Atomistry » Zinc » PDB 5uqa-5v2w » 5uub
Atomistry »
  Zinc »
    PDB 5uqa-5v2w »
      5uub »

Zinc 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:

Calcium (Ca) 3 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc where determined in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant, PDB code: 5uub:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5uub

Go back to Zinc Binding Sites List in 5uub
Zinc binding site 1 out of 7 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 Zinc with other atoms in the Zn 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:Zn402

b:16.3
occ:1.00
 OD2 A:ASP185 2.0 14.2 1.0
OE2 A:GLU190 2.1 13.2 1.0
O A:HOH535 2.1 13.7 1.0
OE2 A:GLU177 2.1 12.8 1.0
O A:ASN183 2.3 14.9 1.0
CG A:ASP185 2.9 15.2 1.0
CD A:GLU177 3.0 12.5 1.0
CD A:GLU190 3.1 11.4 1.0
OD1 A:ASP185 3.4 13.6 1.0
HG3 A:GLU190 3.4 14.7 1.0
HA A:PRO184 3.4 20.4 1.0
C A:ASN183 3.5 16.7 1.0
OE1 A:GLU177 3.6 13.2 1.0
CA A:CA401 3.6 13.0 1.0
HB2 A:ASN183 3.6 23.9 1.0
CG A:GLU190 3.7 12.3 1.0
HG2 A:GLU190 3.7 14.7 1.0
O A:LYS182 3.9 24.9 1.0
HG2 A:GLU177 4.0 16.4 1.0
CA A:PRO184 4.0 17.0 1.0
CG A:GLU177 4.0 13.7 1.0
OD2 A:ASP191 4.0 18.8 1.0
H A:ASP185 4.0 15.6 1.0
OD1 A:ASP191 4.1 16.5 1.0
N A:ASP185 4.1 13.0 1.0
C A:PRO184 4.1 17.7 1.0
OE1 A:GLU190 4.1 13.5 1.0
HG3 A:GLU177 4.2 16.4 1.0
HB3 A:ASN183 4.2 23.9 1.0
CB A:ASP185 4.2 13.5 1.0
N A:PRO184 4.2 15.5 1.0
CB A:ASN183 4.2 19.9 1.0
HB3 A:ASP185 4.3 16.2 1.0
O A:HOH631 4.4 34.4 1.0
CG A:ASP191 4.4 15.6 1.0
CA A:ASN183 4.5 15.3 1.0
O A:PRO184 4.7 17.6 1.0
CA A:ASP185 4.8 12.7 1.0
C A:LYS182 4.9 25.6 1.0
HB2 A:ASP185 4.9 16.2 1.0

Zinc binding site 2 out of 7 in 5uub

Go back to Zinc Binding Sites List in 5uub
Zinc binding site 2 out of 7 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 Zinc with other atoms in the Zn 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:Zn405

