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Chlorine in PDB 5uub: Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant

Enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant:
3.4.24.27;

Protein crystallography data

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant, PDB code: 5uub was solved by D.H.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.90 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.707, 96.707, 105.611, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 16.5

Other elements in 5uub:

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant also contains other interesting chemical elements:

Zinc (Zn) 7 atoms
Calcium (Ca) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant (pdb code 5uub). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant, PDB code: 5uub:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5uub

Go back to Chlorine Binding Sites List in 5uub
Chlorine binding site 1 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:24.3
occ:0.69
 ZN A:ZN409 2.2 15.9 0.6
HA3 A:GLY248 2.8 20.3 1.0
HZ3 A:LYS239 2.8 28.5 1.0
HE2 A:TYR242 2.9 23.9 1.0
O A:HOH712 3.2 17.4 1.0
HD21 A:LEU243 3.3 20.4 1.0
CL A:CL412 3.4 44.7 0.7
HZ1 A:LYS239 3.4 28.5 1.0
O A:HOH619 3.5 31.7 1.0
HD23 A:LEU243 3.5 20.4 1.0
NZ A:LYS239 3.5 23.8 1.0
O A:HOH837 3.7 51.5 1.0
CA A:GLY248 3.7 16.9 1.0
O A:GLY247 3.8 15.6 1.0
CE2 A:TYR242 3.8 19.9 1.0
CD2 A:LEU243 3.8 17.0 1.0
H A:THR249 3.9 19.5 1.0
HA2 A:GLY248 4.0 20.3 1.0
HZ2 A:LYS239 4.1 28.5 1.0
HE3 A:LYS239 4.2 21.0 1.0
HD22 A:LEU243 4.3 20.4 1.0
N A:THR249 4.4 16.2 1.0
HD2 A:TYR242 4.4 20.8 1.0
C A:GLY248 4.4 17.9 1.0
O A:THR249 4.5 23.1 1.0
CE A:LYS239 4.5 17.5 1.0
CD2 A:TYR242 4.6 17.4 1.0
HB2 A:HIS250 4.6 19.7 1.0
OH A:TYR242 4.6 29.1 1.0
C A:GLY247 4.6 15.1 1.0
N A:GLY248 4.7 16.7 1.0
CZ A:TYR242 4.7 22.8 1.0
HE2 A:LYS239 4.8 21.0 1.0

Chlorine binding site 2 out of 4 in 5uub

Go back to Chlorine Binding Sites List in 5uub
Chlorine binding site 2 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:44.7
occ:0.73
 ZN A:ZN409 2.1 15.9 0.6
HZ3 A:LYS239 3.0 28.5 1.0
HZ2 A:LYS239 3.1 28.5 1.0
NZ A:LYS239 3.4 23.8 1.0
CL A:CL411 3.4 24.3 0.7
O A:HOH712 3.4 17.4 1.0
HZ1 A:LYS239 3.6 28.5 1.0
O A:SER206 3.7 16.5 1.0
CL A:CL413 3.9 21.6 1.0
HB2 A:ASP207 4.2 20.6 1.0
HO3B A:XYP417 4.4 53.2 0.5
ZN A:ZN410 4.4 17.9 0.9
HE2 A:TYR242 4.6 23.9 1.0
CE A:LYS239 4.7 17.5 1.0
HE2 A:LYS239 4.8 21.0 1.0
C A:SER206 4.8 15.7 1.0
HA A:ASP207 4.9 17.4 1.0
H3B A:XYP417 4.9 52.2 0.5
CB A:ASP207 5.0 17.1 1.0
HB2 A:SER206 5.0 19.3 1.0

Chlorine binding site 3 out of 4 in 5uub

Go back to Chlorine Binding Sites List in 5uub
Chlorine binding site 3 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:21.6
occ:0.99
 ZN A:ZN410 2.3 17.9 0.9
HE1 A:HIS250 3.0 19.4 1.0
HZ2 A:LYS239 3.3 28.5 1.0
ND1 A:HIS250 3.4 15.0 1.0
CE1 A:HIS250 3.5 16.2 1.0
O A:HOH530 3.5 19.3 1.0
O A:HOH712 3.5 17.4 1.0
HE2 A:LYS239 3.6 21.0 1.0
OD2 A:ASP215 3.6 15.7 1.0
O A:HOH595 3.7 29.7 1.0
HZ3 A:LYS239 3.8 28.5 1.0
ZN A:ZN409 3.8 15.9 0.6
OD1 A:ASP207 3.8 21.3 1.0
CL A:CL414 3.8 16.8 0.9
NZ A:LYS239 3.8 23.8 1.0
CL A:CL412 3.9 44.7 0.7
HA A:ASP207 4.1 17.4 1.0
CE A:LYS239 4.2 17.5 1.0
HD3 A:LYS239 4.4 20.4 1.0
HZ1 A:LYS239 4.6 28.5 1.0
CG A:ASP207 4.7 21.3 1.0
NE2 A:HIS250 4.7 14.6 1.0
HB2 A:ASP215 4.7 16.2 1.0
CG A:ASP215 4.8 15.2 1.0
CG A:HIS250 4.8 15.1 1.0
O A:SER206 4.8 16.5 1.0
CD A:LYS239 4.9 17.0 1.0
HD2 A:PRO208 4.9 17.6 1.0
HE3 A:LYS239 5.0 21.0 1.0

Chlorine binding site 4 out of 4 in 5uub

Go back to Chlorine Binding Sites List in 5uub
Chlorine binding site 4 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:16.8
occ:0.95
 ZN A:ZN410 2.2 17.9 0.9
H A:TYR251 2.6 19.0 1.0
HA A:HIS250 2.7 18.2 1.0
N A:TYR251 3.4 15.8 1.0
ND1 A:HIS250 3.5 15.0 1.0
O A:HOH712 3.6 17.4 1.0
CA A:HIS250 3.7 15.1 1.0
CL A:CL413 3.8 21.6 1.0
O A:THR249 3.9 23.1 1.0
C A:HIS250 4.1 15.6 1.0
CE1 A:HIS250 4.3 16.2 1.0
CG A:HIS250 4.3 15.1 1.0
HA A:TYR251 4.3 18.7 1.0
HE1 A:HIS250 4.3 19.4 1.0
CB A:HIS250 4.4 16.4 1.0
CA A:TYR251 4.5 15.6 1.0
N A:HIS250 4.6 17.1 1.0
C A:THR249 4.6 20.5 1.0
HB2 A:HIS250 4.6 19.7 1.0
H A:GLY252 4.7 20.2 1.0
CD2 A:TYR251 5.0 14.6 1.0
HD2 A:TYR251 5.0 17.5 1.0

Reference:

D.H.Juers, C.A.Farley, C.P.Saxby, R.A.Cotter, J.K.B.Cahn, R.C.Holton-Burke, K.Harrison, Z.Wu. The Impact of Cryosolution Thermal Contraction on Proteins and Protein Crystals: Volumes, Conformation and Order. Acta Crystallogr D Struct V. 74 922 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198901
DOI: 10.1107/S2059798318008793
Page generated: Fri Jul 26 18:20:45 2024

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