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Zinc in PDB 5uue: Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol As Cryoprotectant

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

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

Protein crystallography data

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol As Cryoprotectant, PDB code: 5uue 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) 20.80 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.149, 96.149, 104.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.5

Other elements in 5uue:

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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 50% Methanol As Cryoprotectant (pdb code 5uue). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol As Cryoprotectant, PDB code: 5uue:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5uue

Go back to Zinc Binding Sites List in 5uue
Zinc binding site 1 out of 6 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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 50% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:21.8
occ:1.00
 OD2 A:ASP185 2.0 18.0 1.0
OE2 A:GLU190 2.1 14.7 1.0
O A:HOH596 2.1 17.0 1.0
O A:HOH562 2.1 19.1 1.0
OE2 A:GLU177 2.2 16.9 1.0
O A:ASN183 2.3 17.2 1.0
CD A:GLU177 3.0 16.9 1.0
CG A:ASP185 3.0 23.9 1.0
CD A:GLU190 3.1 13.9 1.0
OD1 A:ASP185 3.4 18.4 1.0
HG3 A:GLU190 3.4 22.0 1.0
C A:ASN183 3.4 20.0 1.0
HA A:PRO184 3.5 29.9 1.0
OE1 A:GLU177 3.5 15.0 1.0
CA A:CA401 3.6 16.6 1.0
CG A:GLU190 3.7 18.4 1.0
HB2 A:ASN183 3.7 27.1 1.0
HG2 A:GLU190 3.8 22.0 1.0
O A:LYS182 4.0 29.3 1.0
HG2 A:GLU177 4.0 20.8 1.0
CG A:GLU177 4.0 17.3 1.0
CA A:PRO184 4.0 24.9 1.0
OD2 A:ASP191 4.1 20.1 1.0
H A:ASP185 4.1 23.1 1.0
OD1 A:ASP191 4.1 18.4 1.0
N A:ASP185 4.1 19.2 1.0
OE1 A:GLU190 4.1 14.3 1.0
C A:PRO184 4.1 23.6 1.0
HB3 A:ASN183 4.1 27.1 1.0
HG3 A:GLU177 4.2 20.8 1.0
N A:PRO184 4.2 22.4 1.0
CB A:ASP185 4.3 20.9 1.0
CB A:ASN183 4.3 22.6 1.0
HB3 A:ASP185 4.3 25.1 1.0
O A:HOH527 4.4 35.4 1.0
CG A:ASP191 4.4 19.1 1.0
CA A:ASN183 4.5 18.0 1.0
O A:PRO184 4.7 22.8 1.0
CA A:ASP185 4.8 16.4 1.0
C A:LYS182 5.0 25.9 1.0
HB2 A:ASP185 5.0 25.1 1.0

