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Calcium in PDB 244d: The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex

Protein crystallography data

The structure of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex, PDB code: 244d was solved by G.Laughlan, A.I.H.Murchie, D.G.Norman, M.H.Moore, P.C.E.Moody, 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) 8.00 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 28.760, 35.470, 56.770, 74.39, 77.64, 89.73
R / Rfree (%) 12.4 / 17.6

Other elements in 244d:

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

Sodium (Na) 14 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex (pdb code 244d). 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 High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex, PDB code: 244d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 244d

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


Mono view


Stereo pair view

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

b:8.4
occ:1.00
 O D:HOH420 2.4 23.2 1.0
O A:HOH182 2.4 8.1 1.0
O D:HOH321 2.4 21.1 1.0
O D:HOH196 2.4 8.7 1.0
O D:HOH300 2.4 19.1 1.0
O D:HOH339 2.4 22.0 1.0
O D:HOH186 2.5 8.6 1.0
O G:HOH185 2.5 9.3 1.0
OP2 D:DG32 4.3 9.6 1.0
OP1 D:DG32 4.4 8.9 1.0
O F:HOH235 4.4 11.0 1.0
N2 A:DG2 4.5 5.8 1.0
N2 G:DG62 4.5 7.3 1.0
O F:HOH600 4.5 37.3 1.0
O4' A:DG3 4.5 7.7 1.0
O F:HOH357 4.6 28.7 1.0
O4' G:DG63 4.6 10.2 1.0
O D:HOH595 4.7 35.7 1.0
O D:HOH303 4.8 26.2 1.0
O D:HOH341 4.8 27.9 1.0
P D:DG32 4.9 7.8 1.0
N3 A:DG2 4.9 5.4 1.0
N3 G:DG62 4.9 7.0 1.0
C4' A:DG3 4.9 7.8 1.0
O G:HOH302 4.9 23.2 1.0

Calcium binding site 2 out of 9 in 244d

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


Mono view


Stereo pair view

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

b:11.1
occ:1.00
 O D:HOH292 2.4 17.1 1.0
O D:HOH233 2.4 16.1 1.0
O D:HOH227 2.4 13.1 1.0
O D:HOH276 2.5 16.7 1.0
O A:HOH323 2.5 16.6 1.0
O D:HOH298 2.5 16.9 1.0
O D:HOH231 2.5 12.5 1.0
OP2 D:DG34 4.4 13.6 1.0
O3' A:DG5 4.5 10.8 1.0
OP1 D:DG33 4.5 11.0 1.0
C4' A:DG5 4.5 10.0 1.0
O D:HOH248 4.7 13.9 1.0
OP1 A:DT6 4.8 14.5 1.0
OP2 D:DG33 4.8 10.4 1.0
O D:HOH512 4.9 38.4 1.0

Calcium binding site 3 out of 9 in 244d

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


Mono view


Stereo pair view

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

b:7.1
occ:1.00
 O A:HOH180 2.4 8.3 1.0
O B:HOH193 2.4 7.6 1.0
O A:HOH266 2.4 14.7 1.0
O E:HOH220 2.4 10.3 1.0
O I:HOH218 2.4 12.2 1.0
O F:HOH183 2.5 7.5 1.0
O A:HOH181 2.5 7.5 1.0
O B:HOH210 4.3 12.4 1.0
OP2 A:DG2 4.3 10.5 1.0
N2 F:DG52 4.4 6.4 1.0
N2 B:DG12 4.5 6.8 1.0
O A:HOH279 4.5 22.6 1.0
O I:HOH224 4.5 12.8 1.0
OP1 A:DG2 4.5 9.9 1.0
O A:HOH254 4.6 17.7 1.0
O4' B:DG13 4.6 8.4 1.0
O E:HOH230 4.6 12.0 1.0
O4' F:DG53 4.6 8.0 1.0
C4' B:DG13 4.8 9.4 1.0
N3 F:DG52 4.9 5.9 1.0
O5' E:DT41 4.9 11.6 1.0
O E:HOH386 4.9 23.0 1.0
N3 B:DG12 4.9 5.6 1.0
C5' B:DG13 4.9 10.3 1.0
P A:DG2 5.0 9.2 1.0
O I:HOH282 5.0 17.5 1.0

