PDBsum entry 1aqp

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protein metals links
Hydrolase (phosphoric diester) PDB id
Protein chain
124 a.a. *
_CU ×2
Waters ×249
* Residue conservation analysis
PDB id:
Name: Hydrolase (phosphoric diester)
Title: Ribonuclease a copper complex
Structure: Ribonuclease a. Chain: a. Synonym: rnase a. Other_details: copper complex
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.200    
Authors: N.Ramasubbu
Key ref:
R.Balakrishnan et al. (1997). Crystal structures of the copper and nickel complexes of RNase A: metal-induced interprotein interactions and identification of a novel copper binding motif. Proc Natl Acad Sci U S A, 94, 9620-9625. PubMed id: 9275172 DOI: 10.1073/pnas.94.18.9620
31-Jul-97     Release date:   27-May-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     6 terms  


DOI no: 10.1073/pnas.94.18.9620 Proc Natl Acad Sci U S A 94:9620-9625 (1997)
PubMed id: 9275172  
Crystal structures of the copper and nickel complexes of RNase A: metal-induced interprotein interactions and identification of a novel copper binding motif.
R.Balakrishnan, N.Ramasubbu, K.I.Varughese, R.Parthasarathy.
We report the crystal structures of the copper and nickel complexes of RNase A. The overall topology of these two complexes is similar to that of other RNase A structures. However, there are significant differences in the mode of binding of copper and nickel. There are two copper ions per molecule of the protein, but there is only one nickel ion per molecule of the protein. Significant changes occur in the interprotein interactions as a result of differences in the coordinating groups at the common binding site around His-105. Consequently, the copper- and nickel-ion-bound dimers of RNase A act as nucleation sites for generating different crystal lattices for the two complexes. A second copper ion is present at an active site residue His-119 for which all the ligands are from one molecule of the protein. At this second site, His-119 adopts an inactive conformation (B) induced by the copper. We have identified a novel copper binding motif involving the alpha-amino group and the N-terminal residues.
  Selected figure(s)  
Figure 1.
Fig. 1. Stereo view of the coordination spheres at the metal binding sites in the complexes. (A) Copper at the His-105 site. (B) Nickel at the His-105 site. (C) Copper at the His-119 site.
Figure 4.
Fig. 4. Superposition of the atoms N1 and the copper metal ions in the copper binding motif involving the -amino terminus and ligands from the first two residues in Gly-Gly-Gly (broken line), thioredoxin (light line), and RNase-Cu structures (thick line).
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
12756270 K.Gamerdinger, C.Moulon, D.R.Karp, J.Van Bergen, F.Koning, D.Wild, U.Pflugfelder, and H.U.Weltzien (2003).
A new type of metal recognition by human T cells: contact residues for peptide-independent bridging of T cell receptor and major histocompatibility complex by nickel.
  J Exp Med, 197, 1345-1353.  
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