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Calcium in PDB 2gw0: A D(Tggggt)- Sodium and Calcium Complex.

Protein crystallography data

The structure of A D(Tggggt)- Sodium and Calcium Complex., PDB code: 2gw0 was solved by M.P.H.Lee, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 27.357, 27.911, 34.969, 89.11, 75.63, 79.70
R / Rfree (%) 17.4 / 22.4

Other elements in 2gw0:

The structure of A D(Tggggt)- Sodium and Calcium Complex. also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the A D(Tggggt)- Sodium and Calcium Complex. (pdb code 2gw0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the A D(Tggggt)- Sodium and Calcium Complex., PDB code: 2gw0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 1 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca54

b:13.6
occ:1.00
 O6 B:DG9 2.6 9.5 1.0
O6 C:DG15 2.7 10.5 1.0
O6 A:DG3 2.7 7.3 1.0
O6 D:DG21 2.7 7.3 1.0
O6 B:DG8 2.9 8.6 1.0
O6 D:DG20 2.9 10.4 1.0
O6 C:DG14 2.9 8.2 1.0
O6 A:DG2 3.0 8.6 1.0
CA A:CA55 3.5 14.4 1.0
CA D:CA53 3.6 19.4 1.0
C6 B:DG9 3.6 9.0 1.0
C6 C:DG15 3.7 13.3 1.0
C6 D:DG20 3.7 9.3 1.0
C6 D:DG21 3.7 6.9 1.0
C6 B:DG8 3.7 7.8 1.0
C6 C:DG14 3.7 7.3 1.0
C6 A:DG3 3.7 7.7 1.0
C6 A:DG2 3.8 7.0 1.0
N1 C:DG15 4.0 12.1 1.0
N1 D:DG21 4.0 9.8 1.0
N1 D:DG20 4.0 5.6 1.0
N1 B:DG9 4.0 8.8 1.0
N1 C:DG14 4.0 6.5 1.0
N1 B:DG8 4.0 8.8 1.0
N1 A:DG2 4.1 7.2 1.0
N1 A:DG3 4.1 9.1 1.0
C5 D:DG20 4.8 8.1 1.0
C5 C:DG14 4.8 9.0 1.0
C5 B:DG8 4.8 10.2 1.0
C5 A:DG2 4.9 3.6 1.0
C5 B:DG9 4.9 10.0 1.0
C5 C:DG15 4.9 8.2 1.0
C5 D:DG21 4.9 11.7 1.0
C5 A:DG3 5.0 9.1 1.0

Calcium binding site 2 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 2 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca55

b:14.4
occ:1.00
 O6 C:DG14 2.6 8.2 1.0
O6 B:DG8 2.7 8.6 1.0
O6 D:DG20 2.7 10.4 1.0
O6 F:DG32 2.8 8.9 1.0
O6 E:DG26 2.8 7.6 1.0
O6 A:DG2 2.8 8.6 1.0
O6 G:DG38 2.8 11.3 1.0
O6 H:DG44 2.8 11.0 1.0
NA F:NA50 3.3 9.6 1.0
CA A:CA54 3.5 13.6 1.0
C6 C:DG14 3.6 7.3 1.0
C6 E:DG26 3.6 6.6 1.0
C6 F:DG32 3.6 9.5 1.0
C6 G:DG38 3.6 14.1 1.0
C6 H:DG44 3.6 9.8 1.0
C6 D:DG20 3.7 9.3 1.0
C6 B:DG8 3.7 7.8 1.0
C6 A:DG2 3.8 7.0 1.0
N1 E:DG26 3.9 6.0 1.0
N1 C:DG14 3.9 6.5 1.0
N1 F:DG32 3.9 6.8 1.0
N1 H:DG44 3.9 5.8 1.0
N1 G:DG38 3.9 8.0 1.0
N1 D:DG20 4.0 5.6 1.0
N1 B:DG8 4.0 8.8 1.0
N1 A:DG2 4.1 7.2 1.0
C5 F:DG32 4.8 11.6 1.0
C5 E:DG26 4.8 10.9 1.0
C5 C:DG14 4.8 9.0 1.0
C5 G:DG38 4.8 11.2 1.0
C5 H:DG44 4.9 10.6 1.0
C5 D:DG20 4.9 8.1 1.0
C5 B:DG8 5.0 10.2 1.0

