Atomistry » Chlorine » PDB 5up0-5uwr » 5uub
Atomistry »
  Chlorine »
    PDB 5up0-5uwr »
      5uub »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy