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Zinc in PDB 6n4z: Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K

Enzymatic activity of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K

All present enzymatic activity of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K:
3.4.24.27;

Protein crystallography data

The structure of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K, PDB code: 6n4z was solved by D.H.Juers, K.Harrison, B.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 1.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.725, 96.725, 106.535, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 16.1

Other elements in 6n4z:

The structure of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K (pdb code 6n4z). 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 (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K, PDB code: 6n4z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6n4z

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Zinc binding site 1 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:24.4
occ:0.50
 O A:HOH824 2.0 17.9 0.9
ND1 A:HIS250 2.2 16.2 1.0
O A:HOH832 2.3 24.8 1.0
O A:HOH536 3.0 30.0 0.8
CE1 A:HIS250 3.0 17.5 1.0
HE1 A:HIS250 3.0 21.0 1.0
HA A:HIS250 3.1 18.6 1.0
HZ1 A:LYS239 3.2 27.1 1.0
CG A:HIS250 3.3 15.6 1.0
HE2 A:LYS239 3.5 22.1 1.0
ZN A:ZN410 3.6 57.0 0.6
HB2 A:HIS250 3.6 18.5 1.0
CB A:HIS250 3.8 15.4 1.0
NZ A:LYS239 3.8 22.5 1.0
HZ3 A:LYS239 3.8 27.1 1.0
CA A:HIS250 3.8 15.5 1.0
H A:TYR251 3.9 20.5 1.0
CE A:LYS239 4.1 18.4 1.0
NE2 A:HIS250 4.2 16.8 1.0
O A:THR249 4.3 23.5 1.0
CD2 A:HIS250 4.3 16.6 1.0
O A:HOH870 4.4 54.1 1.0
N A:TYR251 4.6 17.1 1.0
HZ2 A:LYS239 4.6 27.1 1.0
HE3 A:LYS239 4.6 22.1 1.0
C A:HIS250 4.7 16.0 1.0
HB3 A:HIS250 4.7 18.5 1.0
OD2 A:ASP215 4.8 19.0 1.0
N A:HIS250 4.9 16.1 1.0
HE2 A:HIS250 4.9 20.2 1.0
C A:THR249 5.0 19.9 1.0

Zinc binding site 2 out of 7 in 6n4z

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Zinc binding site 2 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:13.6
occ:0.94
 O A:HOH758 1.9 15.6 1.0
OE1 A:GLU166 2.0 15.0 0.5
OE2 A:GLU166 2.0 11.9 0.5
NE2 A:HIS142 2.0 12.2 1.0
NE2 A:HIS146 2.0 13.0 1.0
CD A:GLU166 2.8 15.1 0.5
CD A:GLU166 2.9 12.5 0.5
OE2 A:GLU166 2.9 16.8 0.5
CE1 A:HIS146 3.0 12.8 1.0
CD2 A:HIS142 3.0 11.8 1.0
CE1 A:HIS142 3.0 12.2 1.0
CD2 A:HIS146 3.1 12.5 1.0
OE1 A:GLU166 3.1 12.7 0.5
HE1 A:HIS146 3.1 15.3 1.0
HD2 A:HIS142 3.2 14.2 1.0
HH A:TYR157 3.2 24.7 0.4
HE1 A:HIS142 3.2 14.7 1.0
HD2 A:HIS146 3.3 15.1 1.0
ZN A:ZN408 3.3 30.4 0.5
ZN A:ZN409 3.4 26.6 0.5
O A:HOH733 3.5 55.0 1.0
OE2 A:GLU143 3.7 19.9 1.0
HA A:GLU166 3.8 14.8 0.5
HA A:GLU166 3.8 14.6 0.5
OH A:TYR157 3.9 20.6 0.4
HB2 A:SER169 4.0 14.3 1.0
NE2 A:HIS231 4.1 22.9 1.0
ND1 A:HIS146 4.1 12.9 1.0
ND1 A:HIS142 4.1 12.3 1.0
O A:HOH754 4.1 30.4 1.0
CG A:HIS142 4.2 11.5 1.0
HE1 A:TYR157 4.2 22.7 0.4
CG A:HIS146 4.2 12.9 1.0
CG A:GLU166 4.2 14.3 0.5
CG A:GLU166 4.3 12.9 0.5
HB3 A:SER169 4.3 14.3 1.0
HG2 A:GLU166 4.4 15.4 0.5
CD A:GLU143 4.5 16.9 1.0
HB3 A:GLU166 4.5 15.7 0.5
CB A:SER169 4.5 11.9 1.0
O A:HOH742 4.6 48.5 1.0
HD2 A:HIS231 4.6 26.6 1.0
HG3 A:GLU166 4.6 17.1 0.5
O A:HOH683 4.6 53.2 1.0
OG A:SER169 4.7 12.9 1.0
CA A:GLU166 4.7 12.2 0.5
CB A:GLU166 4.7 13.1 0.5
CD2 A:HIS231 4.7 22.2 1.0
CA A:GLU166 4.7 12.4 0.5
OE1 A:GLU143 4.8 17.7 1.0
HG2 A:GLU166 4.8 17.1 0.5
HH22 A:ARG203 4.8 17.2 0.7
CE1 A:TYR157 4.8 18.9 0.4
CZ A:TYR157 4.8 19.5 0.4
HG3 A:GLU166 4.9 15.4 0.5
HD1 A:HIS146 4.9 15.5 1.0
O A:HOH839 4.9 38.4 1.0
HD1 A:HIS142 4.9 14.8 1.0
HA A:GLU143 4.9 14.2 1.0

Zinc binding site 3 out of 7 in 6n4z

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Zinc binding site 3 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:32.2
occ:0.37
 ND1 A:HIS231 1.8 21.6 1.0
OD1 A:ASP226 2.1 28.1 1.0
CE1 A:HIS231 2.6 22.6 1.0
HE1 A:HIS231 2.8 27.1 1.0
CG A:HIS231 2.8 20.7 1.0
CG A:ASP226 2.9 25.3 1.0
HB2 A:HIS231 2.9 22.1 1.0
OD2 A:ASP226 3.2 23.1 1.0
CB A:HIS231 3.4 18.4 1.0
NE2 A:HIS231 3.6 22.9 1.0
O A:HOH558 3.7 30.6 0.8
O A:HOH631 3.7 40.0 0.9
CD2 A:HIS231 3.7 22.2 1.0
H A:HIS231 3.8 18.8 1.0
HB3 A:HIS231 4.0 22.1 1.0
HG23 A:VAL230 4.1 21.2 1.0
CB A:ASP226 4.2 24.4 1.0
HG22 A:VAL230 4.2 21.2 1.0
HB2 A:ASP226 4.3 29.3 1.0
HA A:ASP226 4.3 29.5 1.0
N A:HIS231 4.4 15.7 1.0
CA A:HIS231 4.5 16.9 1.0
HD2 A:HIS231 4.6 26.6 1.0
CG2 A:VAL230 4.6 17.7 1.0
CA A:ASP226 4.8 24.6 1.0
HB3 A:ASP226 4.9 29.3 1.0
ZN A:ZN408 4.9 30.4 0.5
HG21 A:VAL230 5.0 21.2 1.0

Zinc binding site 4 out of 7 in 6n4z

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Zinc binding site 4 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:16.3
occ:0.93
 OD2 A:ASP185 2.0 15.3 1.0
OE1 A:GLU190 2.1 14.0 1.0
O A:HOH522 2.1 15.0 1.0
OE2 A:GLU177 2.1 14.5 1.0
O A:ASN183 2.3 16.1 0.6
O A:ASN183 2.3 18.1 0.5
CG A:ASP185 2.9 15.3 1.0
CD A:GLU177 3.0 14.7 1.0
CD A:GLU190 3.1 14.6 1.0
OD1 A:ASP185 3.3 14.8 1.0
HA A:PRO184 3.4 19.4 1.0
HG3 A:GLU190 3.4 18.4 1.0
C A:ASN183 3.5 18.1 0.5
C A:ASN183 3.5 17.1 0.6
CA A:CA402 3.5 13.9 1.0
OE1 A:GLU177 3.6 14.5 1.0
CG A:GLU190 3.6 15.3 1.0
HG2 A:GLU190 3.6 18.4 1.0
HB2 A:ASN183 3.7 23.1 0.5
O A:LYS182 3.8 15.5 0.3
HG2 A:GLU177 4.0 17.9 1.0
CA A:PRO184 4.0 16.2 1.0
OD2 A:ASP191 4.0 21.3 1.0
CG A:GLU177 4.0 14.9 1.0
OD1 A:ASN183 4.1 16.6 0.6
OE2 A:GLU190 4.1 15.2 1.0
C A:PRO184 4.1 16.5 1.0
OD1 A:ASP191 4.1 18.6 1.0
HB2 A:ASN183 4.1 20.9 0.6
N A:ASP185 4.1 14.8 1.0
H A:ASP185 4.1 17.8 1.0
HB3 A:ASN183 4.2 23.1 0.5
HG3 A:GLU177 4.2 17.9 1.0
CB A:ASP185 4.2 15.0 1.0
N A:PRO184 4.2 17.0 1.0
CG A:ASN183 4.2 17.4 0.6
CB A:ASN183 4.3 19.2 0.5
HB3 A:ASP185 4.3 18.0 1.0
CG A:ASP191 4.4 18.3 1.0
CB A:ASN183 4.5 17.4 0.6
CA A:ASN183 4.5 18.8 0.5
CA A:ASN183 4.6 17.8 0.6
O A:PRO184 4.7 18.5 1.0
ND2 A:ASN183 4.7 18.9 0.6
C A:LYS182 4.8 15.9 0.3
CA A:ASP185 4.8 14.7 1.0
HB2 A:ASP185 4.9 18.0 1.0
HD21 A:ASN183 4.9 22.6 0.6
H A:ASN183 5.0 23.1 0.3

Zinc binding site 5 out of 7 in 6n4z

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Zinc binding site 5 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:30.4
occ:0.49
 NE2 A:HIS231 1.9 22.9 1.0
O A:HOH758 1.9 15.6 1.0
O A:HOH839 2.0 38.4 1.0
CE1 A:HIS231 2.7 22.6 1.0
ZN A:ZN409 2.7 26.6 0.5
HE1 A:HIS231 2.8 27.1 1.0
O A:HOH754 2.9 30.4 1.0
CD2 A:HIS231 3.1 22.2 1.0
ZN A:ZN405 3.3 13.6 0.9
HD2 A:HIS231 3.4 26.6 1.0
O A:HOH733 3.5 55.0 1.0
HH A:TYR157 3.5 24.7 0.4
OE2 A:GLU166 3.6 11.9 0.5
OH A:TYR157 3.6 20.6 0.4
O A:HOH665 3.7 44.5 1.0
O A:HOH742 3.7 48.5 1.0
OE1 A:GLU166 3.8 15.0 0.5
ND1 A:HIS231 3.9 21.6 1.0
O A:HOH582 3.9 26.7 0.8
OE1 A:GLU166 4.0 12.7 0.5
CD A:GLU166 4.0 12.5 0.5
CG A:HIS231 4.1 20.7 1.0
CD A:GLU166 4.2 15.1 0.5
OE2 A:GLU166 4.2 16.8 0.5
OE2 A:GLU143 4.3 19.9 1.0
NE2 A:HIS142 4.4 12.2 1.0
HH12 A:ARG203 4.4 16.7 0.3
HH22 A:ARG203 4.4 17.2 0.7
HH22 A:ARG203 4.8 16.2 0.3
ZN A:ZN406 4.9 32.2 0.4
CZ A:TYR157 5.0 19.5 0.4

