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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ZINC UPTAKE REGULATOR COMPLEXED WITH ZINC AND DNA

Authors :   B. A. Gilston, A. Mondragon, T. V. O'Halloran

Date :   19 Sep 13 (Deposition) - 05 Nov 14 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D,Y,Z

Keywords :   Protein-Dna Complex, Winged-Helix, Dna-Binding Regulatory Protein, Helix-Turn-Helix, Winged Helix, Zinc Regulated Repressor, Dna Binding, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Gilston, S. Wang, M. D. Marcus, M. A. Canalizo-Hernandez, E. P. Swindell, Y. Xue, A. Mondragon, T. V. O'Halloran
Structural And Mechanistic Basis Of Zinc Regulation Across The E. Coli Zur Regulon.
Plos Biol. V. 12 01987 2014
PubMed-ID: 25369000 | Reference-DOI: 10.1371/JOURNAL.PBIO.1001987

Molecule 1 - ZINC UPTAKE REGULATION PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B4046, JW5714, YJBK, ZUR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	ZINC UPTAKE REGULATOR

Molecule 2 - ZNUABC OPERATOR DNA
	Chains	:	Y
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - ZNUABC OPERATOR DNA
	Chains	:	Z
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	Y	Z

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	ZN	8	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:103 , CYS A:106 , CYS A:143 , CYS A:146	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	HIS A:77 , CYS A:88 , HIS A:96 , GLU A:111	BINDING SITE FOR RESIDUE ZN A 202
3	AC3	SOFTWARE	HIS B:77 , CYS B:88 , HIS B:96 , GLU B:111	BINDING SITE FOR RESIDUE ZN B 201
4	AC4	SOFTWARE	CYS B:103 , CYS B:106 , CYS B:143 , CYS B:146	BINDING SITE FOR RESIDUE ZN B 202
5	AC5	SOFTWARE	CYS C:103 , CYS C:106 , CYS C:143 , CYS C:146	BINDING SITE FOR RESIDUE ZN C 201
6	AC6	SOFTWARE	HIS C:77 , CYS C:88 , HIS C:96 , GLU C:111	BINDING SITE FOR RESIDUE ZN C 202
7	AC7	SOFTWARE	CYS D:103 , CYS D:106 , CYS D:143 , CYS D:146	BINDING SITE FOR RESIDUE ZN D 201
8	AC8	SOFTWARE	HIS D:77 , CYS D:88 , HIS D:96 , GLU D:111	BINDING SITE FOR RESIDUE ZN D 202

(no "SS Bond" information available for 4MTD)

(no "Cis Peptide Bond" information available for 4MTD)

(no "SAP(SNP)/Variant" information available for 4MTD)

(no "PROSITE Motif" information available for 4MTD)

(no "Exon" information available for 4MTD)

Asymmetric/Biological 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:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeee....eeee...........eeeee.....eeee.hhhhhhhhhhhhhhh..eeeeeeeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mtd A   4 TTTQELLAQAEKICAQRNVRLTPQRLEVLRLMSLQDGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNSYVLCHLFDQPTHTSAMFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCAACVEVEAC 152
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeee....eeee..........eeeeee.....eeeeehhhhhhhhhhhhhhh..eeeeeeeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mtd B   3 KTTTQELLAQAEKICAQRNVRLTPQRLEVLRLMSLQDGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNSYVLCHLFDQPTHTSAMFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCAACVEVEAC 152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeeehhhheeee..........eeeeee.....eeeeehhhhhhhhhhhhhhh..eeeeeeeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mtd C   5 TTQELLAQAEKICAQRNVRLTPQRLEVLRLMSLQDGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNSYVLCHLFDQPTHTSAMFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCAACVEVEAC 152
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Chain D from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeee....eeee...........eeeee.....eeee.hhhhhhhhhhhhhhh..eeeeeeeeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mtd D   2 EKTTTQELLAQAEKICAQRNVRLTPQRLEVLRLMSLQDGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNSYVLCHLFDQPTHTSAMFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCAACVEVEAC 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain Y from PDB  Type:DNA  Length:33
                                                                 
                 4mtd Y   1 AGAAGTGTGATATTATAACATTTCATGACTATG  33
                                    10        20        30

Chain Z from PDB  Type:DNA  Length:33
                                                                 
                 4mtd Z   1 TAGTCATGAAATGTTATAATATCACACTTCTCA  33
                                    10        20        30

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 4MTD)

(no "CATH Domain" information available for 4MTD)

(no "Pfam Domain" information available for 4MTD)

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4mtd)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

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

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Gene Ontology (4, 4)

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