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Sodium in PDB 3gnk: Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4

Protein crystallography data

The structure of Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4, PDB code: 3gnk was solved by A.Naseer, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.35 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.970, 24.170, 73.890, 90.00, 110.37, 90.00
R / Rfree (%) 21.4 / 30.6

Other elements in 3gnk:

The structure of Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 (pdb code 3gnk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4, PDB code: 3gnk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3gnk

Go back to Sodium Binding Sites List in 3gnk
Sodium binding site 1 out of 2 in the Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na106

b:15.0
occ:1.00
O A:HOH182 2.1 18.8 1.0
O B:HOH108 2.2 10.1 1.0
O B:HOH181 2.3 23.3 1.0
O B:HOH105 2.4 15.9 1.0
O B:HOH107 2.6 11.6 1.0
O4' B:DG13 3.9 19.0 1.0
N2 A:DG9 4.1 9.2 1.0
N3 B:DG13 4.2 15.5 1.0
O B:HOH101 4.4 8.4 1.0
C4' B:DG13 4.5 20.1 1.0
O B:HOH183 4.5 24.5 1.0
O4' B:DG14 4.5 21.4 1.0
O A:HOH100 4.6 5.9 1.0
N2 B:DG13 4.6 15.9 1.0
O2 B:DC12 4.7 12.8 1.0
O B:HOH103 4.8 14.5 1.0
C1' B:DG13 4.8 17.2 1.0
C2 B:DG13 4.8 15.9 1.0
O B:HOH109 4.9 16.5 1.0
C5' B:DG14 5.0 23.0 1.0

Sodium binding site 2 out of 2 in 3gnk

Go back to Sodium Binding Sites List in 3gnk
Sodium binding site 2 out of 2 in the Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na42

b:19.7
occ:1.00
O A:HOH126 2.4 9.2 1.0
O D:HOH165 2.5 16.8 1.0
O D:HOH125 2.7 10.1 1.0
O D:HOH41 3.0 6.9 1.0
C5' D:DG36 3.6 14.2 1.0
O C:HOH144 3.8 25.4 1.0
C5 A:DC2 4.0 12.9 1.0
O C:HOH176 4.1 28.4 1.0
O A:HOH44 4.3 5.2 1.0
C4' D:DG36 4.3 13.7 1.0
OP2 D:DC37 4.5 13.3 1.0
C6 A:DC2 4.5 13.2 1.0
O5' A:DT1 4.5 12.7 1.0
O D:HOH130 4.6 37.3 1.0
N4 D:DC38 4.6 12.1 1.0
O3' D:DC35 4.7 17.9 1.0
OP1 D:DG36 4.8 17.9 1.0
O5' D:DG36 4.8 16.2 1.0
O D:HOH177 4.8 29.3 1.0
O6 A:DG3 4.9 12.8 1.0
O A:HOH55 5.0 9.0 1.0

Reference:

A.Naseer, C.J.Cardin. Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 To Be Published.
Page generated: Tue Dec 15 06:12:35 2020

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