Zinc binding site 6 out of 7 in 6n4z

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Zinc binding site 6 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:26.6
occ:0.47
 OE2 A:GLU143 1.8 19.9 1.0
O A:HOH758 1.9 15.6 1.0
O A:HOH582 2.0 26.7 0.8
O A:HOH839 2.7 38.4 1.0
O A:HOH742 2.7 48.5 1.0
ZN A:ZN408 2.7 30.4 0.5
CD A:GLU143 2.9 16.9 1.0
OE1 A:GLU143 3.3 17.7 1.0
ZN A:ZN405 3.4 13.6 0.9
O A:HOH683 3.5 53.2 1.0
O A:HOH754 3.7 30.4 1.0
O A:ALA113 3.8 17.6 1.0
O A:HOH733 3.8 55.0 1.0
HD2 A:HIS142 3.8 14.2 1.0
CG A:GLU143 4.1 14.4 1.0
NE2 A:HIS142 4.1 12.2 1.0
HD2 A:HIS146 4.2 15.1 1.0
HG2 A:GLU143 4.2 17.3 1.0
HA A:PHE114 4.2 16.3 1.0
CD2 A:HIS142 4.2 11.8 1.0
HG3 A:GLU143 4.3 17.3 1.0
NE2 A:HIS146 4.5 13.0 1.0
HB3 A:PHE114 4.6 17.4 1.0
NE2 A:HIS231 4.6 22.9 1.0
CD2 A:HIS146 4.7 12.5 1.0
OD1 A:ASN112 4.7 29.8 1.0
OE2 A:GLU166 4.9 11.9 0.5
C A:ALA113 4.9 15.4 1.0
OE1 A:GLU166 5.0 15.0 0.5

Zinc binding site 7 out of 7 in 6n4z

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Zinc binding site 7 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn410

b:57.0
occ:0.56
 HZ1 A:LYS239 1.5 27.1 1.0
NZ A:LYS239 2.3 22.5 1.0
HZ2 A:LYS239 2.3 27.1 1.0
HZ3 A:LYS239 2.7 27.1 1.0
O A:HOH536 2.7 30.0 0.8
O A:HOH771 3.1 37.0 1.0
O A:HOH870 3.1 54.1 1.0
CE A:LYS239 3.4 18.4 1.0
HE3 A:LYS239 3.5 22.1 1.0
ZN A:ZN404 3.6 24.4 0.5
HE2 A:LYS239 3.6 22.1 1.0
HE2 A:TYR242 3.7 25.0 1.0
HD21 A:LEU243 3.7 18.3 1.0
O A:HOH832 3.8 24.8 1.0
O A:SER206 4.0 16.7 1.0
HB2 A:HIS250 4.1 18.5 1.0
HD23 A:LEU243 4.4 18.3 1.0
CE2 A:TYR242 4.5 20.8 1.0
CD2 A:LEU243 4.5 15.2 1.0
HA3 A:GLY248 4.6 22.4 1.0
ND1 A:HIS250 4.6 16.2 1.0
HD2 A:TYR242 4.6 21.3 1.0
CD A:LYS239 4.7 17.8 1.0
O A:THR249 4.7 23.5 1.0
HD2 A:LYS239 4.9 21.4 1.0
HH A:TYR242 4.9 32.4 1.0
HD3 A:LYS239 4.9 21.4 1.0
CB A:HIS250 4.9 15.4 1.0
CD2 A:TYR242 4.9 17.8 1.0

Reference:

K.Harrison, Z.Wu, D.H.Juers. A Comparison of Gas Stream Cooling and Plunge Cooling of Macromolecular Crystals. J.Appl.Crystallogr. V. 52 1222 2019.
ISSN: ISSN 0021-8898
PubMed: 31636524
DOI: 10.1107/S1600576719010318
Page generated: Tue Oct 29 03:30:44 2024

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