352D | UDF062 - JenaLib

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Description

Title :   THE CRYSTAL STRUCTURE OF A PARALLEL-STRANDED PARALLEL-STRANDED GUANINE TETRAPLEX AT 0.95 ANGSTROM RESOLUTION

Authors :   K. Phillips, Z. Dauter, A. I. H. Murchie, D. M. J. Lilley, B. Luisi

Date :   04 Sep 97 (Deposition) - 10 Nov 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.95

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F,G,H  (1x)
Biol. Unit 3: I,J,K,L  (1x)
Biol. Unit 4: M,N,O,P  (1x)

Keywords :   U-Dna, Quadruple Helix, Parallel-Stranded (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

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
PubMed-ID: 9367755 | Reference-DOI: 10.1006/JMBI.1997.1292
(for further references see the PDB file header)

Compounds

*Molecule 1 - DNA (5'-D(TPGPGPGPGPT)-3')*
	Chains	:	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
	Engineered	:	YES
	Synthetic	:	YES

Structural Features

Chains, Units

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H
Biological Unit 3 (1x)	:									I	J	K	L
Biological Unit 4 (1x)	:													M	N	O	P

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 23)

Asymmetric Unit (2, 23)

No.	Name	Count	Type	Full Name
1	CA	9	Ligand/Ion	CALCIUM ION
2	NA	14	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Sites (23, 23)

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	NA I:158 , DG M:122 , DG M:123 , DG N:132 , DG N:133 , DG O:142 , DG O:143 , DG P:152 , DG P:153	BINDING SITE FOR RESIDUE NA M 157
02	AC2	SOFTWARE	DG I:82 , DG J:92 , DG K:102 , NA K:162 , DG L:112 , DG M:122 , NA M:157 , DG N:132 , DG O:142 , DG P:152	BINDING SITE FOR RESIDUE NA I 158
03	AC3	SOFTWARE	DG A:2 , DG A:3 , NA A:160 , DG B:12 , DG B:13 , DG C:22 , DG C:23 , DG D:32 , DG D:33	BINDING SITE FOR RESIDUE NA A 159
04	AC4	SOFTWARE	DG A:2 , NA A:159 , DG B:12 , DG C:22 , DG D:32 , DG E:42 , DG F:52 , DG G:62 , NA G:161 , DG H:72	BINDING SITE FOR RESIDUE NA A 160
05	AC5	SOFTWARE	NA A:160 , DG E:42 , DG E:43 , NA E:165 , DG F:52 , DG F:53 , DG G:62 , DG G:63 , DG H:72 , DG H:73	BINDING SITE FOR RESIDUE NA G 161
06	AC6	SOFTWARE	DG I:82 , DG I:83 , NA I:158 , NA I:167 , DG J:92 , DG J:93 , DG K:102 , DG K:103 , DG L:112 , DG L:113	BINDING SITE FOR RESIDUE NA K 162
07	AC7	SOFTWARE	DG M:123 , DG M:124 , DG N:133 , DG N:134 , DG O:143 , DG O:144 , DG P:153 , DG P:154	BINDING SITE FOR RESIDUE NA M 163
08	AC8	SOFTWARE	DG A:3 , DG A:4 , DG B:13 , DG B:14 , DG C:23 , DG C:24 , DG D:33 , DG D:34	BINDING SITE FOR RESIDUE NA B 164
09	AC9	SOFTWARE	DG E:43 , DG E:44 , DG F:53 , DG F:54 , DG G:63 , DG G:64 , NA G:161 , DG H:73 , DG H:74	BINDING SITE FOR RESIDUE NA E 165
10	BC1	SOFTWARE	DG I:85 , DG J:95 , DG K:105 , DG L:115 , HOH M:196	BINDING SITE FOR RESIDUE NA I 166
11	BC2	SOFTWARE	DG I:83 , DG I:84 , DG J:93 , DG J:94 , DG K:103 , DG K:104 , NA K:162 , DG L:113 , DG L:114	BINDING SITE FOR RESIDUE NA I 167
12	BC3	SOFTWARE	HOH H:204 , DG M:125 , DG N:135 , DG O:145 , DG P:155	BINDING SITE FOR RESIDUE NA M 168
13	BC4	SOFTWARE	HOH D:191 , DG E:45 , DG F:55 , DG G:65 , DG H:75	BINDING SITE FOR RESIDUE NA E 169
14	BC5	SOFTWARE	DG A:5 , DG B:15 , DG C:25 , DG D:35 , HOH F:201	BINDING SITE FOR RESIDUE NA A 170
15	BC6	SOFTWARE	HOH E:579 , HOH I:565 , HOH J:571 , HOH M:202 , HOH M:569 , HOH P:209 , HOH P:520	BINDING SITE FOR RESIDUE CA M 171
16	BC7	SOFTWARE	HOH K:221 , HOH K:586 , HOH O:198 , HOH O:597 , HOH O:620 , HOH O:714 , HOH P:189 , HOH P:195	BINDING SITE FOR RESIDUE CA K 172
17	BC8	SOFTWARE	HOH I:186 , HOH M:192 , HOH M:211 , HOH M:581 , HOH M:599 , HOH M:694 , HOH M:718 , HOH N:183	BINDING SITE FOR RESIDUE CA N 173
18	BC9	SOFTWARE	DT G:61 , HOH G:253 , HOH G:593 , HOH L:223 , HOH N:197 , HOH N:203 , HOH O:577	BINDING SITE FOR RESIDUE CA G 174
19	CC1	SOFTWARE	HOH D:217 , HOH D:248 , HOH H:187 , HOH H:226 , HOH K:228	BINDING SITE FOR RESIDUE CA O 175
20	CC2	SOFTWARE	HOH B:210 , HOH B:570 , HOH B:608 , HOH C:188 , HOH C:376 , HOH E:194 , HOH E:513	BINDING SITE FOR RESIDUE CA C 176
21	CC3	SOFTWARE	HOH A:182 , HOH D:193 , HOH D:576 , HOH D:635 , HOH D:636 , HOH F:510 , HOH F:584 , HOH F:607 , HOH G:578	BINDING SITE FOR RESIDUE CA A 177
22	CC4	SOFTWARE	HOH A:180 , HOH A:572 , HOH A:580 , HOH B:181 , HOH B:574 , HOH E:215 , HOH F:190	BINDING SITE FOR RESIDUE CA B 178
23	CC5	SOFTWARE	HOH A:459 , HOH D:225 , HOH D:227 , HOH D:268 , HOH D:282 , HOH D:594 , HOH O:222	BINDING SITE FOR RESIDUE CA A 179

