Structural Evidence for a Copper-Bound Carbonate Intermediate in the Peroxidase and Dismutase Activities of Superoxide Dismutase.

Strange, R.W; Hough, M.A; Antonyuk, S.V; Hasnain, S.S.

Macromolecule Content

Unique protein chains: 1

4B3E

Structure of copper-zinc superoxide dismutase complexed with bicarbonate.

DOI: 10.2210/pdb4b3e/pdb

Classification: OXIDOREDUCTASE
Deposited: 2012-07-23 Released: 2012-09-26
Deposition author(s): Strange, R.W., Hough, M.A., Antonyuk, S.V., Hasnain, S.S.
Organism: Homo sapiens
Expression System: SACCHAROMYCES CEREVISIAE

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215
R-Value Work: 0.175

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: OXIDOREDUCTASE

Total Structure Weight: 161957.53

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
SUPEROXIDE DISMUTASE [CU-ZN]	A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J	154	Homo sapiens	EC#: 1.15.1.1 IUBMB Gene Name(s): SOD1 Gene View
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P00441 UniProt Full Protein Feature View for P00441 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P00441/4B3E

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
SO4 Query on SO4 Download SDF File Download CCD File	F, G, J	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L	Poseview Image of SO4 in 4B3E Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
ZN Query on ZN Download SDF File Download CCD File	A, B, C, D, E, F, G, H, I, J	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N	Poseview Image of ZN in 4B3E Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
CU Query on CU Download SDF File Download CCD File	A, B, C, D, E, F, G, H, I, J	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N	Poseview Image of CU in 4B3E Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
CO3 Query on CO3 Download SDF File Download CCD File	A, B, C, D, E, F, G, H, I, J	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L	Poseview Image of CO3 in 4B3E Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)