2H9J

Structure of Hen egg white lysozyme soaked with Ni2-Xylylbicyclam

Summary for 2H9J

• Entry DOI: 10.2210/pdb2h9j/pdb
• Related: 1YIK 1YIL 2H9K
• Descriptor: Lysozyme C, CHLORIDE ION, SODIUM ION, ... (6 entities in total)
• Functional Keywords: lysozyme, cyclam, hydrolase
• Biological source: Gallus gallus (chicken)
• Cellular location: Secreted: P00698
• Total number of polymer chains: 1
• Total formula weight: 15711.99

Authors

McNae, I.W.,Hunter, T.M.,Sadler, P.J.,Walkinshaw, M.D. (deposition date: 2006-06-10, release date: 2007-04-10, Last modification date: 2024-11-20)

Primary citation

Hunter, T.M.,McNae, I.W.,Simpson, D.P.,Smith, A.M.,Moggach, S.,White, F.,Walkinshaw, M.D.,Parsons, S.,Sadler, P.J.
Configurations of nickel-cyclam antiviral complexes and protein recognition.
Chemistry, 13:40-50, 2007

PubMed Abstract: Nickel(II)-xylylbicyclam is a potent anti-HIV agent and binds strongly to the CXCR4 co-receptor. We have investigated configurational equilibria of Ni(II)-cyclam derivatives, since these are important for receptor recognition. Crystallographic studies show that both trans and cis configurations are readily formed: [Ni(cyclam)(OAc)(2)] x H(2)O adopts the trans-III configuration with axial monodentate acetates, as does [Ni(benzylcyclam)(NO(3))(2)] with axial nitrate ligands, whereas [Ni(benzylcyclam)(OAc)](OAc)2 x H(2)O has an unusual folded cis-V configuration with Ni(II) coordination to bidentate acetate. UV/Vis and NMR studies show that the octahedral trans-III configuration slowly converts to square-planar trans-I in aqueous solution. For Ni(II)-xylylbicyclam, a mixture of cis-V and trans-I configurations was detected in solution. X-ray diffraction studies showed that crystals of lysozyme soaked in Ni(II)-cyclam or Ni(II) (2)-xylylbicyclam contain two major binding sites, one involving Ni(II) coordination to Asp101 and hydrophobic interactions between the cyclam ring and Trp62 and Trp63, and the second hydrophobic interactions with Trp123. For Ni(II)-cyclam bound to Asp101, the cis-V configuration predominates.

PubMed: 17120266
DOI: 10.1002/chem.200601334

Experimental method

X-RAY DIFFRACTION (1.75 Å)