Coordinates of XENON sites in a number of protein complexes

 

Close contacts () around the xenon (or krypton) atoms in the various binding sites, within a sphere of 4.5-4.7 . For each site, the co-ordinates are given. Most of the protein coordinates are available from the PDB. (code given in parentheses).

Protein

Atom type

Coordinates ()

Atom dist. Atom dist.
(residue) () (residue) ()

B/Occ*

Elastase (6EST)

Xe

x=11.032
y=54.172
z=-0.779

Og(S195) 3.40 O(C191) 3.71
Cg2(V216) 3.89 Cg2(T213) 4.0

22.6 / 0.81

Elastase (6EST)

Kr

id

Og(S195) 3.28 O(C191) 3.90
Cg2(V216) 3.75 Cg2(T213) 3.85

18.9 / 0.49

Subtilisin
(1SCA)

Xe

x=80.690
y=67.19
z=54.020

Og(S221) 4.03 Cb(A152) 3.94
Ca(G154) 3.92 Nd2(N155) 3.73
Og2(T220) 4.11 Ca(L126) 3.99
Ow(310) 4.43

29.3 / 0.71

Cutinase
wild-type (1CUS)

Xe

x=10.18
y=52.44
z=14.71

Og(S120) 4.24 Nd2(N84) 3.33
Cg2(T150) 4.19 Cg1(V177) 4.17
Cd2(L182) 3.99

19.1/ 0.81**

Collagenase

(2HLC)

Xe

site A:
x=31.789
y=28.275
z=19.882

site B:
x=22.044
y=47.383
z=31.886

subunit-A : subunit B :
Og(S195a) 3.67 Og(S195b) 3.51
Cg2(V216a) 3.98 Cg2(V216b) 4.01
Cg1(V213a) 4.22 Cg1(V213b) 4.33
Oe1(Q37b) 3.76 Oe1(Q37a) 4.0
O(S214a) 4.53 O(S214b) 4.58
C(C191a) 4.29 C(C191b) 4.27
Ow(234) 3.87 Ow(552) 4.40

28.1 / 0.95

(in site A)

 

31.8 / 0.80

(in site B)

Urate-Oxidase

(1UOX)

Xe

x=24.444
y=34.192
z=38.871

Cd2(L178) 4.33 Cg2(T180) 4.79
Cd1(F219) 4.12 Cg1(V227) 4.14
Cg2(T230) 3.99 Cd2(L252) 3.68

30.5 / 0.85

p64k - N. menin-gitidis) (1OJT)

site #1 :

 

site #2 :

Xe

x=37.72
y=23.75
z= 7.18

 

x=107.57
y=39.12
z= 2.39

Cd2(L323) 3.42 Cb(A176) 3.88
Cb(V319) 4.59 O(L172) 3.66
Cd1(I179) 4.60 Cd2(L202) 3.81
Cb(N175) 4.00 Cg(L172) 4.57

 

Cd(L327) 3.60 Cz(F356) 2.65
C(W348) 3.70 Ce(R355) 3.66
Og1(T318) 3.25 N(L314) 3.45

22.5 / 0.55 **

 

 

 

30.5 / 0.40 **

Lysozyme
(1HEL)

Kr

x= -3.622
y=17.216
z=17.441

Cg2(V92) 3.12 Cd1(L56) 3.38
Cg2(I55) 3.46 Cd1(I88) 4.16
Ce(M12) 3.55 Cb(S91) 3.89

19/0.49***

Lysozyme
(1HEL)

 

site #1 :

(intermolecular)

 

 

site #2 :

(intramolecular)

 

 

site #3 :

(intramolecular)

Xe

 

 

x=15.235
y=15.235
z=18.870

 

 

x= 2.977
y=23.012
z=24.531

 

 

x= -3.559
y=17.301
z=17.381

 

Og1(T43) 3.65 Cb(T43) 4.00
N(R45) 4.25 N(N44) 4.36
Cg2(T51) 4.55 Nh2(R68) 4.49
Ow(20) 4.50
+ symmetry-related

 

Cg2(V92) 3.18 Cd1(L56) 3.33
Cg2(I55) 3.51 Cd1(I88) 4.19
Ce(M12) 3.54 Cb(S91) 3.91

 

Ca(I58) 4.30 Ne1(W108) 3.75
O(Q57) 4.03 Cd1(W108) 3.96
Cd1(I98) 4.30 O(A107) 3.78

 

 

36.2 / 0.33

 

 

 

 

32.9 / 0.28

 

 

 

36.0 / 0.1

CytB
(intermolecular)
(1CBY)

Xe

x=27.94
y=22.24
z=71.17

Cd1(L33) 3.4 Cd1(I54) 4.2
Cd1(I233) 4.7 Cz(F237) 3.9
+ symmetry-related

n.r.

RXR
()

site #1 :

 

site #2 :

 

Xe

 

x= 1.445
y=81.401
z=69.265

 

x=21.216
y=82.534
z=74.611

Cg1(V332) 4.09 O(S336) 4.33
Ca(A337) 3.25 Cb(A340) 3.36
Cg2(V342) 3.41 O(K440) 3.69
Cd2(L441) 4.23 Cb(D444) 3.94

 

Cd1(L370) 2.92 Cb(R421) 4.30
Cd1(L425) 3.78 Cd1(L422) 4.62

n.r.

 

 

 

n.r.

DMSO-reductase

(1DMS)

Xe

x= 7.920
y=29.610
z=133.470

Cz(F110) 3.23 Cb(A428) 3.58
Cg1(V402) 3.56 Ce(M405) 4.05
Cd2(L406) 4.21 Cd2(L452) 4.23
Ch2(W449) 4.29

n.r.

 

*Occ=occupancy factor, B=temperature factor (refined, 2) for Xe or Kr. Refined using PROLSQ (Hendrickson & Konnert, 1985). Standard deviations are within 22 for B factor and 0.1 for Occ.

n.r. = not refined.

Refined with program SHARP (La Fortelle & Bricogne, 1997).

** refined using program MLPHARE (CCP4) after absolute scaling of the data.

*** ( Schiltz et al., 1977b).

Not available, coordinates should be requested to authors.