Calcium binding site 3 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 3 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca59

b:10.5
occ:1.00
 O A:HOH88 2.3 11.8 1.0
O D:HOH84 2.3 16.6 1.0
O D:HOH87 2.4 8.4 1.0
O F:HOH86 2.5 14.3 1.0
O D:HOH85 2.5 17.0 1.0
O A:HOH83 2.5 9.3 1.0
N2 A:DG2 4.2 9.9 1.0
OP2 D:DG20 4.2 8.7 1.0
O D:HOH125 4.3 15.9 1.0
OP1 D:DG20 4.4 10.7 1.0
O F:HOH181 4.4 21.9 1.0
O4' A:DG3 4.5 15.5 1.0
N2 F:DG32 4.5 8.4 1.0
O E:HOH162 4.5 21.1 1.0
O E:HOH108 4.5 12.0 1.0
O4' F:DG33 4.6 14.9 1.0
O D:HOH160 4.7 25.8 1.0
C4' A:DG3 4.8 6.9 1.0
N3 A:DG2 4.8 9.9 1.0
P D:DG20 4.9 10.9 1.0
N3 F:DG32 4.9 8.0 1.0
C4' F:DG33 5.0 13.2 1.0
C2 A:DG2 5.0 11.5 1.0

Calcium binding site 4 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 4 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca60

b:14.9
occ:1.00
 O A:HOH95 2.3 14.5 1.0
O B:HOH94 2.3 13.4 1.0
O B:HOH92 2.4 12.1 1.0
O A:HOH90 2.4 14.3 1.0
O A:HOH91 2.4 20.9 1.0
O A:HOH93 2.4 13.9 1.0
O B:HOH89 2.5 20.5 1.0
OP2 A:DG4 4.3 16.1 1.0
O3' B:DG11 4.3 12.7 1.0
C4' B:DG11 4.4 9.2 1.0
OP1 A:DG3 4.5 14.5 1.0
OP2 A:DG3 4.6 16.1 1.0
O A:HOH133 4.6 13.6 1.0
OP1 B:DT12 4.9 17.2 1.0
P A:DG3 4.9 10.2 1.0
C3' B:DG11 5.0 12.9 1.0

Calcium binding site 5 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 5 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca56

b:10.9
occ:1.00
 O A:HOH67 2.4 15.0 1.0
O B:HOH68 2.4 10.0 1.0
O E:HOH65 2.4 10.6 1.0
O A:HOH64 2.5 9.4 1.0
O A:HOH191 2.5 28.2 1.0
O A:HOH63 2.5 9.9 1.0
O E:HOH66 2.6 21.2 1.0
N2 B:DG8 4.3 8.4 1.0
OP2 A:DG2 4.3 9.1 1.0
O B:HOH110 4.3 17.4 1.0
OP1 A:DG2 4.4 7.8 1.0
N2 E:DG26 4.4 8.4 1.0
O H:HOH223 4.4 37.3 1.0
O A:HOH128 4.5 16.0 1.0
O4' B:DG9 4.5 11.5 1.0
O4' E:DG27 4.6 12.0 1.0
N3 B:DG8 4.8 6.2 1.0
O E:HOH173 4.8 20.1 1.0
P A:DG2 4.9 9.5 1.0
O E:HOH143 4.9 22.6 1.0
N3 E:DG26 4.9 6.8 1.0
C4' B:DG9 5.0 11.1 1.0

Calcium binding site 6 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 6 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca57

b:12.1
occ:1.00
 O C:HOH74 2.4 12.6 1.0
O B:HOH73 2.4 12.5 1.0
O B:HOH70 2.4 14.9 1.0
O B:HOH71 2.5 14.3 1.0
O H:HOH72 2.5 12.0 1.0
O B:HOH69 2.5 10.8 1.0
N2 H:DG44 4.3 8.4 1.0
OP2 B:DG8 4.4 11.6 1.0
OP1 B:DG8 4.4 13.2 1.0
O C:HOH111 4.4 16.8 1.0
N2 C:DG14 4.5 7.7 1.0
O5' B:DT7 4.5 18.9 1.0
O4' C:DG15 4.6 9.3 1.0
O4' H:DG45 4.7 20.8 1.0
N3 H:DG44 4.8 8.0 1.0
O G:HOH158 4.8 23.2 1.0
O H:HOH156 4.8 20.1 1.0
N3 C:DG14 4.9 12.1 1.0
P B:DG8 4.9 12.4 1.0

