Domain ID e4by7I2

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  • A: few secondary structure elements
  • X: Rubredoxin-like
  • H: Rubredoxin-related
  • T: Rubredoxin-related
  • F: RNA_POL_M_15KD
UID: 001098677
Type: Automatic domain
Parent: e1twfI1
Range: I:2-49
Ligands: ZN
PDB: 4by7
PDB Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
UniProt: P27999
Hsap BLAST neighbor: P36954
Species: Saccharomyces cerevisiae

Structure of domain e4by7I2

Domains in the same chain:

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e4by7I2 I:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4by7I1 I:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related

Domains in the same PDB:

e4by7A6 A:2-336 N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit
e4by7A5 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e4by7A1 A:375-435 MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase
e4by7A9 A:520-662 first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit
e4by7A7 A:663-871 second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit
e4by7A2 A:872-1059 helical domain in yeast RNA-polymerases third helical domain in yeast RNA-polymerase II beta-prime subunit third helical domain in yeast RNA-polymerase II beta-prime subunit
e4by7A3 A:1060-1102,A:1301-1455 central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit
e4by7A4 A:1103-1131,A:1243-1300 ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e4by7A8 A:1132-1242 permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e4by7B1 B:20-134,B:164-218,B:405-541 N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase
e4by7B2 B:219-404 insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase
e4by7B3 B:542-630 inserted a+b domain in yeast RNA polymerase beta subunit inserted a+b domain in yeast RNA polymerase beta subunit inserted a+b domain in yeast RNA polymerase beta subunit
e4by7B4 B:631-813 barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase
e4by7B5 B:814-850,B:975-1097 cradle loop barrel RIFT-related double psi
e4by7B6 B:851-974 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4by7B7 B:1098-1224 C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase
e4by7C3 C:3-41,C:173-268 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4by7C4 C:42-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e4by7D1 D:4-71,D:131-221 HhH/H2TH SAM/DNA-glycosylase SAM domain-like
e4by7E2 E:1-143 Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain
e4by7E1 E:144-215 RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit
e4by7F1 F:69-155 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e4by7G4 G:1-68 Dodecin subunit-like Flavin-binding protein dodecin-like Flavin-binding protein dodecin-like
e4by7G3 G:69-171 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4by7H1 H:2-146 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4by7I2 I:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4by7I1 I:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4by7J1 J:1-65 HTH RPB10 RPB10
e4by7K1 K:1-115 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4by7L1 L:25-70 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4by7X1 X:232-365 RuvA-C Elongation factor TFIIS domain 2/ Kix domain of creb binding protein Elongation factor TFIIS domain 2/ Kix domain of creb binding protein

Structural contacts of domain e4by7I2 of H-group "Rubredoxin-related":

The domain and its neighboring domains (both within the asymmetric unit and to crystallographic symmetry mates) are represented by spheres and linked by lines. Distances between the center of the domain and interfaces are shown for each contact.

Domain IDSymmetry operatorH-groupVisualization
e4by7A8 I:x,y,z->A:X,Y,Z permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit Interaction Interface Pymol
e4by7A4 I:x,y,z->A:X,Y,Z ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit Interaction Interface Pymol
e4by7B2 I:x,y,z->B:X,Y,Z insertion domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e4by7A2 I:x,y,z->A:X-1/2,-Y+1/2,-Z third helical domain in yeast RNA-polymerase II beta-prime subunit Interaction Interface Pymol