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Bacillus halodurans RNase H catalytic domain mutant D192N in complex with 12-mer RNA/DNA hybrid

Analyse Bacillus halodurans RNase H catalytic domain mutant D192N in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1ZBL
Type
protein + DNA + RNA
Length
290 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3'; 5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'…
EC
3.1.26.4
Ligands
MG

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3'rna12——
D5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'dna12——
A, BRibonuclease H-related protein (EC 3.1.26.4)protein13334% helix, 24% strand—

Ligands and binding sites

  • MG · Magnesium ion · metal · 4 copies · chains C, A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

5 interfaces between chains.

  • C–D · 553 Ų buried · 56 hydrogen bonds · nucleic-nucleic
  • C–A · 484 Ų buried · 19 hydrogen bonds · protein-nucleic
  • C–B · 468 Ų buried · 21 hydrogen bonds · protein-nucleic
  • D–B · 418 Ų buried · 18 hydrogen bonds · protein-nucleic
  • D–A · 410 Ų buried · 15 hydrogen bonds · protein-nucleic

Compared structures

  • 1ZBL · Bacillus halodurans RNase H catalytic domain mutant D192N in complex with 12-mer RNA/DNA… · the same entry in another collection · chain C against C, TM-score 1.00

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