5TYY

DNA Polymerase Mu Product Complex, Mn2+ (60 min)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 5TYY

Classification: Transferase / DNA

Total Structure Weight: 46522.24


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed DNA/RNA polymerase mu A 356 Homo sapiens EC#: 2.7.7.7 IUBMB
Fragment: UNP residues 132-494
Mutation: ΔP398, ΔG399, ΔA400, ΔA401, ΔV402, ΔG403, ΔG404, ΔS405, ΔT406, ΔR407, ΔP408, ΔC409, P410G
Gene Name(s): POLM Gene View polmu
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3') T 9 Unidentified
DNA (5'-D(*CP*GP*TP*AP*T)-3') P 5 Unidentified
DNA (5'-D(P*GP*CP*CP*G)-3') D 4 Unidentified

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EPE
Query on EPE

A 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PPV
Query on PPV

A PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DTT
Query on DTT

A 2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL (Synonym)
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

P 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, P, T MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.186
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 59.99 α = 90.00
b = 68.67 β = 90.00
c = 110.18 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-11-21
  • Released Date: 2017-08-30
  • Deposition author(s): Jamsen, J.A., Wilson, S.H.

Revision History

  • Version 1_0: 2017-08-30

    Type: Initial release

  • Version 1_1: 2017-09-27

    Type: Author supporting evidence