2EB8 | pdb_00002eb8

Crystal Structure of Cu(II)(Sal-Phe)/apo-Myoglobin

• PDB DOI: https://doi.org/10.2210/pdb2EB8/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-07 Released: 2007-07-03 
• Deposition Author(s): Abe, S., Okazaki, S., Ueno, T., Hikage, T., Suzuki, A., Yamane, T., Watanabe, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Design and Structure Analysis of Artificial Metalloproteins: Selective Coordination of His64 to Copper Complexes with Square-Planar Structure in the apo-Myoglobin Scaffold

Abe, S., Ueno, T., Reddy, P.A.N., Okazaki, S., Hikage, T., Suzuki, A., Yamane, T., Nakajima, H., Watanabe, Y.

(2007) Inorg Chem 46: 5137-5139

• PubMed: 17523632 
• DOI: https://doi.org/10.1021/ic070289m
• Primary Citation Related Structures: 
  2EB8, 2EB9


• PubMed Abstract: 
  

  apo-Myoglobin (apo-Mb) was reconstituted with three copper complexes: CuII(Sal-Phe) (1; Sal-Phe = N-salicylidene-L-phenylalanato), CuII(Sal-Leu) (2; Sal-Leu = N-salicylidene-L-leucinato), and CuII(Sal-Ala) (3; Sal-Ala = N-salicylidene-L-alanato). The crystal structures of 1.apo-Mb (1.65 Angstrom resolution) and 2.apo-Mb (1.8 Angstrom resolution) show that the coordination geometry around the CuII atom in apo-Mb is distorted square-planar with tridentate Sal-X and a Nepsilon atom of His64 in the apo-Mb cavity and the plane of these copper complexes is perpendicular to that of heme. These results suggest that the apo-Mb cavity can hold metal complexes with various coordination geometries.

---

Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.17 kDa 
• Atom Count: 1,422 
• Modeled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CUP	G [auth A]	(N-SALICYLIDEN-L-PHENYLALANATO)-COPPER(II) C16 H13 Cu N O3 YEXSLHMEGKWMMU-VNKRLIBXSA-L
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.691	α = 90
b = 59.132	β = 90
c = 74.188	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Abe, S., Okazaki, S., Ueno, T., Hikage, T., Suzuki, A., Yamane, T., Watanabe, Y.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description