Calcium binding site 7 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 7 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca53

b:19.4
occ:1.00
 O6 D:DG22 2.5 10.4 1.0
O6 C:DG16 2.5 10.4 1.0
O6 B:DG10 2.6 8.0 1.0
O6 A:DG4 2.6 9.9 1.0
O6 A:DG3 3.0 7.3 1.0
O6 D:DG21 3.1 7.3 1.0
O6 B:DG9 3.1 9.5 1.0
O6 C:DG15 3.2 10.5 1.0
C6 D:DG22 3.4 9.3 1.0
C6 C:DG16 3.5 9.5 1.0
C6 B:DG10 3.6 10.3 1.0
CA A:CA54 3.6 13.6 1.0
C6 A:DG4 3.6 6.6 1.0
C6 A:DG3 3.8 7.7 1.0
N1 D:DG22 3.8 14.4 1.0
C6 D:DG21 3.8 6.9 1.0
N1 B:DG10 3.9 9.4 1.0
C6 B:DG9 3.9 9.0 1.0
N1 C:DG16 3.9 10.7 1.0
N1 A:DG4 3.9 8.7 1.0
C6 C:DG15 3.9 13.3 1.0
N1 A:DG3 4.1 9.1 1.0
N1 D:DG21 4.2 9.8 1.0
N1 B:DG9 4.2 8.8 1.0
N1 C:DG15 4.2 12.1 1.0
NA A:NA49 4.4 13.6 1.0
C5 D:DG22 4.7 11.1 1.0
C5 C:DG16 4.8 10.7 1.0
C5 B:DG10 4.9 11.2 1.0
O6 C:DG17 4.9 11.5 1.0
C5 A:DG4 4.9 11.2 1.0
C5 A:DG3 4.9 9.1 1.0
O6 B:DG11 4.9 7.9 1.0
C5 D:DG21 4.9 11.7 1.0
C5 B:DG9 5.0 10.0 1.0
O6 D:DG23 5.0 11.7 1.0

Calcium binding site 8 out of 8 in 2gw0

Go back to Calcium Binding Sites List in 2gw0
Calcium binding site 8 out of 8 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca58

b:11.5
occ:1.00
 O C:HOH82 2.3 25.2 1.0
O C:HOH78 2.4 17.9 1.0
O D:HOH75 2.4 11.3 1.0
O G:HOH76 2.4 13.3 1.0
O D:HOH77 2.5 21.7 1.0
O D:HOH80 2.5 14.2 1.0
O D:HOH81 2.5 17.9 1.0
O C:HOH79 2.6 9.6 1.0
N2 G:DG38 4.3 9.2 1.0
O F:HOH224 4.3 28.2 1.0
O D:HOH184 4.3 32.0 1.0
N2 D:DG20 4.4 8.8 1.0
OP2 C:DG14 4.4 15.2 1.0
O D:HOH129 4.4 18.1 1.0
O4' D:DG21 4.5 9.3 1.0
O4' G:DG39 4.5 12.0 1.0
OP1 C:DG14 4.5 14.3 1.0
O G:HOH149 4.7 31.1 1.0
C4' D:DG21 4.8 9.2 1.0
N3 G:DG38 4.8 9.3 1.0
O C:HOH153 4.9 21.5 1.0
N3 D:DG20 4.9 7.3 1.0
O C:HOH233 4.9 33.8 1.0
P C:DG14 5.0 17.7 1.0

Reference:

M.P.Lee, G.N.Parkinson, P.Hazel, S.Neidle. Observation of the Coexistence of Sodium and Calcium Ions in A Dna G-Quadruplex Ion Channel. J.Am.Chem.Soc. V. 129 10106 2007.
ISSN: ISSN 0002-7863
PubMed: 17661470
DOI: 10.1021/JA0740869
Page generated: Fri Jul 12 12:43:10 2024

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