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Zinc 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:

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% Dmf As Cryoprotectant (pdb code 5uud). 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% Dmf As Cryoprotectant, PDB code: 5uud:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5uud

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Zinc binding site 1 out of 6 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf 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% Dmf As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:22.0
occ:1.00
 OD2 A:ASP185 2.0 19.0 1.0
O A:HOH523 2.1 17.9 1.0
OE2 A:GLU190 2.1 17.2 1.0
OE2 A:GLU177 2.1 16.4 1.0
O A:ASN183 2.4 21.1 0.5
O A:ASN183 2.4 18.9 0.6
CG A:ASP185 3.0 21.7 1.0
CD A:GLU177 3.0 18.4 1.0
CD A:GLU190 3.1 15.1 1.0
OD1 A:ASP185 3.4 17.9 1.0
HA A:PRO184 3.4 26.9 1.0
HG3 A:GLU190 3.4 21.1 1.0
C A:ASN183 3.5 22.0 0.6
OE1 A:GLU177 3.5 17.1 1.0
CA A:CA401 3.5 16.9 1.0
C A:ASN183 3.5 23.3 0.5
CG A:GLU190 3.7 17.6 1.0
HG2 A:GLU190 3.7 21.1 1.0
O A:LYS182 3.7 25.3 0.6
HB2 A:ASN183 3.8 34.3 0.6
OD1 A:ASN183 3.9 42.0 0.6
HB2 A:ASN183 3.9 32.6 0.5
HG2 A:GLU177 4.0 21.9 1.0
OD2 A:ASP191 4.0 21.8 1.0
CG A:GLU177 4.0 18.3 1.0
CA A:PRO184 4.0 22.4 1.0
OD1 A:ASP191 4.1 19.6 1.0
OE1 A:GLU190 4.1 17.9 1.0
C A:PRO184 4.1 23.0 1.0
N A:ASP185 4.2 19.2 1.0
HG3 A:GLU177 4.2 21.9 1.0
H A:ASP185 4.2 23.0 1.0
CB A:ASP185 4.2 18.4 1.0
N A:PRO184 4.2 23.4 1.0
OD1 A:ASN183 4.3 27.5 0.5
HB3 A:ASP185 4.3 22.1 1.0
CG A:ASP191 4.4 21.1 1.0
CB A:ASN183 4.4 28.6 0.6
CB A:ASN183 4.5 27.1 0.5
CA A:ASN183 4.5 23.5 0.6
CG A:ASN183 4.6 36.0 0.6
CG A:ASN183 4.6 31.0 0.5
O A:PRO184 4.6 24.0 1.0
CA A:ASN183 4.7 24.0 0.5
C A:LYS182 4.8 23.4 0.6
CA A:ASP185 4.8 16.6 1.0
HB2 A:ASP185 4.9 22.1 1.0

Zinc binding site 2 out of 6 in 5uud

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

b:16.2
occ:1.00
 O A:HOH746 1.9 16.1 1.0
OE2 A:GLU166 2.0 19.2 1.0
NE2 A:HIS146 2.0 13.3 1.0
NE2 A:HIS142 2.0 12.2 1.0
CD A:GLU166 2.9 22.3 1.0
CE1 A:HIS146 3.0 14.0 1.0
CE1 A:HIS142 3.0 13.6 1.0
CD2 A:HIS142 3.0 12.9 1.0
CD2 A:HIS146 3.0 14.9 1.0
HE1 A:HIS146 3.1 16.8 1.0
OE1 A:GLU166 3.2 21.6 1.0
O A:HOH520 3.2 26.2 1.0
HD2 A:HIS142 3.2 15.5 1.0
HE1 A:HIS142 3.2 16.3 1.0
HD2 A:HIS146 3.3 17.8 1.0
HH A:TYR157 3.3 35.8 1.0
ZN A:ZN406 3.4 18.3 0.6
ZN A:ZN407 3.5 34.1 0.3
OE2 A:GLU143 3.6 21.7 1.0
O A:HOH642 3.9 47.4 1.0
HA A:GLU166 3.9 15.5 1.0
OH A:TYR157 4.0 29.8 1.0
HC A:DMF418 4.0 35.7 0.9
ND1 A:HIS146 4.1 13.0 1.0
ND1 A:HIS142 4.1 12.8 1.0
HB2 A:SER169 4.1 16.7 1.0
CG A:HIS146 4.2 13.2 1.0
CG A:HIS142 4.2 13.6 1.0
CG A:GLU166 4.2 17.3 1.0
HE1 A:TYR157 4.3 31.7 1.0
HG2 A:GLU166 4.3 20.8 1.0
NE2 A:HIS231 4.3 22.0 1.0
HB3 A:SER169 4.4 16.7 1.0
CD A:GLU143 4.4 18.5 1.0
O A:DMF418 4.5 32.3 0.9
O A:HOH573 4.5 37.7 1.0
C A:DMF418 4.6 29.8 0.9
CB A:SER169 4.6 13.9 1.0
O A:HOH799 4.7 30.2 1.0
OG A:SER169 4.8 13.9 1.0
CA A:GLU166 4.8 12.9 1.0
HD2 A:HIS231 4.8 27.4 1.0
OE1 A:GLU143 4.8 19.0 1.0
HG3 A:GLU166 4.8 20.8 1.0
HH22 A:ARG203 4.8 19.6 1.0
HD1 A:HIS146 4.9 15.6 1.0
CZ A:TYR157 4.9 27.2 1.0
CE1 A:TYR157 4.9 26.4 1.0
HA A:GLU143 4.9 17.7 1.0
HD1 A:HIS142 4.9 15.4 1.0
O A:HOH815 4.9 27.7 1.0
CD2 A:HIS231 4.9 22.8 1.0