b:14.6
occ:1.00
 O A:HOH737 1.9 17.4 1.0
OE2 A:GLU166 2.0 17.5 1.0
NE2 A:HIS146 2.0 12.7 1.0
NE2 A:HIS142 2.0 10.6 1.0
CD A:GLU166 2.9 21.8 1.0
CE1 A:HIS146 2.9 13.7 1.0
CD2 A:HIS142 3.0 11.7 1.0
CE1 A:HIS142 3.0 10.3 1.0
CD2 A:HIS146 3.1 13.6 1.0
HE1 A:HIS146 3.1 16.4 1.0
HD2 A:HIS142 3.2 14.1 1.0
OE1 A:GLU166 3.2 23.6 1.0
HE1 A:HIS142 3.3 12.3 1.0
HD2 A:HIS146 3.3 16.3 1.0
O A:HOH507 3.3 18.9 0.9
HH A:TYR157 3.3 23.0 0.5
HA A:MRD420 3.4 33.4 0.9
ZN A:ZN406 3.5 27.2 0.4
ZN A:ZN407 3.6 22.3 0.4
OE2 A:GLU143 3.8 28.5 1.0
O A:HOH506 3.8 29.2 1.0
HA A:GLU166 3.9 11.8 1.0
O4 A:MRD420 4.0 27.8 0.9
OH A:TYR157 4.0 19.2 0.5
ND1 A:HIS146 4.1 12.8 1.0
HB2 A:SER169 4.1 15.2 1.0
O A:HOH547 4.1 27.1 0.6
ND1 A:HIS142 4.1 11.2 1.0
CG A:HIS142 4.1 11.4 1.0
CG A:HIS146 4.2 11.9 1.0
NE2 A:HIS231 4.2 29.0 1.0
CG A:GLU166 4.2 14.5 1.0
HB3 A:SER169 4.3 15.2 1.0
HE1 A:TYR157 4.3 19.1 0.5
HG2 A:GLU166 4.3 17.4 1.0
O A:HOH695 4.3 47.7 1.0
CD A:GLU143 4.5 15.9 1.0
CB A:SER169 4.5 12.7 1.0
OE1 A:GLU143 4.6 19.1 1.0
OG A:SER169 4.7 12.5 1.0
CA A:GLU166 4.8 9.8 1.0
HD2 A:HIS231 4.8 34.4 1.0
HH22 A:ARG203 4.8 18.6 1.0
HG3 A:GLU166 4.8 17.4 1.0
HD1 A:HIS146 4.8 15.4 1.0
CD2 A:HIS231 4.9 28.7 1.0
CZ A:TYR157 4.9 15.2 0.5
HA A:GLU143 4.9 13.6 1.0
CE1 A:TYR157 4.9 15.9 0.5
HD1 A:HIS142 4.9 13.5 1.0
CB A:GLU166 5.0 11.9 1.0

Zinc binding site 3 out of 7 in 5uub

Go back to Zinc Binding Sites List in 5uub
Zinc binding site 3 out of 7 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 Zinc with other atoms in the Zn 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:Zn406

b:27.2
occ:0.44
 O A:HOH547 1.9 27.1 0.6
NE2 A:HIS231 1.9 29.0 1.0
O A:HOH737 2.2 17.4 1.0
CE1 A:HIS231 2.6 26.1 1.0
HE1 A:HIS231 2.7 31.4 1.0
O A:HOH506 2.7 29.2 1.0
ZN A:ZN407 3.1 22.3 0.4
CD2 A:HIS231 3.1 28.7 1.0
O A:HOH507 3.1 18.9 0.9
HH A:TYR157 3.4 23.0 0.5
HD2 A:HIS231 3.5 34.4 1.0
ZN A:ZN405 3.5 14.6 1.0
OH A:TYR157 3.5 19.2 0.5
OE2 A:GLU166 3.7 17.5 1.0
O4 A:MRD420 3.7 27.8 0.9
HA A:MRD420 3.8 33.4 0.9
ND1 A:HIS231 3.8 27.6 1.0
O A:HOH554 3.8 19.4 1.0
O2 A:MRD420 3.9 32.8 0.9
CD A:GLU166 4.0 21.8 1.0
OE1 A:GLU166 4.1 23.6 1.0
CG A:HIS231 4.1 24.0 1.0
H2 A:MRD420 4.1 39.3 0.9
O A:HOH749 4.1 36.9 1.0
OE2 A:GLU143 4.6 28.5 1.0
O A:HOH695 4.7 47.7 1.0
NE2 A:HIS142 4.7 10.6 1.0
HH22 A:ARG203 4.8 18.6 1.0
CZ A:TYR157 4.9 15.2 0.5

