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

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

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

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites., PDB code: 1l4j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca101 b:19.2 occ:1.00 O A:HOH543 2.1 21.6 1.0 O A:HOH542 2.3 28.4 1.0 O A:HOH540 2.4 18.6 1.0 O D:HOH544 2.4 21.1 1.0 O D:HOH502 2.5 15.6 1.0 O A:HOH541 2.5 16.7 1.0 O A:HOH503 2.7 18.6 1.0 O4' A:DG3 4.2 22.2 1.0 N2 D:DG39 4.4 18.1 1.0 O D:HOH539 4.4 19.1 1.0 O A:HOH580 4.5 21.4 1.0 C4' A:DG3 4.5 24.1 1.0 O A:HOH605 4.5 33.8 1.0 O A:HOH526 4.6 22.1 1.0 O D:HOH520 4.6 46.5 1.0 N3 A:DG3 4.6 18.0 1.0 O A:HOH501 4.6 17.6 1.0 O2 A:DC2 4.7 13.9 1.0 N2 A:DG3 4.7 15.5 1.0 O D:HOH644 4.7 32.7 1.0 O4' A:DG4 4.8 19.2 1.0 O D:HOH510 4.8 19.1 1.0

Calcium binding site 2 out of 4 in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca102 b:28.4 occ:1.00 O B:HOH592 2.2 24.1 1.0 O B:HOH591 2.4 14.6 1.0 O B:HOH589 2.4 30.8 1.0 O B:HOH512 2.5 12.3 0.5 O B:HOH590 2.5 33.1 1.0 O A:HOH588 2.6 21.9 1.0 O A:HOH577 2.7 20.1 1.0 O4' B:DG13 3.9 25.5 1.0 O B:HOH621 4.1 31.1 1.0 N2 A:DG9 4.2 14.2 1.0 C4' B:DG13 4.3 30.6 1.0 N3 B:DG13 4.4 17.9 1.0 O A:HOH527 4.5 17.5 1.0 O B:HOH622 4.5 19.8 1.0 O B:HOH508 4.5 15.7 1.0 O4' B:DG14 4.6 30.0 1.0 O2 B:DC12 4.7 15.5 1.0 O A:HOH576 4.7 15.2 1.0 C5' B:DG14 4.8 31.6 1.0 O B:HOH552 4.8 21.0 1.0 N2 B:DG13 4.8 14.2 1.0 C1' B:DG13 4.8 26.3 1.0 C4' B:DG14 5.0 31.8 1.0 C2 B:DG13 5.0 16.9 1.0

Calcium binding site 3 out of 4 in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Holliday Junction Tcggtaccga with Na and Ca Binding Sites. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca104 b:29.2 occ:1.00 O C:HOH584 2.2 33.4 1.0 O B:HOH538 2.4 20.3 1.0 O C:HOH583 2.4 22.9 1.0 O C:HOH582 2.4 26.1 1.0 O C:HOH531 2.4 24.0 1.0 O C:HOH587 2.4 34.0 1.0 O4' C:DG23 3.8 29.2 1.0 N3 C:DG23 4.2 21.5 1.0 N2 B:DG19 4.3 21.9 1.0 C4' C:DG23 4.3 29.0 1.0 O B:HOH565 4.4 19.0 1.0 O C:HOH534 4.4 33.5 1.0 O2 C:DC22 4.6 20.2 1.0 O C:HOH537 4.7 29.9 1.0 N2 C:DG23 4.7 21.9 1.0 C1' C:DG23 4.7 25.0 1.0 C2 C:DG23 4.8 22.2 1.0 O B:HOH641 4.9 19.6 1.0 O C:HOH596 4.9 29.3 1.0 O B:HOH530 4.9 21.5 1.0 O4' C:DG24 4.9 24.4 1.0

Calcium binding site 4 out of 4 in the Holliday Junction Tcggtaccga with Na and Ca Binding Sites.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Holliday Junction Tcggtaccga with Na and Ca Binding Sites. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca103 b:22.7 occ:1.00 O D:HOH572 2.2 37.8 1.0 O D:HOH585 2.3 21.8 1.0 O C:HOH570 2.3 22.2 1.0 O D:HOH581 2.4 21.6 1.0 O C:HOH571 2.4 22.0 1.0 O D:HOH586 2.5 24.4 1.0 O D:HOH515 2.6 20.5 1.0 O4' D:DG33 4.0 26.7 1.0 N2 C:DG29 4.3 13.8 1.0 O D:HOH604 4.3 26.7 1.0 O D:HOH569 4.4 20.9 1.0 C4' D:DG33 4.5 30.5 1.0 N3 D:DG33 4.5 23.9 1.0 O D:HOH648 4.6 29.3 1.0 O C:HOH573 4.6 19.7 1.0 O C:HOH557 4.6 20.7 1.0 O2 D:DC32 4.7 16.9 1.0 O4' D:DG34 4.8 25.1 1.0 N2 D:DG33 4.9 18.9 1.0

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