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Calcium in PDB 352d: The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution

Protein crystallography data

The structure of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution, PDB code: 352d was solved by K.Phillips, Z.Dauter, A.I.H.Murchie, D.M.J.Lilley, B.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 0.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 28.280, 34.780, 56.230, 74.31, 77.68, 89.81
R / Rfree (%) 15.2 / n/a

Other elements in 352d:

The structure of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution also contains other interesting chemical elements:

Sodium (Na) 14 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution (pdb code 352d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution, PDB code: 352d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 352d

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Calcium binding site 1 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca177

b:5.9
occ:1.00
 O F:HOH584 2.3 10.3 0.5
O F:HOH510 2.4 20.8 1.0
O A:HOH182 2.4 6.1 1.0
O D:HOH193 2.4 6.9 1.0
O F:HOH607 2.4 12.7 1.0
O D:HOH635 2.4 12.1 0.5
O D:HOH576 2.4 6.3 1.0
O G:HOH578 2.5 6.7 1.0
O D:HOH636 2.5 18.4 0.5
OP2 D:DG32 4.2 8.0 1.0
OP1 D:DG32 4.4 6.5 1.0
O F:HOH229 4.4 6.0 1.0
N2 G:DG62 4.4 5.7 1.0
N2 A:DG2 4.4 4.8 1.0
O4' A:DG3 4.4 6.0 1.0
O4' G:DG63 4.5 7.6 1.0
O F:HOH585 4.5 12.6 1.0
O G:HOH340 4.6 21.8 1.0
O A:HOH292 4.6 14.8 1.0
N3 A:DG2 4.8 4.3 1.0
C4' A:DG3 4.8 6.0 1.0
N3 G:DG62 4.8 5.6 1.0
P D:DG32 4.9 6.3 1.0
C5' A:DG3 5.0 6.0 1.0
O G:HOH184 5.0 14.1 1.0
C4' G:DG63 5.0 8.3 1.0

Calcium binding site 2 out of 9 in 352d

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Calcium binding site 2 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca179

b:8.6
occ:1.00
 O D:HOH594 2.3 12.4 1.0
O D:HOH268 2.4 11.6 1.0
O D:HOH227 2.4 10.8 1.0
O D:HOH282 2.4 12.8 1.0
O D:HOH225 2.4 8.9 1.0
O A:HOH459 2.4 13.0 1.0
O3' A:DG5 4.3 7.8 1.0
OP2 D:DG34 4.3 9.8 1.0
C4' A:DG5 4.4 6.9 1.0
OP1 D:DG33 4.6 9.5 1.0
O D:HOH241 4.6 9.8 1.0
OP2 D:DG33 4.7 8.7 1.0
OP1 A:DT6 4.9 11.4 1.0
C5' A:DG5 5.0 6.8 1.0

Calcium binding site 3 out of 9 in 352d

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Calcium binding site 3 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca178

b:4.9
occ:1.00
 O B:HOH574 2.4 5.3 1.0
O A:HOH180 2.4 5.6 1.0
O E:HOH215 2.4 6.8 1.0
O A:HOH572 2.4 7.0 1.0
O A:HOH580 2.4 7.8 1.0
O F:HOH190 2.4 4.9 1.0
O B:HOH181 2.5 4.9 1.0
OP2 A:DG2 4.2 8.2 1.0
O B:HOH206 4.2 7.5 1.0
O A:HOH271 4.4 9.3 1.0
N2 F:DG52 4.4 5.0 1.0
N2 B:DG12 4.4 4.3 1.0
O I:HOH219 4.5 4.6 1.0
O4' B:DG13 4.5 5.6 1.0
O E:HOH224 4.5 6.7 1.0
O A:HOH246 4.5 8.0 1.0
O4' F:DG53 4.5 5.3 1.0
OP1 A:DG2 4.5 8.2 1.0
O5' E:DT41 4.8 6.6 1.0
C5' B:DG13 4.8 8.8 0.6
C4' B:DG13 4.8 7.3 1.0
N3 F:DG52 4.8 4.3 1.0
N3 B:DG12 4.8 4.1 1.0
P A:DG2 4.9 6.5 1.0
O E:HOH365 4.9 12.2 1.0
O I:HOH274 4.9 8.6 1.0
C4' F:DG53 5.0 5.9 1.0

Calcium binding site 4 out of 9 in 352d

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Calcium binding site 4 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca176

b:6.3
occ:1.00
 O C:HOH376 2.3 17.6 1.0
O B:HOH608 2.3 13.0 1.0
O B:HOH210 2.4 6.8 1.0
O C:HOH188 2.4 7.0 1.0
O E:HOH513 2.4 12.1 1.0
O E:HOH194 2.4 7.0 1.0
O B:HOH570 2.5 6.1 1.0
OP2 B:DG12 4.3 7.3 1.0
N2 E:DG42 4.3 5.7 1.0
O4' C:DG23 4.4 7.0 1.0
N2 C:DG22 4.4 4.4 1.0
O H:HOH265 4.4 12.5 1.0
OP1 B:DG12 4.5 7.0 1.0
O4' E:DG43 4.5 7.5 1.0
O H:HOH284 4.6 22.8 1.0
O E:HOH439 4.6 15.8 1.0
O B:HOH275 4.6 11.8 1.0
O C:HOH289 4.6 11.4 1.0
C4' C:DG23 4.7 7.0 1.0
O B:HOH326 4.7 9.5 1.0
N3 E:DG42 4.8 4.9 1.0
N3 C:DG22 4.8 4.7 1.0
P B:DG12 4.9 6.2 1.0
C5' C:DG23 5.0 6.9 1.0

