1Q3M

1H NMR structure bundle of bovine Ca2+-osteocalcin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 13 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Three-Dimensional Structure of Bovine Calcium Ion-Bound Osteocalcin Using 1H NMR Spectroscopy

Dowd, T.L.Rosen, J.F.Li, L.Gundberg, C.M.

(2003) Biochemistry 42: 7769-7779

  • DOI: 10.1021/bi034470s

  • PubMed Abstract: 
  • Structural information on osteocalcin or other noncollagenous bone proteins is very limited. We have solved the three-dimensional structure of calcium bound osteocalcin using (1)H 2D NMR techniques and proposed a mechanism for mineral binding. The pr ...

    Structural information on osteocalcin or other noncollagenous bone proteins is very limited. We have solved the three-dimensional structure of calcium bound osteocalcin using (1)H 2D NMR techniques and proposed a mechanism for mineral binding. The protons in the 49 amino acid sequence were assigned using standard two-dimensional homonuclear NMR experiments. Distance constraints, dihedral angle constraints, hydrogen bonds, and (1)H and (13)C chemical shifts were all used to calculate a family of 13 structures. The tertiary structure of the protein consisted of an unstructured N terminus and a C-terminal loop (residues 16-49) formed by long-range hydrophobic interactions. Elements of secondary structure within residues 16-49 include type III turns (residues 20-25) and two alpha-helical regions (residues 27-35 and 41-44). The three Gla residues project from the same face of the helical turns and are surface exposed. The genetic algorithm-molecular dynamics simulation approach was used to place three calcium atoms on the NMR-derived structure. One calcium atom was coordinated by three side chain oxygen atoms, two from Asp30, and one from Gla24. The second calcium atom was coordinated to four oxygen atoms, two from the side chain in Gla 24, and two from the side chain of Gla 21. The third calcium atom was coordinated to two oxygen atoms of the side chain of Gla17. The best correlation of the distances between the uncoordinated Gla oxygen atoms is with the intercalcium distance of 9.43 A in hydroxyapatite. The structure may provide further insight into the function of osteocalcin.


    Organizational Affiliation

    Department of Pediatrics, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York 10467, USA. dowd@aecom.yu.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Osteocalcin
A
49Bos taurusGene Names: BGLAP
Find proteins for P02820 (Bos taurus)
Go to Gene View: BGLAP
Go to UniProtKB:  P02820
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
A
L-PEPTIDE LINKINGC6 H9 N O6GLU
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 13 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1Q3M Olderado
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance