Download MendeleyStructures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities
Shi, Y., Hellinga, H.W., Beese, L.S.To be published.
7MXT
Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (cmr)
- PDB DOI: https://doi.org/10.2210/pdb7MXT/pdb
- NAKB: 7MXT
- Classification: HYDROLASE/DNA
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2021-05-19 Released: 2023-05-10
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.05 Å
- R-Value Free: 0.260
- R-Value Work: 0.211
- R-Value Observed: 0.215
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Exonuclease 1 | A [auth Z] | 358 | Homo sapiens | Mutation(s): 0 Gene Names: EXO1, EXOI, HEX1 EC: 3.1 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UQ84 (Homo sapiens) Explore Q9UQ84 Go to UniProtKB: Q9UQ84 | |||||
PHAROS: Q9UQ84 GTEx: ENSG00000174371 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UQ84 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3') | B [auth A] | 13 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*CP*GP*AP*CP*TP*AP*GP*CP*G)-3') | C [auth B] | 9 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MN (Subject of Investigation/LOI) Query on MN | D [auth Z], E [auth Z], G [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| NA Query on NA | F [auth Z] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.05 Å
- R-Value Free: 0.260
- R-Value Work: 0.211
- R-Value Observed: 0.215
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.857 | α = 90 |
| b = 72.857 | β = 90 |
| c = 181.382 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-05-10 Deposition Author(s): Shi, Y., Beese, L.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | R01 GM091487 |
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | P01 CA092584 |
Revision History (Full details and data files)
- Version 1.0: 2023-05-10
Type: Initial release - Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
