1NUV | UR0030 - JenaLib

Title :   THE LEADZYME RIBOZYME BOUND TO MG(H2O)6(II) AND SR(II) AT 1.8 A RESOLUTION

Authors :   J. E. Wedekind, D. B. Mckay

Date :   01 Feb 03 (Deposition) - 19 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: G,H  (1x)

Keywords :   Ribozyme, Leadzyme, Lead-Dependent Cleavage, Rna, Mg(H2O) 6(Ii), Bulged Nucleotides, Hydrated Magnesium, Sr(Ii), Pseudohelical Packing, Sticky Ends, Alternate Conformation, Homopurine Base Pairs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Wedekind, D. B. Mckay
Crystal Structure Of The Leadzyme At 1. 8 A Resolution: Metal Ion Binding And The Implications For Catalytic Mechanism And Allo Site Ion Regulation.
Biochemistry V. 42 9554 2003
PubMed-ID: 12911297 | Reference-DOI: 10.1021/BI0300783
(for further references see the PDB file header)

Compounds

*Molecule 1 - 5'-R(CPGPGPAPCPCPGPAPGPCPCPAPG)-3'**
	Chains	:	A, C, E, G
	Engineered	:	YES
	Other Details	:	THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK
	Synthetic	:	YES

*Molecule 2 - 5'-R(GPCPUPGPGPGPAPGPUPCPC)-3'**
	Chains	:	B, D, F, H
	Engineered	:	YES
	Other Details	:	THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Asymmetric Unit (2, 16)

No.	Name	Count	Type	Full Name
1	MG	10	Ligand/Ion	MAGNESIUM ION
2	SR	6	Ligand/Ion	STRONTIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SR	-1	Ligand/Ion	STRONTIUM ION

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:412 , HOH A:413 , HOH A:414 , HOH A:415 , HOH A:416 , HOH B:425	BINDING SITE FOR RESIDUE MG A 410
02	AC2	SOFTWARE	HOH A:417 , HOH A:418 , HOH A:419 , HOH A:420 , HOH B:426 , HOH B:427	BINDING SITE FOR RESIDUE MG A 411
03	AC3	SOFTWARE	HOH A:421 , HOH A:422 , HOH A:423 , HOH B:428 , HOH B:429 , HOH B:430	BINDING SITE FOR RESIDUE MG B 412
04	AC4	SOFTWARE	HOH G:222 , HOH G:224 , HOH G:225 , HOH H:221 , HOH H:223 , HOH H:226	BINDING SITE FOR RESIDUE MG G 413
05	AC5	SOFTWARE	HOH G:202 , HOH G:203 , HOH G:205 , HOH G:206 , HOH H:201 , HOH H:204	BINDING SITE FOR RESIDUE MG G 414
06	AC6	SOFTWARE	HOH G:228 , HOH G:229 , HOH G:231 , HOH H:227 , HOH H:230 , HOH H:232	BINDING SITE FOR RESIDUE MG H 415
07	AC7	SOFTWARE	HOH E:90 , HOH E:93 , HOH E:112 , HOH E:117 , HOH E:305 , HOH F:294	BINDING SITE FOR RESIDUE MG E 416
08	AC8	SOFTWARE	HOH E:285 , HOH E:287 , HOH E:302 , HOH E:367 , HOH E:370 , HOH F:293	BINDING SITE FOR RESIDUE MG E 417
09	AC9	SOFTWARE	HOH C:180 , HOH C:198 , HOH C:286 , HOH C:371 , HOH D:372	BINDING SITE FOR RESIDUE MG C 418
10	BC1	SOFTWARE	HOH C:130 , HOH C:136 , HOH D:158 , HOH D:348	BINDING SITE FOR RESIDUE MG C 419
11	BC2	SOFTWARE	C C:23 , A C:25 , HOH C:147 , HOH C:157 , HOH C:325 , HOH C:395 , A D:45	BINDING SITE FOR RESIDUE SR C 420
12	BC3	SOFTWARE	C E:23 , A E:25 , HOH E:82 , HOH E:83 , HOH E:329 , A F:45 , HOH F:114	BINDING SITE FOR RESIDUE SR E 421
13	BC4	SOFTWARE	HOH D:121 , HOH D:123 , HOH D:192	BINDING SITE FOR RESIDUE SR D 422
14	BC5	SOFTWARE	HOH G:284 , HOH H:236 , HOH H:243 , HOH H:270 , HOH H:283	BINDING SITE FOR RESIDUE SR H 423
15	BC6	SOFTWARE	HOH B:456 , HOH B:465 , HOH B:466 , HOH B:467	BINDING SITE FOR RESIDUE SR B 424
16	BC7	SOFTWARE	HOH F:330 , HOH F:331 , HOH F:392	BINDING SITE FOR RESIDUE SR F 425

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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Chain A from PDB  Type:RNA  Length:13
                                            
                  1nuv A 18 CGGACCGAGCCAG 30
                                    27

Chain B from PDB  Type:RNA  Length:11
                                          
                  1nuv B 39 GCUGGGAGUCC 49
                                    48

Chain C from PDB  Type:RNA  Length:13
                                            
                  1nuv C 18 CGGACCGAGCCAG 30
                                    27

Chain D from PDB  Type:RNA  Length:11
                                          
                  1nuv D 39 GCUGGGAGUCC 49
                                    48

Chain E from PDB  Type:RNA  Length:13
                                            
                  1nuv E 18 CGGACCGAGCCAG 30
                                    27

Chain F from PDB  Type:RNA  Length:11
                                          
                  1nuv F 39 GCUGGGAGUCC 49
                                    48

Chain G from PDB  Type:RNA  Length:13
                                            
                  1nuv G 18 CGGACCGAGCCAG 30
                                    27

Chain H from PDB  Type:RNA  Length:11
                                          
                  1nuv H 39 GCUGGGAGUCC 49
                                    48

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