Atomistry » Zinc » PDB 6mm1-6n7l » 6n4z
Atomistry »
  Zinc »
    PDB 6mm1-6n7l »
      6n4z »

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

Go back to Zinc Binding Sites List in 6n4z
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

Go back to Zinc Binding Sites List in 6n4z
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

Go back to Zinc Binding Sites List in 6n4z
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

Go back to Zinc Binding Sites List in 6n4z
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

Go back to Zinc Binding Sites List in 6n4z
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

Go back to Zinc Binding Sites List in 6n4z
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

Go back to Zinc Binding Sites List in 6n4z
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy