Table 2 Cavities and xenon binding sites in the human PrP ^a .

Binding Site	Cavities/pockets in 3D structures
	Surrounding residues ^b	PrP(90–237) (2KUN)		PrP(90–230) (1QM1)
	0.12 nm probe	0.12 nm probe ^c	0.22 nm probe ^c	0.12 nm probe ^c	0.22 nm probe ^c
	0.12 nm probe	Volume [nm³]
A₁	G131, S132, M134, V161, Y162, Y163, F175, V176, C179, C214, I215, Q217, Y218, E219, R220	0.058 (0.023) 18/20	0.002 (0.007) 1/20	0.045 (0.037) 15/20	0.0 0/20
A₂	R164, E168, S170, N171, N173, N174	0.041 (0.025) 19/20	0.005 (0.017) 2/20	0.049 (0.039) 16/20	0.011 (0.024) 4/20
B	I138, I139, F141, E146, D147, Y150, Y157, M205, R208, Y209	0.017 (0.025) 8/20	0.0 0/20	0.069 (0.019) 20/20	0.0 0/20
C	Y149, Y150, N153, R156, Y157, Q186, H187, T190, T191, K194, E196, N197, F198, D202, M205, M206	0.144 (0.049) 20/20	0.080 (0.040) 18/20	0.146 (0.075) 20/20	0.042 (0.035) 14/20
D	A120, V121, V122, G123, G124, L125, Y128, Y162, K185, Q186, V189, T193	0.081 (0.114) 14/20	0.044 (0.090) 5/20	– ^d	– ^d

^aCavities were calculated with CASTp using two different probe radii (water, 0.12 nm; Xe, 0.22 nm). The structural ensembles of the PDB entries 2KUN and 1QM1 have been used for the analysis.
^bResidues contributing at least one atom to the surface of the cavities determined with a sphere of 0.12 nm radius in the 20^th structure of the ensembles of the PDB entry 2KUN and the 1^st structure of the PDB ensemble 1QM1, respectively. Residues in bold letters show significant xenon effects above σ₀.
^cThe cavities were calculated for all 40 structures of the two PDB data sets deposited. The mean volume and the standard deviation of the mean value (values in brackets) are listed for the cavities defined by a probe of the size of a water molecule and a xenon atom, respectively. In addition, the number of structures is listed where a cavity can be detected that is large enough for accepting a water molecule or a xenon atom.
^dN-terminal part is not contained in the PDB entry 1QM1.

Search