Zinc binding site 2 out of 6 in 5uue

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Zinc binding site 2 out of 6 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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 50% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:17.8
occ:1.00
 OE2 A:GLU166 1.7 12.1 0.5
O A:HOH589 1.8 23.0 1.0
NE2 A:HIS146 2.0 14.5 1.0
NE2 A:HIS142 2.1 11.7 1.0
OE1 A:GLU166 2.1 17.1 0.5
CD A:GLU166 2.7 13.8 0.5
CD A:GLU166 2.9 14.0 0.5
CE1 A:HIS146 3.0 13.3 1.0
CE1 A:HIS142 3.0 12.9 1.0
OE2 A:GLU166 3.0 17.3 0.5
OE1 A:GLU166 3.0 13.8 0.5
CD2 A:HIS146 3.1 16.7 1.0
CD2 A:HIS142 3.1 15.4 1.0
HE1 A:HIS146 3.1 16.0 1.0
HE1 A:HIS142 3.2 15.5 1.0
HH A:TYR157 3.2 25.1 0.6
O A:HOH501 3.3 34.9 1.0
HD2 A:HIS142 3.3 18.5 1.0
HD2 A:HIS146 3.3 20.0 1.0
ZN A:ZN406 3.3 23.2 0.5
OE2 A:GLU143 3.7 22.0 1.0
O A:HOH655 3.8 45.5 1.0
OH A:TYR157 3.9 20.9 0.6
HA A:GLU166 3.9 16.2 0.5
HA A:GLU166 3.9 16.0 0.5
O A:HOH795 4.0 38.7 1.0
CG A:GLU166 4.0 16.2 0.5
HB2 A:SER169 4.0 17.4 1.0
O A:HOH532 4.1 39.9 1.0
HG2 A:GLU166 4.1 19.4 0.5
ND1 A:HIS146 4.1 14.0 1.0
NE2 A:HIS231 4.1 28.8 1.0
ND1 A:HIS142 4.1 13.0 1.0
CG A:HIS146 4.2 16.4 1.0
CG A:HIS142 4.2 15.3 1.0
HB3 A:SER169 4.2 17.4 1.0
HE1 A:TYR157 4.3 22.3 0.6
CG A:GLU166 4.4 15.1 0.5
O A:HOH537 4.4 45.0 1.0
CB A:SER169 4.5 14.5 1.0
HB3 A:GLU166 4.6 15.7 0.5
CD A:GLU143 4.6 18.5 1.0
HG3 A:GLU166 4.6 19.4 0.5
OG A:SER169 4.7 14.6 1.0
HD2 A:HIS231 4.7 36.7 1.0
CA A:GLU166 4.7 13.3 0.5
CA A:GLU166 4.7 13.5 0.5
HH22 A:ARG203 4.7 19.3 1.0
CZ A:TYR157 4.8 19.7 0.6
CD2 A:HIS231 4.8 30.6 1.0
CB A:GLU166 4.8 13.1 0.5
HG3 A:GLU166 4.8 18.2 0.5
O A:HOH623 4.9 34.9 1.0
CE1 A:TYR157 4.9 18.6 0.6
CB A:GLU166 4.9 13.5 0.5
HG2 A:GLU166 4.9 18.2 0.5
HD1 A:HIS146 4.9 16.8 1.0
HD1 A:HIS142 4.9 15.6 1.0
OE1 A:GLU143 4.9 18.9 1.0
HA A:GLU143 5.0 18.5 1.0

Zinc binding site 3 out of 6 in 5uue

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Zinc binding site 3 out of 6 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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 50% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:23.2
occ:0.47
 O A:HOH589 1.9 23.0 1.0
NE2 A:HIS231 2.0 28.8 1.0
O A:HOH819 2.1 42.3 1.0
O A:HOH532 2.3 39.9 1.0
O A:HOH795 2.5 38.7 1.0
O A:HOH501 2.6 34.9 1.0
CE1 A:HIS231 2.8 30.9 1.0
HE1 A:HIS231 2.8 37.1 1.0
CD2 A:HIS231 3.1 30.6 1.0
ZN A:ZN405 3.3 17.8 1.0
HD2 A:HIS231 3.4 36.7 1.0
HH A:TYR157 3.6 25.1 0.6
OE2 A:GLU166 3.6 12.1 0.5
O A:HOH703 3.7 30.8 1.0
OH A:TYR157 3.7 20.9 0.6
O A:HOH537 3.9 45.0 1.0
O A:HOH767 3.9 30.7 1.0
O A:HOH655 3.9 45.5 1.0
ND1 A:HIS231 4.0 27.5 1.0
O A:HOH835 4.0 47.4 1.0
OE1 A:GLU166 4.0 13.8 0.5
CD A:GLU166 4.0 13.8 0.5
OE1 A:GLU166 4.0 17.1 0.5
CG A:HIS231 4.2 29.6 1.0
OE2 A:GLU166 4.2 17.3 0.5
OE2 A:GLU143 4.4 22.0 1.0
CD A:GLU166 4.4 14.0 0.5
NE2 A:HIS142 4.4 11.7 1.0
HH22 A:ARG203 4.6 19.3 1.0
HH12 A:ARG203 4.8 22.5 1.0

Zinc binding site 4 out of 6 in 5uue

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Zinc binding site 4 out of 6 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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 50% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:48.1
occ:0.48
 OD1 A:ASP226 1.6 28.9 1.0
ND1 A:HIS231 2.0 27.5 1.0
O A:HOH724 2.1 64.1 1.0
CG A:ASP226 2.6 29.8 1.0
HB2 A:HIS231 2.7 34.1 1.0
CE1 A:HIS231 2.9 30.9 1.0
CG A:HIS231 2.9 29.6 1.0
O A:HOH772 2.9 53.1 1.0
OD2 A:ASP226 3.1 31.0 1.0
HE1 A:HIS231 3.1 37.1 1.0
CB A:HIS231 3.3 28.4 1.0
O A:HOH798 3.4 53.5 1.0
H A:HIS231 3.7 23.1 1.0
CB A:ASP226 3.8 28.8 1.0
HA A:ASP226 3.8 34.8 1.0
NE2 A:HIS231 3.9 28.8 1.0
CD2 A:HIS231 3.9 30.6 1.0
HB3 A:HIS231 3.9 34.1 1.0
HB2 A:ASP226 4.0 34.6 1.0
HG23 A:VAL230 4.0 26.9 1.0
HG22 A:VAL230 4.1 26.9 1.0
N A:HIS231 4.3 19.2 1.0
CA A:ASP226 4.3 29.0 1.0
CA A:HIS231 4.4 23.4 1.0
CG2 A:VAL230 4.5 22.4 1.0
HB3 A:ASP226 4.6 34.6 1.0
HD2 A:HIS231 4.8 36.7 1.0
O A:ASP226 4.8 26.0 1.0
HG21 A:VAL230 4.8 26.9 1.0
C A:ASP226 4.9 27.6 1.0
HA A:HIS231 5.0 28.1 1.0