Zinc binding site 4 out of 7 in 5uub

Go back to Zinc Binding Sites List in 5uub
Zinc binding site 4 out of 7 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 Zinc with other atoms in the Zn 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:Zn407

b:22.3
occ:0.42
 OE2 A:GLU143 1.7 28.5 1.0
O A:HOH507 1.7 18.9 0.9
HA A:MRD420 1.9 33.4 0.9
O A:HOH737 2.1 17.4 1.0
O A:HOH554 2.1 19.4 1.0
O4 A:MRD420 2.2 27.8 0.9
H2 A:MRD420 2.4 39.3 0.9
O2 A:MRD420 2.5 32.8 0.9
CD A:GLU143 2.9 15.9 1.0
ZN A:ZN406 3.1 27.2 0.4
H4 A:MRD420 3.2 27.4 0.9
C4 A:MRD420 3.2 22.9 0.9
OE1 A:GLU143 3.5 19.1 1.0
O A:HOH506 3.5 29.2 1.0
HMC3 A:MRD420 3.5 31.0 0.9
C2 A:MRD420 3.6 27.9 0.9
ZN A:ZN405 3.6 14.6 1.0
HD2 A:HIS142 3.8 14.1 1.0
O A:HOH695 3.8 47.7 1.0
O A:ALA113 3.8 17.0 1.0
C3 A:MRD420 3.9 22.2 0.9
O A:HOH547 3.9 27.1 0.6
CM A:MRD420 4.0 25.8 0.9
CG A:GLU143 4.0 13.9 1.0
HG2 A:GLU143 4.0 16.7 1.0
NE2 A:HIS142 4.0 10.6 1.0
CD2 A:HIS142 4.1 11.7 1.0
HG3 A:GLU143 4.2 16.7 1.0
HMC1 A:MRD420 4.3 31.0 0.9
H3C2 A:MRD420 4.3 26.6 0.9
C5 A:MRD420 4.4 17.8 0.9
HA A:PHE114 4.5 17.8 1.0
HD2 A:HIS146 4.5 16.3 1.0
H5C3 A:MRD420 4.6 21.3 0.9
H5C1 A:MRD420 4.6 21.3 0.9
OD1 A:ASN112 4.6 21.4 0.9
HD22 A:ASN112 4.8 27.4 0.1
H3C1 A:MRD420 4.8 26.6 0.9
C1 A:MRD420 4.8 28.8 0.9
NE2 A:HIS146 4.8 12.7 1.0
NE2 A:HIS231 4.9 29.0 1.0
HMC2 A:MRD420 4.9 31.0 0.9
H1C3 A:MRD420 4.9 34.6 0.9
C A:ALA113 4.9 16.3 1.0
H A:ALA113 5.0 17.2 1.0

Zinc binding site 5 out of 7 in 5uub

Go back to Zinc Binding Sites List in 5uub
Zinc binding site 5 out of 7 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 Zinc with other atoms in the Zn binding site number 5 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:Zn408

b:66.0
occ:0.62
 ND1 A:HIS231 2.0 27.6 1.0
OD1 A:ASP226 2.0 30.6 1.0
CG A:ASP226 2.7 32.0 1.0
HB2 A:HIS231 2.8 25.1 1.0
CE1 A:HIS231 2.8 26.1 1.0
CG A:HIS231 2.9 24.0 1.0
OD2 A:ASP226 3.0 28.5 1.0
HE1 A:HIS231 3.0 31.4 1.0
CB A:HIS231 3.3 20.9 1.0
H A:HIS231 3.6 18.4 1.0
NE2 A:HIS231 3.8 29.0 1.0
O A:HOH692 3.8 47.0 1.0
CD2 A:HIS231 3.9 28.7 1.0
CB A:ASP226 3.9 26.9 1.0
HB3 A:HIS231 4.0 25.1 1.0
HG23 A:VAL230 4.0 24.1 1.0
HG22 A:VAL230 4.0 24.1 1.0
HB2 A:ASP226 4.1 32.3 1.0
HA A:ASP226 4.1 32.9 1.0
N A:HIS231 4.3 15.3 1.0
CA A:HIS231 4.4 17.3 1.0
CG2 A:VAL230 4.5 20.0 1.0
CA A:ASP226 4.6 27.4 1.0
HB3 A:ASP226 4.7 32.3 1.0
HD2 A:HIS231 4.7 34.4 1.0
HG21 A:VAL230 4.8 24.1 1.0
O A:ASP226 4.9 23.8 1.0

