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Title :   BACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER FRNA/DNA HYBRID

Authors :   P. S. Pallan, M. Egli

Date :   08 Aug 16 (Deposition) - 21 Sep 16 (Release) - 12 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C,D  (1x)
Biol. Unit 2: B,C,D  (1x)

Keywords :   Rnase H, Rna/Dna Hybrid, Hydrolase-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. S. Pallan, T. P. Prakash, A. R. De Leon, M. Egli
Limits Of Rna 2'-Oh Mimicry By Fluorine: Crystal Structure Of Bacillus Halodurans Rnase H Bound To A 2'-Frna:Dna Hybrid.
Biochemistry V. 55 5321 2016
PubMed-ID: 27611889 | Reference-DOI: 10.1021/ACS.BIOCHEM.6B00849

Molecule 1 - RIBONUCLEASE H
	Chains	:	A, B
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	BACILLUS HALODURANS
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 PLYSS
	Expression System Taxid	:	86665
	Gene	:	RNHA
	Mutation	:	YES
	Organism Scientific	:	BACILLUS HALODURANS
	Organism Taxid	:	86665
	Synonym	:	RNASE H

Molecule 2 - RNA (12-MER)
	Chains	:	C
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Molecule 3 - DNA (12-MER)
	Chains	:	D
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C	D
Biological Unit 2 (1x)	:		B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (9, 17)

No.	Name	Count	Type	Full Name
1	AF2	3	OTHER	2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2	BRU	1	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
3	CFZ	4	OTHER	2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
4	CL	1	Ligand/Ion	CHLORIDE ION
5	GF2	2	OTHER	2'-DEOXY-2'-FLUOROGUANOSINE 5'-(DIHYDROGEN PHOSPHATE)
6	GOL	1	Ligand/Ion	GLYCEROL
7	NA	1	Ligand/Ion	SODIUM ION
8	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
9	UFT	3	OTHER	2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

Biological Unit 1 (7, 15)

No.	Name	Count	Type	Full Name
1	AF2	3	OTHER	2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2	BRU	1	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
3	CFZ	4	OTHER	2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	GF2	2	OTHER	2'-DEOXY-2'-FLUOROGUANOSINE 5'-(DIHYDROGEN PHOSPHATE)
6	GOL	1	Ligand/Ion	GLYCEROL
7	NA	-1	Ligand/Ion	SODIUM ION
8	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
9	UFT	3	OTHER	2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

Biological Unit 2 (6, 14)

No.	Name	Count	Type	Full Name
1	AF2	3	OTHER	2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2	BRU	1	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
3	CFZ	4	OTHER	2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	GF2	2	OTHER	2'-DEOXY-2'-FLUOROGUANOSINE 5'-(DIHYDROGEN PHOSPHATE)
6	GOL	1	Ligand/Ion	GLYCEROL
7	NA	-1	Ligand/Ion	SODIUM ION
8	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
9	UFT	3	OTHER	2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:132 , THR A:183 , GLU A:188 , ILE A:189 , HOH A:302	binding site for residue NA A 201
2	AC2	SOFTWARE	LEU A:117 , LYS A:121 , TYR A:174 , THR A:176 , HOH A:384	binding site for residue CL A 202
3	AC3	SOFTWARE	TYR A:83 , ARG A:97 , LEU A:111 , HIS A:115 , HOH A:337 , HOH A:373 , ASN B:170	binding site for residue PEG A 203
4	AC4	SOFTWARE	GLY B:76 , ASN B:77 , GF2 C:1 , AF2 C:2 , UFT C:7 , GF2 C:8 , CFZ C:12 , DG D:1 , DA D:2 , DA D:3 , DG D:7 , DG D:8 , HOH D:221	binding site for residue GOL D 101

(no "SS Bond" information available for 5SWM)

Asymmetric Unit

No.	Residues
1	Asn A:77	-	Pro A:78
2	Asn B:77	-	Pro B:78

(no "SAP(SNP)/Variant" information available for 5SWM)

(no "PROSITE Motif" information available for 5SWM)

(no "Exon" information available for 5SWM)

Asymmetric Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee...eeeeeeeee.....eeee...eeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhh.......eee.hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5swm A  63 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY 193
                                    72        82        92       102       112       122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...eeeeeeeee.....eeee...eeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhh.......eee.hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5swm B  62 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYG 194
                                    71        81        91       101       111       121       131       141       151       161       171       181       191

Chain C from PDB  Type:OTHER  Length:12
                                            
                 5swm C   1 xxxxxxxxxxxx  12
                            ||||||||10||
                            1-GF2|||10-UFT
                             2-AF2|||11-UFT
                              3-CFZ|| 12-CFZ
                               4-AF2|   
                                5-CFZ   
                                 6-CFZ  
                                  7-UFT 
                                   8-GF2
                                    9-AF2

Chain D from PDB  Type:DNA  Length:12
                                            
                 5swm D   1 GAAuCAGGTGTC  12
                               |    10  
                               |        
                               4-BRU

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

(no "SCOP Domain" information available for 5SWM)

(no "CATH Domain" information available for 5SWM)

(no "Pfam Domain" information available for 5SWM)

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		Asn A:77 - Pro A:78	[ RasMol ]
		Asn B:77 - Pro B:78	[ RasMol ]

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Ligands, Modified Residues, Ions (9, 17)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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