Calcium binding site 4 out of 9 in 244d

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


Mono view


Stereo pair view

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

b:9.2
occ:1.00
 O C:HOH191 2.4 10.2 1.0
O B:HOH428 2.4 21.5 1.0
O B:HOH215 2.4 9.4 1.0
O B:HOH356 2.4 27.8 1.0
O B:HOH400 2.4 22.0 1.0
O E:HOH197 2.5 9.7 1.0
O B:HOH187 2.5 8.9 1.0
O E:HOH382 2.6 29.0 1.0
N2 E:DG42 4.4 8.2 1.0
OP2 B:DG12 4.4 9.9 1.0
N2 C:DG22 4.5 5.7 1.0
O C:HOH273 4.5 14.8 1.0
OP1 B:DG12 4.5 9.7 1.0
O4' C:DG23 4.5 9.6 1.0
O4' E:DG43 4.5 9.9 1.0
O B:HOH435 4.6 42.6 1.0
O B:HOH283 4.6 21.6 1.0
O B:HOH344 4.7 19.3 1.0
C4' C:DG23 4.8 10.6 1.0
N3 E:DG42 4.9 6.5 1.0
O E:HOH295 4.9 24.9 1.0
N3 C:DG22 4.9 5.5 1.0
P B:DG12 4.9 9.1 1.0

Calcium binding site 5 out of 9 in 244d

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca175

b:9.5
occ:1.00
 O D:HOH256 2.4 11.5 1.0
O C:HOH507 2.4 19.2 1.0
O C:HOH190 2.4 10.7 1.0
O C:HOH234 2.4 17.7 1.0
O H:HOH232 2.5 10.7 1.0
O D:HOH222 2.5 10.4 1.0
OP2 C:DG22 4.3 12.2 1.0
O D:HOH239 4.4 13.4 1.0
N2 D:DG32 4.4 7.6 1.0
N2 H:DG72 4.4 8.1 1.0
O4' D:DG33 4.5 9.8 1.0
OP1 C:DG22 4.6 13.9 1.0
O C:HOH473 4.6 31.5 1.0
O4' H:DG73 4.8 13.0 1.0
N3 D:DG32 4.8 5.6 1.0
N3 H:DG72 4.9 7.6 1.0
O H:HOH330 4.9 33.2 1.0
P C:DG22 4.9 11.3 1.0
C4' D:DG33 5.0 9.9 1.0

Calcium binding site 6 out of 9 in 244d

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca174

b:7.8
occ:1.00
 O L:HOH261 2.4 12.4 1.0
O O:HOH229 2.4 10.1 1.0
O N:HOH201 2.4 8.2 1.0
O L:HOH244 2.4 13.3 1.0
O N:HOH207 2.5 7.7 1.0
O L:HOH228 2.5 9.5 1.0
OP2 N:DG132 4.3 10.2 1.0
N2 L:DG112 4.4 7.2 1.0
O O:HOH255 4.4 14.7 1.0
N2 O:DG142 4.4 7.1 1.0
O L:HOH290 4.4 21.0 1.0
OP1 N:DG132 4.5 12.0 1.0
O4' O:DG143 4.7 8.2 1.0
O4' L:DG113 4.8 11.1 1.0
O L:HOH296 4.8 25.4 1.0
N3 O:DG142 4.8 6.3 1.0
O L:HOH360 4.8 29.7 1.0
N3 L:DG112 4.9 6.0 1.0
P N:DG132 4.9 9.4 1.0

