PDBsum entry 2kkd

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protein metals links
Electron transport PDB id
Protein chain
52 a.a. *
* Residue conservation analysis
PDB id:
Name: Electron transport
Title: Nmr structure of ni substitued desulfovibrio vulgaris rubredoxin
Structure: Rubredoxin. Chain: a. Synonym: rd. Engineered: yes
Source: Desulfovibrio vulgaris str. Hildenborough. Organism_taxid: 882. Strain: hidenborough/atcc 29579/ncimb 8303. Gene: rub, dvu_3184. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 15 models
Authors: S.G.Nunes,B.F.Volkman,J.J.G.Moura,I.Moura,A.L.Macedo, J.L.Markley,I.C.Duarte
Key ref: B.J.Goodfellow et al. (2010). An NMR structural study of nickel-substituted rubredoxin. J Biol Inorg Chem, 15, 409-420. PubMed id: 19997764
18-Jun-09     Release date:   22-Dec-09    
Supersedes: 2qkz
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00269  (RUBR_DESVH) -  Rubredoxin
52 a.a.
52 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     3 terms  


J Biol Inorg Chem 15:409-420 (2010)
PubMed id: 19997764  
An NMR structural study of nickel-substituted rubredoxin.
B.J.Goodfellow, I.C.Duarte, A.L.Macedo, B.F.Volkman, S.G.Nunes, I.Moura, J.L.Markley, J.J.Moura.
The Ni(II) and Zn(II) derivatives of Desulfovibrio vulgaris rubredoxin (DvRd) have been studied by NMR spectroscopy to probe the structure at the metal centre. The beta CH(2) proton pairs from the cysteines that bind the Ni(II) atom have been identified using 1D nuclear Overhauser enhancement (NOE) difference spectra and sequence specifically assigned via NOE correlations to neighbouring protons and by comparison with the published X-ray crystal structure of a Ni(II) derivative of Clostridium pasteurianum rubredoxin. The solution structures of DvRd(Zn) and DvRd(Ni) have been determined and the paramagnetic form refined using pseudocontact shifts. The determination of the magnetic susceptibility anisotropy tensor allowed the contact and pseudocontact contributions to the observed chemical shifts to be obtained. Analysis of the pseudocontact and contact chemical shifts of the cysteine H beta protons and backbone protons close to the metal centre allowed conclusions to be drawn as to the geometry and hydrogen-bonding pattern at the metal binding site. The importance of NH-S hydrogen bonds at the metal centre for the delocalization of electron spin density is confirmed for rubredoxins and can be extrapolated to metal centres in Cu proteins: amicyanin, plastocyanin, stellacyanin, azurin and pseudoazurin.