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Zinc in PDB 6n4w: Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 K

Enzymatic activity of Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 K

All present enzymatic activity of Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 K:
3.4.24.27;

Protein crystallography data

The structure of Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 K, PDB code: 6n4w 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) 30.59 / 1.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.739, 96.739, 106.425, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 15.7

Other elements in 6n4w:

The structure of Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K (pdb code 6n4w). 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) Cryocooled in A Nitrogen Gas Stream to 100 K, PDB code: 6n4w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6n4w

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Zinc binding site 1 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:14.2
occ:1.00
 O A:HOH738 1.8 15.0 1.0
OE2 A:GLU166 2.0 11.4 0.5
OE1 A:GLU166 2.0 12.6 0.5
NE2 A:HIS142 2.0 12.0 1.0
NE2 A:HIS146 2.0 12.2 1.0
CD A:GLU166 2.8 13.2 0.5
CD A:GLU166 2.9 12.4 0.5
OE2 A:GLU166 2.9 15.2 0.5
CE1 A:HIS146 3.0 12.2 1.0
CD2 A:HIS142 3.0 12.1 1.0
CE1 A:HIS142 3.0 12.4 1.0
CD2 A:HIS146 3.1 12.4 1.0
OE1 A:GLU166 3.1 12.4 0.5
HE1 A:HIS146 3.1 14.7 1.0
HH A:TYR157 3.2 25.1 0.5
HD2 A:HIS142 3.2 14.5 1.0
HE1 A:HIS142 3.2 14.9 1.0
HD2 A:HIS146 3.3 14.9 1.0
ZN A:ZN407 3.3 27.7 0.5
ZN A:ZN409 3.4 26.0 0.4
OE2 A:GLU143 3.6 18.5 1.0
HA A:GLU166 3.8 14.2 0.5
HA A:GLU166 3.8 14.0 0.5
OH A:TYR157 3.9 20.9 0.5
HB2 A:SER169 4.1 13.7 1.0
HE1 A:TYR157 4.1 23.5 0.5
ND1 A:HIS146 4.1 12.3 1.0
NE2 A:HIS231 4.1 22.0 1.0
ND1 A:HIS142 4.1 11.4 1.0
O A:HOH747 4.1 30.9 1.0
CG A:HIS142 4.2 11.0 1.0
CG A:HIS146 4.2 12.1 1.0
HB3 A:SER169 4.2 13.7 1.0
CG A:GLU166 4.2 12.8 0.5
CG A:GLU166 4.3 12.6 0.5
HG2 A:GLU166 4.4 15.3 0.5
CD A:GLU143 4.5 15.2 1.0
CB A:SER169 4.5 11.4 1.0
HB3 A:GLU166 4.5 15.0 0.5
O A:HOH767 4.6 44.5 1.0
HD2 A:HIS231 4.7 26.0 1.0
HG3 A:GLU166 4.7 15.1 0.5
CA A:GLU166 4.7 11.7 0.5
OG A:SER169 4.7 12.4 1.0
CE1 A:TYR157 4.7 19.6 0.5
CZ A:TYR157 4.7 19.9 0.5
CB A:GLU166 4.7 12.5 0.5
CA A:GLU166 4.7 11.9 0.5
CD2 A:HIS231 4.8 21.7 1.0
OE1 A:GLU143 4.8 15.0 1.0
HG2 A:GLU166 4.8 15.1 0.5
HH22 A:ARG203 4.8 15.5 0.7
HG3 A:GLU166 4.8 15.3 0.5
HD1 A:HIS146 4.9 14.7 1.0
HD1 A:HIS142 4.9 13.7 1.0
O A:HOH840 4.9 34.9 1.0
HA A:GLU143 4.9 13.7 1.0

Zinc binding site 2 out of 7 in 6n4w

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Zinc binding site 2 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:50.2
occ:0.63
 ND1 A:HIS250 2.5 16.1 1.0
O A:HOH764 2.8 34.3 1.0
HA A:HIS250 3.0 17.9 1.0
O A:HOH527 3.0 28.9 0.8
CE1 A:HIS250 3.3 16.5 1.0
HE1 A:HIS250 3.3 19.8 1.0
CG A:HIS250 3.6 15.2 1.0
H A:TYR251 3.7 20.7 1.0
HZ1 A:LYS239 3.7 26.0 1.0
CA A:HIS250 3.8 14.9 1.0
ZN A:ZN410 3.9 80.1 0.8
HB2 A:HIS250 3.9 17.7 1.0
HZ3 A:LYS239 4.0 26.0 1.0
CB A:HIS250 4.0 14.8 1.0
O A:THR249 4.1 22.3 1.0
HE2 A:LYS239 4.1 20.4 1.0
NZ A:LYS239 4.2 21.6 1.0
N A:TYR251 4.4 17.2 1.0
O A:HOH642 4.4 16.8 0.5
NE2 A:HIS250 4.5 16.3 1.0
O A:HOH876 4.6 56.9 1.0
C A:HIS250 4.6 15.9 1.0
CD2 A:HIS250 4.7 15.6 1.0
CE A:LYS239 4.7 17.0 1.0
N A:HIS250 4.9 16.3 1.0
C A:THR249 4.9 18.7 1.0
HB3 A:HIS250 5.0 17.7 1.0

