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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

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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

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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

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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

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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

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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

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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

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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

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