1LFI

METAL SUBSTITUTION IN TRANSFERRINS: THE CRYSTAL STRUCTURE OF HUMAN COPPER-LACTOFERRIN AT 2.1 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Metal substitution in transferrins: the crystal structure of human copper-lactoferrin at 2.1-A resolution.

Smith, C.A.Anderson, B.F.Baker, H.M.Baker, E.N.

(1992) Biochemistry 31: 4527-4533


  • PubMed Abstract: 
  • The structural consequences of binding a metal other than iron to a transferrin have been examined by crystallographic analysis of human copper-lactoferrin, Cu2Lf. X-ray diffraction data were collected from crystals of Cu2Lf, using a diffractometer, ...

    The structural consequences of binding a metal other than iron to a transferrin have been examined by crystallographic analysis of human copper-lactoferrin, Cu2Lf. X-ray diffraction data were collected from crystals of Cu2Lf, using a diffractometer, to 2.6-A resolution, and oscillation photography on a synchrotron source, to 2.1-A resolution. The structure was refined crystallographically, by restrained least-squares methods, starting with a model based on the isomorphous diferric structure from which the ligands, metal ions, anions, and solvent molecules had been deleted. The final model, comprising 5321 protein atoms (691 residues), 2 Cu2+ ions, 2 (bi)carbonate ions, and 308 solvent molecules has good stereochemistry (rms deviation of bond lengths from standard values of 0.018 A) and gives a crystallographic R value of 0.196 for 43,525 reflections in the range 7.5-2.1-A resolution. The copper coordination is different in the two binding sites. In the N-terminal site, the geometry is square pyramidal, with equatorial bonds to Asp 60, Tyr 192, His 253, and a monodentate anion and a longer apical bond to Tyr 92. In the C-terminal site, the geometry is distorted octahedral, with bonds to Asp 395, Tyr 435, Tyr 528, and His 597 and an asymmetrically bidentate anion. The protein structure is the same as for the diferric protein, Fe2Lf, demonstrating that the closure of the protein domains over the metal is the same in each case irrespective of whether Fe3+ or Cu2+ is bound and that copper could be transported and delivered to cells equally well as iron. The differences in metal coordination are achieved by small movements of the metal ion and anion within each binding site, which do not affect the protein structure.


    Related Citations: 
    • Preliminary Crystallographic Studies of Copper(II)-and Oxalate-Substituted Human Lactoferrin
      Smith, C.A.,Baker, H.M.,Baker, E.N.
      (1991) J.Mol.Biol. 219: 155
    • Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 Angstroms Resolution
      Anderson, B.F.,Baker, H.M.,Norris, G.E.,Rice, D.W.,Baker, E.N.
      (1989) J.Mol.Biol. 209: 711
    • Structure of Human Lactoferrin at 3.2 Angstroms Resolution
      Anderson, B.F.,Baker, H.M.,Dodson, E.J.,Norris, G.E.,Rumball, S.V.,Waters, J.M.,Baker, E.N.
      (1987) Proc.Natl.Acad.Sci.USA 84: 1769


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LACTOFERRIN
A
691Homo sapiensMutation(s): 0 
Gene Names: LTF (GIG12, LF)
EC: 3.4.21.-
Find proteins for P02788 (Homo sapiens)
Go to Gene View: LTF
Go to UniProtKB:  P02788
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 155.900α = 90.00
b = 97.000β = 90.00
c = 56.000γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other