Zinc binding site 3 out of 7 in 6n4w

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Zinc binding site 3 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:16.0
occ:0.95
 OD2 A:ASP185 2.0 14.8 1.0
O A:HOH536 2.1 14.8 1.0
OE2 A:GLU190 2.1 13.6 1.0
OE2 A:GLU177 2.1 14.0 1.0
O A:ASN183 2.3 15.9 0.7
O A:ASN183 2.3 16.9 0.3
CG A:ASP185 3.0 15.2 1.0
CD A:GLU177 3.0 13.8 1.0
CD A:GLU190 3.1 14.2 1.0
HA A:PRO184 3.3 18.2 1.0
OD1 A:ASP185 3.3 13.9 1.0
HG3 A:GLU190 3.4 17.9 1.0
C A:ASN183 3.5 16.5 0.7
C A:ASN183 3.5 16.9 0.3
CA A:CA401 3.5 13.4 1.0
OE1 A:GLU177 3.6 13.6 1.0
HG2 A:GLU190 3.6 17.9 1.0
CG A:GLU190 3.6 14.9 1.0
HB2 A:ASN183 3.8 21.5 0.3
O A:LYS182 3.8 15.7 0.3
OD2 A:ASP191 3.9 20.0 1.0
CA A:PRO184 3.9 15.2 1.0
HG2 A:GLU177 4.0 16.9 1.0
CG A:GLU177 4.0 14.1 1.0
HB2 A:ASN183 4.1 20.1 0.7
C A:PRO184 4.1 15.6 1.0
OE1 A:GLU190 4.1 14.3 1.0
OD1 A:ASN183 4.1 16.9 0.7
OD1 A:ASP191 4.1 17.9 1.0
N A:ASP185 4.1 14.5 1.0
H A:ASP185 4.2 17.4 1.0
HG3 A:GLU177 4.2 16.9 1.0
N A:PRO184 4.2 16.0 1.0
CG A:ASN183 4.2 17.9 0.7
CB A:ASP185 4.2 14.9 1.0
HB3 A:ASN183 4.3 21.5 0.3
HB3 A:ASP185 4.3 17.9 1.0
CB A:ASN183 4.3 17.9 0.3
CG A:ASP191 4.4 17.1 1.0
CB A:ASN183 4.5 16.7 0.7
CA A:ASN183 4.6 17.8 0.3
CA A:ASN183 4.6 17.8 0.7
O A:PRO184 4.6 17.6 1.0
ND2 A:ASN183 4.7 19.6 0.7
C A:LYS182 4.8 16.6 0.3
CA A:ASP185 4.8 14.8 1.0
HB2 A:ASP185 4.9 17.9 1.0
HD21 A:ASN183 4.9 23.5 0.7

Zinc binding site 4 out of 7 in 6n4w

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Zinc binding site 4 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:27.7
occ:0.53
 NE2 A:HIS231 1.9 22.0 1.0
O A:HOH738 1.9 15.0 1.0
O A:HOH840 1.9 34.9 1.0
CE1 A:HIS231 2.7 21.9 1.0
HE1 A:HIS231 2.8 26.3 1.0
ZN A:ZN409 2.8 26.0 0.4
O A:HOH747 2.9 30.9 1.0
CD2 A:HIS231 3.1 21.7 1.0
ZN A:ZN404 3.3 14.2 1.0
HD2 A:HIS231 3.4 26.0 1.0
HH A:TYR157 3.4 25.1 0.5
OH A:TYR157 3.5 20.9 0.5
OE2 A:GLU166 3.6 11.4 0.5
O A:HOH785 3.7 45.8 1.0
OE1 A:GLU166 3.8 12.6 0.5
O A:HOH636 3.9 29.0 0.9
O A:HOH767 3.9 44.5 1.0
ND1 A:HIS231 3.9 20.9 1.0
OE1 A:GLU166 4.0 12.4 0.5
CD A:GLU166 4.0 12.4 0.5
CG A:HIS231 4.1 19.8 1.0
OE2 A:GLU166 4.1 15.2 0.5
CD A:GLU166 4.2 13.2 0.5
OE2 A:GLU143 4.3 18.5 1.0
NE2 A:HIS142 4.5 12.0 1.0
HH22 A:ARG203 4.6 15.5 0.7
HD1 A:HIS231 4.6 25.1 1.0
HH12 A:ARG203 4.6 17.3 0.3
O A:HOH873 4.7 60.3 1.0
CZ A:TYR157 4.9 19.9 0.5
HH22 A:ARG203 4.9 16.8 0.3
ZN A:ZN408 5.0 53.7 0.5