Zinc binding site 5 out of 6 in 5uue

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Zinc binding site 5 out of 6 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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 50% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:19.0
occ:0.64
 HZ1 A:LYS239 1.2 33.3 1.0
O A:HOH579 1.9 20.5 1.0
NZ A:LYS239 2.1 27.7 1.0
CL A:CL411 2.2 56.1 0.8
CL A:CL410 2.2 29.7 0.9
HZ3 A:LYS239 2.4 33.3 1.0
HZ2 A:LYS239 2.5 33.3 1.0
CE A:LYS239 3.1 19.7 1.0
HE2 A:LYS239 3.1 23.6 1.0
HE3 A:LYS239 3.2 23.6 1.0
ZN A:ZN409 3.4 20.2 0.9
HD21 A:LEU243 3.7 18.8 1.0
CL A:CL412 3.8 25.0 1.0
O A:HOH860 3.9 50.9 1.0
O A:SER206 3.9 21.6 1.0
HE2 A:TYR242 4.1 21.1 1.0
HB2 A:HIS250 4.2 21.1 1.0
O A:THR249 4.3 27.1 1.0
CD A:LYS239 4.4 13.7 1.0
ND1 A:HIS250 4.5 16.8 1.0
CD2 A:LEU243 4.6 15.6 1.0
HD23 A:LEU243 4.6 18.8 1.0
HD2 A:LYS239 4.6 16.4 1.0
HD2 A:TYR242 4.7 22.4 1.0
HD3 A:LYS239 4.7 16.4 1.0
CE2 A:TYR242 4.7 17.6 1.0
HA A:HIS250 4.9 22.0 1.0
HA3 A:GLY248 4.9 26.8 1.0
CB A:HIS250 5.0 17.6 1.0

Zinc binding site 6 out of 6 in 5uue

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Zinc binding site 6 out of 6 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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 50% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:20.2
occ:0.89
 ND1 A:HIS250 2.1 16.8 1.0
O A:HOH579 2.2 20.5 1.0
CL A:CL413 2.2 20.1 1.0
CL A:CL412 2.2 25.0 1.0
HA A:HIS250 2.9 22.0 1.0
CE1 A:HIS250 2.9 19.9 1.0
HE1 A:HIS250 3.0 23.9 1.0
HE2 A:LYS239 3.2 23.6 1.0
CG A:HIS250 3.2 16.1 1.0
ZN A:ZN408 3.4 19.0 0.6
HB2 A:HIS250 3.6 21.1 1.0
CA A:HIS250 3.7 18.3 1.0
CB A:HIS250 3.7 17.6 1.0
HZ1 A:LYS239 3.7 33.3 1.0
H A:TYR251 3.9 23.4 1.0
CE A:LYS239 4.0 19.7 1.0
O A:THR249 4.0 27.1 1.0
HE3 A:LYS239 4.1 23.6 1.0
NE2 A:HIS250 4.1 16.8 1.0
NZ A:LYS239 4.2 27.7 1.0
CD2 A:HIS250 4.3 14.9 1.0
HZ3 A:LYS239 4.4 33.3 1.0
CL A:CL411 4.5 56.1 0.8
N A:TYR251 4.5 19.5 1.0
C A:HIS250 4.6 19.0 1.0
HB3 A:HIS250 4.6 21.1 1.0
N A:HIS250 4.7 20.5 1.0
C A:THR249 4.7 23.5 1.0
HE2 A:HIS250 4.8 20.2 1.0
OD2 A:ASP215 4.9 19.0 1.0
HD2 A:TYR251 5.0 21.8 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 12:22:20 2024

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