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Chlorine in PDB 5uud: Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant

Enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant:
3.4.24.27;

Protein crystallography data

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant, PDB code: 5uud 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) 19.89 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.440, 96.440, 105.529, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.3

Other elements in 5uud:

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Calcium (Ca) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant (pdb code 5uud). 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 50% Dmf As Cryoprotectant, PDB code: 5uud:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5uud

Go back to Chlorine Binding Sites List in 5uud
Chlorine binding site 1 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf 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 50% Dmf As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:33.7
occ:0.78
 ZN A:ZN408 2.4 22.3 0.6
HA3 A:GLY248 2.9 25.9 1.0
HE2 A:TYR242 3.0 23.9 1.0
HZ1 A:LYS239 3.2 32.4 1.0
HD21 A:LEU243 3.5 22.3 1.0
HD23 A:LEU243 3.6 22.3 1.0
O A:HOH539 3.6 33.2 1.0
O A:HOH774 3.6 32.9 1.0
O A:GLY247 3.7 17.7 1.0
HZ2 A:LYS239 3.7 32.4 1.0
CA A:GLY248 3.8 21.6 1.0
NZ A:LYS239 3.9 27.0 1.0
CE2 A:TYR242 3.9 19.9 1.0
CD2 A:LEU243 4.0 18.6 1.0
CL A:CL411 4.0 54.0 0.9
HA2 A:GLY248 4.1 25.9 1.0
H A:THR249 4.2 26.7 1.0
HH A:TYR242 4.3 31.2 1.0
HD2 A:TYR242 4.3 22.1 1.0
HD22 A:LEU243 4.4 22.3 1.0
HZ3 A:LYS239 4.4 32.4 1.0
N A:THR249 4.5 22.3 1.0
C A:GLY248 4.5 22.8 1.0
C A:GLY247 4.6 17.7 1.0
CD2 A:TYR242 4.6 18.4 1.0
HE3 A:LYS239 4.6 25.9 1.0
O A:THR249 4.6 24.5 1.0
N A:GLY248 4.7 20.1 1.0
CE A:LYS239 4.9 21.6 1.0
HB2 A:HIS250 4.9 23.2 1.0
CZ A:TYR242 4.9 23.4 1.0
OH A:TYR242 5.0 26.0 1.0

Chlorine binding site 2 out of 4 in 5uud

Go back to Chlorine Binding Sites List in 5uud
Chlorine binding site 2 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf 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 50% Dmf As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:54.0
occ:0.89
 ZN A:ZN408 2.4 22.3 0.6
HZ3 A:LYS239 3.1 32.4 1.0
HZ1 A:LYS239 3.1 32.4 1.0
O A:HOH774 3.4 32.9 1.0
NZ A:LYS239 3.5 27.0 1.0
CL A:CL412 3.5 26.7 0.6
O A:SER206 3.6 19.0 1.0
HB2 A:ASP207 3.8 24.4 1.0
HZ2 A:LYS239 3.8 32.4 1.0
CL A:CL410 4.0 33.7 0.8
ZN A:ZN409 4.2 23.1 0.6
HA A:ASP207 4.5 23.3 1.0
CB A:ASP207 4.6 20.4 1.0
C A:SER206 4.6 18.3 1.0
HE2 A:LYS239 4.7 25.9 1.0
CG A:ASP207 4.8 28.2 1.0
CE A:LYS239 4.8 21.6 1.0
OD1 A:ASP207 4.9 28.8 1.0
HB2 A:SER206 5.0 23.6 1.0
CA A:ASP207 5.0 19.4 1.0

Chlorine binding site 3 out of 4 in 5uud

Go back to Chlorine Binding Sites List in 5uud
Chlorine binding site 3 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf 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 50% Dmf As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:26.7
occ:0.61
 ZN A:ZN409 2.3 23.1 0.6
HE1 A:HIS250 3.0 23.1 1.0
HZ3 A:LYS239 3.4 32.4 1.0
O A:HOH774 3.5 32.9 1.0
CE1 A:HIS250 3.5 19.2 1.0
HE2 A:LYS239 3.5 25.9 1.0
CL A:CL411 3.5 54.0 0.9
O A:HOH512 3.6 31.3 1.0
ND1 A:HIS250 3.6 18.0 1.0
OD2 A:ASP215 3.6 19.8 1.0
OD1 A:ASP207 3.7 28.8 1.0
HZ1 A:LYS239 3.8 32.4 1.0
CL A:CL413 3.8 25.9 0.8
HA A:ASP207 3.9 23.3 1.0
ZN A:ZN408 3.9 22.3 0.6
NZ A:LYS239 4.0 27.0 1.0
CE A:LYS239 4.2 21.6 1.0
HD3 A:LYS239 4.5 21.4 1.0
CG A:ASP207 4.5 28.2 1.0
O A:SER206 4.6 19.0 1.0
HB2 A:ASP215 4.7 23.4 1.0
CG A:ASP215 4.7 18.6 1.0
NE2 A:HIS250 4.8 20.9 1.0
HZ2 A:LYS239 4.8 32.4 1.0
HD2 A:PRO208 4.8 17.9 1.0
CA A:ASP207 4.8 19.4 1.0
HB2 A:ASP207 4.8 24.4 1.0
CG A:HIS250 4.9 19.6 1.0
CD A:LYS239 4.9 17.8 1.0
HE3 A:LYS239 5.0 25.9 1.0
CB A:ASP207 5.0 20.4 1.0

Chlorine binding site 4 out of 4 in 5uud

Go back to Chlorine Binding Sites List in 5uud
Chlorine binding site 4 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf 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 50% Dmf As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:25.9
occ:0.77
 ZN A:ZN409 2.1 23.1 0.6
H A:TYR251 2.7 23.3 1.0
HA A:HIS250 2.8 24.0 1.0
ND1 A:HIS250 3.3 18.0 1.0
O A:HOH774 3.5 32.9 1.0
N A:TYR251 3.6 19.4 1.0
CA A:HIS250 3.7 20.0 1.0
CL A:CL412 3.8 26.7 0.6
O A:HOH687 3.9 29.5 1.0
O A:THR249 4.0 24.5 1.0
CE1 A:HIS250 4.1 19.2 1.0
HE1 A:HIS250 4.2 23.1 1.0
C A:HIS250 4.2 18.3 1.0
CG A:HIS250 4.2 19.6 1.0
HA A:TYR251 4.4 24.0 1.0
CB A:HIS250 4.5 19.3 1.0
CA A:TYR251 4.6 20.0 1.0
HB2 A:HIS250 4.6 23.2 1.0
N A:HIS250 4.7 20.4 1.0
C A:THR249 4.7 21.9 1.0
H A:GLY252 4.9 26.9 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 18:20:55 2024

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