structure D(Tcggtaccga)4 J.Mol.Biol. V. 327 97 2003.
ISSN: ISSN 0022-2836
PubMed: 12614611
DOI: 10.1016/S0022-2836(03)00088-3
Page generated: Tue Dec 15 05:29:15 2020

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