Zinc binding site 3 out of 6 in 5uud

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

b:18.3
occ:0.58
 NE2 A:HIS231 1.9 22.0 1.0
O A:HOH746 2.0 16.1 1.0
O A:HOH815 2.0 27.7 1.0
O A:HOH799 2.1 30.2 1.0
O A:HOH520 2.2 26.2 1.0
CE1 A:HIS231 2.9 22.8 1.0
CD2 A:HIS231 2.9 22.8 1.0
ZN A:ZN407 3.0 34.1 0.3
HE1 A:HIS231 3.1 27.4 1.0
HD2 A:HIS231 3.1 27.4 1.0
ZN A:ZN405 3.4 16.2 1.0
HH A:TYR157 3.6 35.8 1.0
O A:HOH642 3.7 47.4 1.0
OE2 A:GLU166 3.7 19.2 1.0
OH A:TYR157 3.7 29.8 1.0
O A:HOH654 3.9 24.5 0.9
O A:HOH593 4.0 40.0 1.0
O A:DMF418 4.0 32.3 0.9
OE1 A:GLU166 4.0 21.6 1.0
ND1 A:HIS231 4.0 22.8 1.0
CD A:GLU166 4.0 22.3 1.0
O A:HOH791 4.0 29.9 1.0
CG A:HIS231 4.1 19.4 1.0
C A:DMF418 4.1 29.8 0.9
HC A:DMF418 4.3 35.7 0.9
OE2 A:GLU143 4.4 21.7 1.0
NE2 A:HIS142 4.5 12.2 1.0
HH22 A:ARG203 4.6 19.6 1.0
N A:DMF418 4.7 26.3 0.9
HH12 A:ARG203 4.7 23.0 1.0
H11 A:DMF418 4.7 33.5 0.9
HD1 A:HIS231 4.8 27.4 1.0
H13 A:DMF418 4.9 33.5 0.9

Zinc binding site 4 out of 6 in 5uud

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

b:34.1
occ:0.34
 OE2 A:GLU143 1.8 21.7 1.0
O A:HOH654 1.9 24.5 0.9
O A:HOH746 2.0 16.1 1.0
H11 A:DMF418 2.7 33.5 0.9
CD A:GLU143 2.8 18.5 1.0
ZN A:ZN406 3.0 18.3 0.6
O A:HOH573 3.1 37.7 1.0
HC A:DMF418 3.1 35.7 0.9
O A:HOH799 3.1 30.2 1.0
O A:HOH815 3.3 27.7 1.0
OE1 A:GLU143 3.3 19.0 1.0
ZN A:ZN405 3.5 16.2 1.0
O A:HOH642 3.5 47.4 1.0
C A:DMF418 3.6 29.8 0.9
C1 A:DMF418 3.6 27.9 0.9
H13 A:DMF418 3.7 33.5 0.9
O A:ALA113 3.7 18.0 1.0
N A:DMF418 4.0 26.3 0.9
O A:HOH520 4.0 26.2 1.0
HD2 A:HIS142 4.0 15.5 1.0
CG A:GLU143 4.0 13.9 1.0
HD2 A:HIS146 4.0 17.8 1.0
HA A:PHE114 4.1 20.1 1.0
HG2 A:GLU143 4.1 16.7 1.0
O A:DMF418 4.2 32.3 0.9
HG3 A:GLU143 4.3 16.7 1.0
NE2 A:HIS142 4.3 12.2 1.0
HB3 A:PHE114 4.4 20.9 1.0
CD2 A:HIS142 4.4 12.9 1.0
O A:HOH593 4.5 40.0 1.0
NE2 A:HIS146 4.5 13.3 1.0
H12 A:DMF418 4.5 33.5 0.9
CD2 A:HIS146 4.6 14.9 1.0
O A:HOH780 4.6 36.6 1.0
OD1 A:ASN112 4.7 26.2 1.0
C A:ALA113 4.9 18.7 1.0
CA A:PHE114 4.9 16.7 1.0
NE2 A:HIS231 4.9 22.0 1.0
CB A:PHE114 4.9 17.4 1.0
HB2 A:PHE114 4.9 20.9 1.0
OE2 A:GLU166 4.9 19.2 1.0