Zinc binding site 6 out of 7 in 5uub

Go back to Zinc Binding Sites List in 5uub
Zinc binding site 6 out of 7 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 Zinc with other atoms in the Zn binding site number 6 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:Zn409

b:15.9
occ:0.58
 HZ3 A:LYS239 1.3 28.5 1.0
O A:HOH712 1.9 17.4 1.0
NZ A:LYS239 2.1 23.8 1.0
CL A:CL412 2.1 44.7 0.7
CL A:CL411 2.2 24.3 0.7
HZ2 A:LYS239 2.3 28.5 1.0
HZ1 A:LYS239 2.5 28.5 1.0
CE A:LYS239 3.2 17.5 1.0
HE2 A:LYS239 3.3 21.0 1.0
HE3 A:LYS239 3.4 21.0 1.0
ZN A:ZN410 3.4 17.9 0.9
HD21 A:LEU243 3.7 20.4 1.0
CL A:CL413 3.8 21.6 1.0
HE2 A:TYR242 3.9 23.9 1.0
O A:SER206 4.0 16.5 1.0
HB2 A:HIS250 4.1 19.7 1.0
ND1 A:HIS250 4.4 15.0 1.0
O A:THR249 4.4 23.1 1.0
CD A:LYS239 4.5 17.0 1.0
HD23 A:LEU243 4.6 20.4 1.0
CD2 A:LEU243 4.6 17.0 1.0
CE2 A:TYR242 4.6 19.9 1.0
HD3 A:LYS239 4.6 20.4 1.0
HA3 A:GLY248 4.7 20.3 1.0
HD2 A:TYR242 4.7 20.8 1.0
HD2 A:LYS239 4.7 20.4 1.0
CB A:HIS250 4.9 16.4 1.0
HA A:HIS250 4.9 18.2 1.0
CG A:HIS250 5.0 15.1 1.0

Zinc binding site 7 out of 7 in 5uub

Go back to Zinc Binding Sites List in 5uub
Zinc binding site 7 out of 7 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 Zinc with other atoms in the Zn binding site number 7 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:Zn410

b:17.9
occ:0.90
 ND1 A:HIS250 2.0 15.0 1.0
O A:HOH712 2.1 17.4 1.0
CL A:CL414 2.2 16.8 0.9
CL A:CL413 2.3 21.6 1.0
CE1 A:HIS250 2.9 16.2 1.0
HA A:HIS250 2.9 18.2 1.0
HE1 A:HIS250 3.0 19.4 1.0
CG A:HIS250 3.2 15.1 1.0
HE2 A:LYS239 3.3 21.0 1.0
ZN A:ZN409 3.4 15.9 0.6
HB2 A:HIS250 3.5 19.7 1.0
HZ3 A:LYS239 3.5 28.5 1.0
CB A:HIS250 3.6 16.4 1.0
CA A:HIS250 3.7 15.1 1.0
H A:TYR251 3.8 19.0 1.0
HZ2 A:LYS239 3.9 28.5 1.0
O A:THR249 4.0 23.1 1.0
NZ A:LYS239 4.0 23.8 1.0
CE A:LYS239 4.1 17.5 1.0
NE2 A:HIS250 4.1 14.6 1.0
CD2 A:HIS250 4.2 14.3 1.0
CL A:CL412 4.4 44.7 0.7
N A:TYR251 4.4 15.8 1.0
HE3 A:LYS239 4.5 21.0 1.0
C A:HIS250 4.6 15.6 1.0
HB3 A:HIS250 4.6 19.7 1.0
N A:HIS250 4.7 17.1 1.0
OD2 A:ASP215 4.7 15.7 1.0
C A:THR249 4.8 20.5 1.0
HE2 A:HIS250 4.8 17.5 1.0
HZ1 A:LYS239 4.9 28.5 1.0
HD2 A:TYR251 4.9 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: Mon Oct 28 12:20:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy