Table A23.3.1.3

Dickerson, R. E.

doi:10.1107/97809553602060000716

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 23.3, pp. 619-622

Table A23.3.1.3

R. E. Dickerson^a ^*

^a Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095–1570, USA
Correspondence e-mail: red@mbi.ucla.edu

Table A23.3.1.3 | top | pdf |
X-ray analyses of Z helices

See introductory notes to Table A23.3.1.1. odm = 6H,8H-3,4-dihydropyrimido[4,5c][1,2]oxazin-7-one.

(a) Hexadecamers

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCGCGTTTTCGCGCG (hairpin)	C 2	4	8	1988, UCLA	UDP011	(Z20, Z25)

(b) Decamers (disordered)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
GCGCGCGCGC	$[P6_{5}]$	6	2	1996, Ohio State	ZDJ050	(Z46)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCICICG	$[P6_{5}]$	6	8	1992, Thomas Jefferson	ZDH030	(Z32)
CGCGCGCG	$[P6_{5}]$	6	8	1985, MIT	(ZDH017)	(Z10)
CGCATGCG	$[P6_{5}]$	6	8	1985, MIT	(ZDH016)	(Z10)

(d) Heptamers (overhanging 5′ bases)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
GCGCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Oregon State	ZDG054	(Z50)
G^5meCGCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Oregon State	ZDG055	(Z50)
GCGCGCG/GCGCGCT	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Oregon State	ZDG056	(Z50)
GCGCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1997, Ohio State	ZDG057	(Z51)

(e) Hexamers

(1) Alternating CG: Pu-Py alternation retained

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCGCG, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	ZDF002	(Z23)
CGCGCG, DL racemate	$[P\overline{1}]$	2	6	1993, Osaka	ZDF040	(Z36)
CGCGCG/spermine	$[P2_{1}2_{1}2_{1}]$	4	6	1991, MIT	ZDF029	(Z29)
CGCGCG/spermine, 163 K	$[P2_{1}2_{1}2_{1}]$	4	6	1994, MIT	ZDF035	(Z41)
CGCGCG/spermine, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1979, MIT	ZDF001	(Z1, Z23)
CGCGCG/spermidine	$[P2_{1}2_{1}2_{1}]$	4	6	1996, MIT	ZDF052	(Z47)
CGCGCG/thermospermidine	$[P2_{1}2_{1}2_{1}]$	4	6	1996, MIT	ZDF053	(Z48)
CGCGCG, Co, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1985, MIT	(ZDF019)	(Z11)
CGCGCG, Co, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	(ZDF044)	(Z37)
CGCGCG/spermine, Co	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	(ZDF045)	(Z37)
CGCGCG, Ru	$[P2_{1}2_{1}2_{1}]$	4	6	1987, MIT	(ZDF007)	(Z18)
CG c g CG	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	(ZHF026)	(Z24)

(2) Alternating CG: Pu-Py alternation broken

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CCGCGG	$[C222_{1}]$	8	6	1994, Moscow	UDF025	(Z42)

(3) Modified CG bases: Pu-Py alternation retained

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CG^araCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	(ZDFS27)	(Z24)
CGC^6moGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1990, Rutgers	ZDFB21	(Z26)
CGCG^4moCG	$[P2_{1}2_{1}2_{1}]$	4	6	1990, Cambridge	ZDFB25	(Z27)
CGCG^4moCG	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Manchester	ZDFB36	(Z35)
CGCG^5brCG	$[P2_{1}2_{1}2_{1}]$	4	6	1996, Manchester	ZDFB51	(Z49)
CGCG^odmCG	$[P2_{1}2_{1}2_{1}]$	4	6	1995, Cambridge	ZDFB43	(Z43)
^5me CG^5meCG^5meCG	$[P2_{1}2_{1}2_{1}]$	4	6	1982, MIT	ZDFB03	(Z6, Z7)
^5br CG^5brCG^5brCG, 291 K	$[P2_{1}2_{1}2_{1}]$	4	6	1986, Strasbourg	ZDFB04	(Z16, Z19)
^5br CG^5brCG^5brCG, 310 K	$[P2_{1}2_{1}2_{1}]$	4	6	1986, Strasbourg	ZDFB05	(Z16, Z19)
Aminohexyl-CG^5brCGCG	C 2	4	6	1993, Illinois	(ZDFA32)	(Z38)
^ara CG^araCG^araCG (disordered)	$[P6_{5}22]$	12	2	1992, Illinois	ZDFS33	(Z34)