Zinc binding site 5 out of 6 in 5uud

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

b:22.3
occ:0.56
 HZ1 A:LYS239 1.3 32.4 1.0
O A:HOH774 1.8 32.9 1.0
NZ A:LYS239 2.2 27.0 1.0
CL A:CL411 2.4 54.0 0.9
CL A:CL410 2.4 33.7 0.8
HZ3 A:LYS239 2.4 32.4 1.0
HZ2 A:LYS239 2.5 32.4 1.0
CE A:LYS239 3.2 21.6 1.0
HE2 A:LYS239 3.3 25.9 1.0
HE3 A:LYS239 3.4 25.9 1.0
ZN A:ZN409 3.5 23.1 0.6
HD21 A:LEU243 3.6 22.3 1.0
O A:SER206 3.9 19.0 1.0
CL A:CL412 3.9 26.7 0.6
HB2 A:HIS250 4.1 23.2 1.0
HE2 A:TYR242 4.1 23.9 1.0
ND1 A:HIS250 4.4 18.0 1.0
HD23 A:LEU243 4.5 22.3 1.0
CD2 A:LEU243 4.5 18.6 1.0
O A:THR249 4.5 24.5 1.0
CD A:LYS239 4.6 17.8 1.0
HD2 A:TYR242 4.6 22.1 1.0
HD3 A:LYS239 4.7 21.4 1.0
HD2 A:LYS239 4.8 21.4 1.0
CE2 A:TYR242 4.8 19.9 1.0
HA3 A:GLY248 4.9 25.9 1.0
CB A:HIS250 4.9 19.3 1.0
HA A:HIS250 4.9 24.0 1.0
CG A:HIS250 5.0 19.6 1.0

Zinc binding site 6 out of 6 in 5uud

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

b:23.1
occ:0.64
 ND1 A:HIS250 2.0 18.0 1.0
O A:HOH774 2.0 32.9 1.0
CL A:CL413 2.1 25.9 0.8
CL A:CL412 2.3 26.7 0.6
CE1 A:HIS250 2.8 19.2 1.0
HE1 A:HIS250 2.8 23.1 1.0
HA A:HIS250 3.1 24.0 1.0
CG A:HIS250 3.2 19.6 1.0
HE2 A:LYS239 3.3 25.9 1.0
ZN A:ZN408 3.5 22.3 0.6
HZ1 A:LYS239 3.6 32.4 1.0
HB2 A:HIS250 3.7 23.2 1.0
CB A:HIS250 3.8 19.3 1.0
CA A:HIS250 3.8 20.0 1.0
H A:TYR251 3.9 23.3 1.0
NE2 A:HIS250 4.0 20.9 1.0
HZ3 A:LYS239 4.1 32.4 1.0
CE A:LYS239 4.1 21.6 1.0
NZ A:LYS239 4.1 27.0 1.0
O A:THR249 4.2 24.5 1.0
CD2 A:HIS250 4.2 17.2 1.0
CL A:CL411 4.2 54.0 0.9
HE3 A:LYS239 4.4 25.9 1.0
N A:TYR251 4.5 19.4 1.0
OD2 A:ASP215 4.6 19.8 1.0
C A:HIS250 4.7 18.3 1.0
HB3 A:HIS250 4.7 23.2 1.0
HE2 A:HIS250 4.7 25.1 1.0
N A:HIS250 4.9 20.4 1.0
HZ2 A:LYS239 4.9 32.4 1.0
C A:THR249 5.0 21.9 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: Mon Oct 28 12:20:08 2024

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