Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).

Ligands and binding sites

• DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains T, P, A
• PPV · Pyrophosphate · ligand · chains P, A
• NA · Sodium ion · metal · 2 copies · chains P, A
• MN · Manganese (II) ion · metal · 2 copies · chains P, A
• MG · Magnesium ion · metal · chains P, A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• T–A · 921 Ų buried · 18 hydrogen bonds · protein-nucleic
• P–A · 537 Ų buried · 21 hydrogen bonds · protein-nucleic
• D–A · 375 Ų buried · 18 hydrogen bonds · protein-nucleic
• T–P · 314 Ų buried · 28 hydrogen bonds · nucleic-nucleic
• T–D · 193 Ų buried · 20 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 2PFQ · Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal · the same entry in another collection · chain T against T, TM-score 1.00
• Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9UGP5
• Elsewhere: RCSB PDB 2PFQ · PDBe 2PFQ · UniProt Q9UGP5