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B. halodurans RNase H catalytic domain D132N mutant in complex with MG2+ and RNA/DNA hybrid (non-P nick at the active site)

Analyse B. halodurans RNase H catalytic domain D132N mutant in complex with MG2+ and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2G8U
Type
protein + DNA + RNA
Length
144 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-R(*UP*CP*GP*AP*CP*A)-3'; 5'-D(*AP*TP*GP*TP*CP*G)-3'; Ribonuclease H
EC
3.1.26.4
UniProt
Q9KEI9
Ligands
MG

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-R(*UP*CP*GP*AP*CP*A)-3'rna6——
C5'-D(*AP*TP*GP*TP*CP*G)-3'dna6——
ARibonuclease H (EC 3.1.26.4)protein13232% helix, 23% strandQ9KEI9

Ligands and binding sites

  • MG · Magnesium ion · metal · 2 copies · chains B, A

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

Interfaces

3 interfaces between chains.

  • C–A · 407 Ų buried · 19 hydrogen bonds · protein-nucleic
  • B–C · 258 Ų buried · 27 hydrogen bonds · nucleic-nucleic
  • B–A · 252 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 2G8U · B. halodurans RNase H catalytic domain D132N mutant in complex with Mg2+ and RNA/DNA… · the same entry in another collection · chain B against B, TM-score 1.00
  • Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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