Calcium binding site 5 out of 9 in 352d

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Calcium binding site 5 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca174

b:6.3
occ:1.00
 O G:HOH253 2.3 8.8 1.0
O2 G:DT61 2.4 11.6 1.0
O G:HOH593 2.4 12.3 1.0
C2 G:DT61 3.6 10.3 1.0
N3 G:DT61 4.3 9.3 1.0
N1 G:DT61 4.5 13.6 1.0
O D:HOH238 4.6 14.9 1.0

Calcium binding site 6 out of 9 in 352d

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Calcium binding site 6 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca172

b:7.7
occ:1.00
 O O:HOH620 2.3 21.6 1.0
O O:HOH714 2.3 18.3 1.0
O O:HOH597 2.4 14.3 1.0
O P:HOH189 2.4 7.8 1.0
O O:HOH198 2.4 8.2 1.0
O P:HOH195 2.4 6.8 1.0
O K:HOH221 2.5 8.3 1.0
O K:HOH586 2.5 15.4 1.0
OP2 O:DG142 4.3 10.9 1.0
O4' P:DG153 4.4 6.5 1.0
OP1 O:DG142 4.4 11.8 1.0
O O:HOH610 4.4 25.7 1.0
N2 K:DG102 4.4 6.2 1.0
N2 P:DG152 4.4 5.1 1.0
O P:HOH267 4.5 9.6 1.0
O O:HOH626 4.5 36.3 1.0
O4' K:DG103 4.5 9.8 1.0
O O:HOH280 4.5 14.2 1.0
O P:HOH403 4.6 17.1 1.0
C4' P:DG153 4.7 7.2 1.0
O O:HOH373 4.7 14.7 1.0
N3 P:DG152 4.8 5.0 1.0
N3 K:DG102 4.9 6.3 1.0
P O:DG142 4.9 9.1 1.0
C4' K:DG103 5.0 11.8 1.0

Calcium binding site 7 out of 9 in 352d

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Calcium binding site 7 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca171

b:5.5
occ:1.00
 O P:HOH520 2.3 10.4 1.0
O M:HOH202 2.4 5.5 1.0
O I:HOH565 2.4 8.8 1.0
O P:HOH209 2.4 6.2 1.0
O E:HOH579 2.4 8.7 1.0
O J:HOH571 2.4 6.0 1.0
O M:HOH569 2.4 5.9 1.0
O E:HOH622 4.3 20.7 1.0
N2 M:DG122 4.3 4.8 1.0
O M:HOH207 4.3 6.1 1.0
O P:HOH234 4.3 10.9 1.0
O4' M:DG123 4.4 5.6 1.0
N2 J:DG92 4.4 6.0 1.0
OP2 P:DG152 4.4 6.4 1.0
OP1 P:DG152 4.4 6.6 1.0
O P:HOH185 4.4 12.8 1.0
O E:HOH411 4.5 13.0 1.0
O4' J:DG93 4.5 7.2 1.0
O I:HOH583 4.6 11.2 1.0
N3 M:DG122 4.7 5.0 1.0
C4' M:DG123 4.7 6.1 1.0
N3 J:DG92 4.8 5.5 1.0
O I:HOH272 4.8 11.9 1.0
O I:HOH317 4.8 10.6 1.0
P P:DG152 4.9 6.0 1.0
C5' M:DG123 4.9 5.5 1.0
C4' J:DG93 5.0 6.7 1.0

Calcium binding site 8 out of 9 in 352d

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Calcium binding site 8 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca173

b:5.7
occ:1.00
 O M:HOH599 2.3 16.3 1.0
O M:HOH581 2.4 10.6 1.0
O N:HOH183 2.4 5.8 1.0
O M:HOH211 2.4 6.0 1.0
O M:HOH192 2.4 5.5 1.0
O I:HOH186 2.5 5.7 1.0
O M:HOH694 2.5 13.1 1.0
O M:HOH718 2.6 14.8 1.0
O M:HOH567 3.7 35.1 0.5
OP2 M:DG122 4.3 6.3 1.0
OP1 M:DG122 4.4 5.8 1.0
N2 I:DG82 4.4 5.4 1.0
N2 N:DG132 4.4 4.7 1.0
O N:HOH252 4.4 8.3 1.0
O4' N:DG133 4.5 5.2 1.0
O4' I:DG83 4.5 6.8 1.0
O M:HOH645 4.5 24.9 1.0
O M:HOH566 4.6 11.6 0.5
O M:HOH370 4.6 21.3 1.0
O L:HOH402 4.6 23.2 1.0
N3 N:DG132 4.8 4.4 1.0
C4' N:DG133 4.8 5.1 1.0
N3 I:DG82 4.8 4.8 1.0
P M:DG122 4.9 5.2 1.0
C5' N:DG133 5.0 5.7 1.0

Calcium binding site 9 out of 9 in 352d

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Calcium binding site 9 out of 9 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca175

b:7.3
occ:1.00
 O K:HOH228 2.4 11.1 1.0
O K:HOH418 4.6 24.3 1.0

Reference:

K.Phillips, Z.Dauter, A.I.Murchie, D.M.Lilley, B.Luisi. The Crystal Structure of A Parallel-Stranded Guanine Tetraplex at 0.95 A Resolution. J.Mol.Biol. V. 273 171 1997.
ISSN: ISSN 0022-2836
PubMed: 9367755
DOI: 10.1006/JMBI.1997.1292
Page generated: Sat Jul 13 07:02:22 2024

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