Zinc binding site 5 out of 7 in 6n4w

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Zinc binding site 5 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:53.7
occ:0.48
 HD1 A:HIS231 1.6 25.1 1.0
ND1 A:HIS231 2.0 20.9 1.0
OD1 A:ASP226 2.3 27.0 1.0
CE1 A:HIS231 2.7 21.9 1.0
CG A:HIS231 2.8 19.8 1.0
HB2 A:HIS231 2.9 21.4 1.0
HE1 A:HIS231 2.9 26.3 1.0
CG A:ASP226 3.0 25.1 1.0
O A:HOH873 3.0 60.3 1.0
OD2 A:ASP226 3.2 22.9 1.0
CB A:HIS231 3.4 17.9 1.0
O A:HOH631 3.6 28.4 0.9
NE2 A:HIS231 3.6 22.0 1.0
CD2 A:HIS231 3.7 21.7 1.0
H A:HIS231 3.9 18.6 1.0
O A:HOH614 3.9 33.9 0.9
HB3 A:HIS231 3.9 21.4 1.0
CB A:ASP226 4.2 24.0 1.0
HB2 A:ASP226 4.2 28.8 1.0
HG23 A:VAL230 4.4 20.0 1.0
HA A:ASP226 4.4 28.3 1.0
HG22 A:VAL230 4.4 20.0 1.0
N A:HIS231 4.5 15.5 1.0
HD2 A:HIS231 4.5 26.0 1.0
CA A:HIS231 4.5 15.8 1.0
CG2 A:VAL230 4.9 16.7 1.0
CA A:ASP226 4.9 23.6 1.0
HB3 A:ASP226 4.9 28.8 1.0
ZN A:ZN407 5.0 27.7 0.5

Zinc binding site 6 out of 7 in 6n4w

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Zinc binding site 6 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:26.0
occ:0.43
 OE2 A:GLU143 1.8 18.5 1.0
O A:HOH738 1.9 15.0 1.0
O A:HOH636 2.0 29.0 0.9
O A:HOH840 2.8 34.9 1.0
ZN A:ZN407 2.8 27.7 0.5
CD A:GLU143 2.8 15.2 1.0
O A:HOH767 2.9 44.5 1.0
OE1 A:GLU143 3.3 15.0 1.0
ZN A:ZN404 3.4 14.2 1.0
O A:ALA113 3.8 16.7 1.0
O A:HOH747 3.8 30.9 1.0
HD2 A:HIS142 3.9 14.5 1.0
CG A:GLU143 4.0 13.6 1.0
O A:HOH633 4.0 51.8 1.0
HD2 A:HIS146 4.1 14.9 1.0
HG2 A:GLU143 4.1 16.3 1.0
HA A:PHE114 4.2 16.6 1.0
NE2 A:HIS142 4.2 12.0 1.0
HG3 A:GLU143 4.3 16.3 1.0
CD2 A:HIS142 4.3 12.1 1.0
NE2 A:HIS146 4.5 12.2 1.0
HB3 A:PHE114 4.5 19.0 1.0
CD2 A:HIS146 4.6 12.4 1.0
NE2 A:HIS231 4.7 22.0 1.0
OD1 A:ASN112 4.8 29.9 1.0
OE2 A:GLU166 4.9 11.4 0.5
C A:ALA113 4.9 15.0 1.0
HH A:TYR157 5.0 25.1 0.5
CA A:PHE114 5.0 13.8 1.0

Zinc binding site 7 out of 7 in 6n4w

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Zinc binding site 7 out of 7 in the Tetragonal Thermolysin (with 50% Xylose) Cryocooled in A Nitrogen Gas Stream to 100 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) Cryocooled in A Nitrogen Gas Stream to 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn410

b:80.1
occ:0.75
 HZ1 A:LYS239 1.6 26.0 1.0
NZ A:LYS239 2.4 21.6 1.0
HZ2 A:LYS239 2.5 26.0 1.0
O A:HOH527 2.6 28.9 0.8
HZ3 A:LYS239 2.8 26.0 1.0
O A:HOH876 3.2 56.9 1.0
O A:HOH603 3.4 32.8 1.0
CE A:LYS239 3.5 17.0 1.0
HE3 A:LYS239 3.5 20.4 1.0
HD21 A:LEU243 3.6 17.8 1.0
HE2 A:TYR242 3.6 22.6 1.0
HE2 A:LYS239 3.7 20.4 1.0
O A:HOH764 3.7 34.3 1.0
ZN A:ZN405 3.9 50.2 0.6
HB2 A:HIS250 4.0 17.7 1.0
O A:SER206 4.1 15.6 1.0
HD23 A:LEU243 4.3 17.8 1.0
CD2 A:LEU243 4.4 14.8 1.0
CE2 A:TYR242 4.4 18.8 1.0
HA3 A:GLY248 4.5 21.5 1.0
O A:THR249 4.5 22.3 1.0
ND1 A:HIS250 4.6 16.1 1.0
HD2 A:TYR242 4.6 19.1 1.0
HH A:TYR242 4.8 30.4 1.0
CD A:LYS239 4.8 16.0 1.0
CB A:HIS250 4.8 14.8 1.0
HA A:HIS250 4.9 17.9 1.0
HD2 A:LYS239 4.9 19.2 1.0
H A:THR249 5.0 21.9 1.0
CD2 A:TYR242 5.0 15.9 1.0
CG A:HIS250 5.0 15.2 1.0
HD3 A:LYS239 5.0 19.2 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 03:29:43 2024

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