(4) Modified CG bases: Pu-Py alternation broken

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
$[^{\rm 5me}\hbox{CG}\underline{\hbox{G}}\hbox{G}^{\rm 5me}\hbox{CG}]$	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Oregon State	ZDFB37	(Z40)

(5) With A, T, U, I bases: Pu-Py alternation retained

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
^5me CGTA^5meCG	$[P2_{1}2_{1}2_{1}]$	4	6	1984, MIT	ZDFB06	(Z8)
CGT^2amACG	$[P3_{2}21]$	6	3	1995, Rutgers	ZDFB41	(Z44)
CGT^2amACG, Pt	$[P3_{2}21]$	6	3	1995, Rutgers	ZDFB42	(Z44)
CGU^2amACG	$[P2_{1}2_{1}2_{1}]$	4	6	1992, Rutgers	ZDFB31	(Z33)
^5me CGUA^5meCG	$[P2_{1}2_{1}2_{1}]$	4	6	1990, Oregon State	ZDFB24	(Z28)
^5me CGUA^5meCG, Cu	$[P2_{1}2_{1}2_{1}]$	4	5	1991, Oregon State	ZDFB10	(Z30)
CACGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1988, MIT	(ZDF008)	(Z21)
C^2amACGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1986, MIT	ZDFB11	(Z17)
CGCICG	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Thomas Jefferson	(ZDFB34)	(Z39)
CACGCG/CGCGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1995, Madras	ZDF039	(Z45)
CGCACG/CGTGCG	$[P2_{1}]$	2	6	1995, Madras	ZDF038	(Z45)

(6) With A, T, U, I bases: Pu-Py alternation broken

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
$[^{\rm 5br}\hbox{CG}\underline{\hbox{AT}}^{\rm 5br}\hbox{CG}]$	$[P2_{1}2_{1}2_{1}]$	4	6	1985, MIT	(ZDFB09)	(Z13)

(7) With mismatches (underlined)

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCGTG	$[P2_{1}2_{1}2_{1}]$	4	6	1985, MIT	ZDF013	(Z12)
C $[\underline{\hbox{G}}\hbox{CG}^{\rm 5fl}\underline{\hbox{U}}]$ G	$[P2_{1}2_{1}2_{1}]$	4	6	1989, MIT	ZDFB12	(Z22)
$[^{\rm 5br}\underline{\hbox{U}}]$ GCGCG	$[P2_{1}2_{1}2_{1}]$	4	6	1986, Cambridge	ZDFB14	(Z15)
CGCGTG, Co, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	ZDF046	(Z37)
CGCGTG, Cu, Mg	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	ZDF047	(Z37)
$[^{\rm 5me}\hbox{C}\underline{\hbox{G}}^{\rm 5me}\hbox{CG}\underline{\hbox{T}}]$ G, Ba	$[P2_{1}2_{1}2_{1}]$	4	6	1993, Illinois	(ZDFB48)	(Z37)

(f) Tetramers

Sequence	Space group	Z	Ubp	Date, institution	NDB No.	Reference
CGCG	$[C222_{1}]$	8	4	1980, UCLA (CIT)	ZDD015	(Z3, Z4, Z5)
CGCG (disordered)	$[P6_{5}]$	6	6	1980, MIT	ZDD023	(Z2)

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