SS Bonds (0, 0)

(no "SS Bond" information available for 352D)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 352D)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 352D)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 352D)

Exons (0, 0)

(no "Exon" information available for 352D)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:DNA  Length:6
                                      
                 352d A   1 TGGGGT   6

Chain B from PDB  Type:DNA  Length:6
                                      
                 352d B  11 TGGGGT  16

Chain C from PDB  Type:DNA  Length:5
                                     
                 352d C  22 GGGGT  26

Chain D from PDB  Type:DNA  Length:6
                                      
                 352d D  31 TGGGGT  36

Chain E from PDB  Type:DNA  Length:6
                                      
                 352d E  41 TGGGGT  46

Chain F from PDB  Type:DNA  Length:6
                                      
                 352d F  51 TGGGGT  56

Chain G from PDB  Type:DNA  Length:6
                                      
                 352d G  61 TGGGGT  66

Chain H from PDB  Type:DNA  Length:6
                                      
                 352d H  71 TGGGGT  76

Chain I from PDB  Type:DNA  Length:6
                                      
                 352d I  81 TGGGGT  86

Chain J from PDB  Type:DNA  Length:6
                                      
                 352d J  91 TGGGGT  96

Chain K from PDB  Type:DNA  Length:4
                                    
                 352d K 102 GGGG 105

Chain L from PDB  Type:DNA  Length:6
                                      
                 352d L 111 TGGGGT 116

Chain M from PDB  Type:DNA  Length:6
                                      
                 352d M 121 TGGGGT 126

Chain N from PDB  Type:DNA  Length:6
                                      
                 352d N 131 TGGGGT 136

Chain O from PDB  Type:DNA  Length:6
                                      
                 352d O 141 TGGGGT 146

Chain P from PDB  Type:DNA  Length:6
                                      
                 352d P 151 TGGGGT 156

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 352D)

CATH Domains (0, 0)

(no "CATH Domain" information available for 352D)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 352D)

Gene Ontology (0, 0)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 352D)

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