Calcium binding site 7 out of 9 in 244d

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


Mono view


Stereo pair view

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

b:7.9
occ:1.00
 O P:HOH253 2.3 24.0 1.0
O P:HOH541 2.4 18.7 1.0
O M:HOH188 2.4 8.6 1.0
O P:HOH267 2.4 16.3 1.0
O P:HOH213 2.4 8.5 1.0
O J:HOH206 2.4 9.5 1.0
O P:HOH198 2.5 7.6 1.0
N2 J:DG92 4.4 7.4 1.0
O P:HOH534 4.4 23.8 1.0
O M:HOH211 4.4 9.9 1.0
O P:HOH240 4.4 16.9 1.0
O E:HOH613 4.5 38.5 1.0
N2 M:DG122 4.5 6.5 1.0
OP2 P:DG152 4.5 10.0 1.0
O4' M:DG123 4.5 8.3 1.0
OP1 P:DG152 4.5 11.6 1.0
O4' J:DG93 4.6 9.5 1.0
O E:HOH464 4.7 31.9 1.0
C4' M:DG123 4.8 9.3 1.0
O J:HOH331 4.8 21.3 1.0
N3 M:DG122 4.8 5.8 1.0
N3 J:DG92 4.9 7.0 1.0
O I:HOH280 4.9 19.4 1.0
C5' M:DG123 5.0 9.7 1.0
P P:DG152 5.0 8.7 1.0

Calcium binding site 8 out of 9 in 244d

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


Mono view


Stereo pair view

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

b:7.7
occ:1.00
 O M:HOH293 2.4 17.1 1.0
O N:HOH184 2.4 8.1 1.0
O M:HOH291 2.4 19.9 1.0
O M:HOH216 2.4 8.9 1.0
O M:HOH195 2.5 7.4 1.0
O I:HOH189 2.5 7.9 1.0
O M:HOH373 2.5 20.2 1.0
O M:HOH402 2.5 24.2 1.0
O M:HOH616 4.3 41.4 1.0
OP1 M:DG122 4.4 8.5 1.0
OP2 M:DG122 4.4 8.5 1.0
O L:HOH260 4.4 12.6 1.0
N2 I:DG82 4.4 6.4 1.0
N2 N:DG132 4.5 6.2 1.0
O4' N:DG133 4.5 7.8 1.0
O M:HOH558 4.6 31.8 1.0
O4' I:DG83 4.7 9.1 1.0
O L:HOH432 4.7 30.7 1.0
O M:HOH421 4.7 32.4 1.0
O M:HOH691 4.7 25.7 1.0
O I:HOH309 4.9 20.0 1.0
N3 N:DG132 4.9 5.3 1.0
P M:DG122 4.9 7.3 1.0
N3 I:DG82 4.9 5.8 1.0
C4' N:DG133 4.9 7.3 1.0

Calcium binding site 9 out of 9 in 244d

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca172

b:9.4
occ:1.00
 O P:HOH192 2.4 10.1 1.0
O O:HOH202 2.4 10.3 1.0
O O:HOH199 2.4 9.1 1.0
O O:HOH392 2.5 21.3 1.0
O K:HOH226 2.5 9.8 1.0
O P:HOH364 2.5 19.4 1.0
O O:HOH460 2.5 24.9 1.0
O O:HOH409 2.5 27.8 1.0
OP2 O:DG142 4.4 11.4 1.0
N2 K:DG102 4.4 7.8 1.0
OP1 O:DG142 4.4 10.8 1.0
O P:HOH275 4.4 14.7 1.0
O4' P:DG153 4.5 9.4 1.0
N2 P:DG152 4.5 6.6 1.0
O4' K:DG103 4.6 11.7 1.0
O O:HOH308 4.7 21.8 1.0
C4' P:DG153 4.8 10.1 1.0
O K:HOH325 4.8 25.3 1.0
O O:HOH395 4.8 27.1 1.0
O O:HOH372 4.9 21.3 1.0
N3 K:DG102 4.9 7.0 1.0
N3 P:DG152 4.9 5.9 1.0
P O:DG142 5.0 10.2 1.0

Reference:

G.Laughlan, A.I.Murchie, D.G.Norman, M.H.Moore, P.C.Moody, D.M.Lilley, B.Luisi. The High-Resolution Crystal Structure of A Parallel-Stranded Guanine Tetraplex. Science V. 265 520 1994.
ISSN: ISSN 0036-8075
PubMed: 8036494
Page generated: Sat Dec 12 03:30:32 2020

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