Zinc in PDB 8cdb: Proulilysin E229A Structure

Protein crystallography data

The structure of Proulilysin E229A Structure, PDB code: 8cdb was solved by A.Rodriguez-Banqueri, U.Eckhard, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.72 / 4.50
Space group C 2 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 192.1, 544.4, 185.5, 90, 90, 90
R / Rfree (%) 28.9 / 30.2

Other elements in 8cdb:

The structure of Proulilysin E229A Structure also contains other interesting chemical elements:

Calcium (Ca) 14 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Proulilysin E229A Structure (pdb code 8cdb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Proulilysin E229A Structure, PDB code: 8cdb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 8cdb

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Zinc binding site 1 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:180.0
occ:1.00
 NE2 A:HIS238 2.1 182.6 1.0
NE2 A:HIS232 2.1 180.1 1.0
NE2 A:HIS228 2.1 183.9 1.0
SG A:CYS23 2.1 183.2 1.0
CB A:CYS23 2.9 184.4 1.0
CE1 A:HIS238 3.0 183.3 1.0
CD2 A:HIS228 3.0 184.2 1.0
CE1 A:HIS232 3.1 178.8 1.0
CE1 A:HIS228 3.1 182.7 1.0
CD2 A:HIS232 3.1 180.4 1.0
CD2 A:HIS238 3.2 181.1 1.0
ND1 A:HIS238 4.1 182.4 1.0
ND1 A:HIS228 4.1 182.3 1.0
CG A:HIS228 4.1 183.2 1.0
ND1 A:HIS232 4.2 178.4 1.0
CE1 A:TYR292 4.2 186.1 1.0
CG A:HIS232 4.2 179.4 1.0
CG A:HIS238 4.3 180.9 1.0
OH A:TYR292 4.4 187.7 1.0
CA A:CYS23 4.4 186.5 1.0
CB A:ALA25 4.6 186.4 1.0
CZ A:TYR292 4.8 187.4 1.0
C A:CYS23 4.9 186.9 1.0
CA A:ALA229 5.0 182.0 1.0

Zinc binding site 2 out of 14 in 8cdb

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Zinc binding site 2 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:149.7
occ:1.00
 NE2 B:HIS232 2.1 155.8 1.0
NE2 B:HIS238 2.1 150.8 1.0
NE2 B:HIS228 2.1 161.6 1.0
SG B:CYS23 2.1 161.2 1.0
CB B:CYS23 2.9 161.2 1.0
CE1 B:HIS238 3.0 152.1 1.0
CD2 B:HIS228 3.0 159.0 1.0
CE1 B:HIS232 3.1 159.2 1.0
CE1 B:HIS228 3.1 163.8 1.0
CD2 B:HIS232 3.1 154.4 1.0
CD2 B:HIS238 3.2 153.4 1.0
ND1 B:HIS238 4.1 155.6 1.0
CG B:HIS228 4.1 159.7 1.0
ND1 B:HIS228 4.1 162.6 1.0
ND1 B:HIS232 4.2 160.2 1.0
CE1 B:TYR292 4.2 163.5 1.0
CG B:HIS232 4.2 157.2 1.0
CG B:HIS238 4.3 156.5 1.0
CA B:CYS23 4.4 159.1 1.0
OH B:TYR292 4.4 164.0 1.0
CB B:ALA25 4.6 162.8 1.0
CZ B:TYR292 4.8 163.9 1.0
C B:CYS23 5.0 160.5 1.0
CA B:ALA229 5.0 159.9 1.0

Zinc binding site 3 out of 14 in 8cdb

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Zinc binding site 3 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:180.0
occ:1.00
 NE2 C:HIS238 2.1 180.3 1.0
NE2 C:HIS232 2.1 172.1 1.0
SG C:CYS23 2.1 179.6 1.0
NE2 C:HIS228 2.1 179.9 1.0
CB C:CYS23 2.9 181.9 1.0
CE1 C:HIS238 3.0 181.7 1.0
CD2 C:HIS228 3.0 179.6 1.0
CE1 C:HIS232 3.1 170.8 1.0
CE1 C:HIS228 3.1 179.0 1.0
CD2 C:HIS232 3.1 171.8 1.0
CD2 C:HIS238 3.2 178.9 1.0
ND1 C:HIS228 4.1 178.2 1.0
CG C:HIS228 4.1 178.5 1.0
ND1 C:HIS238 4.1 181.2 1.0
ND1 C:HIS232 4.2 169.8 1.0
CE1 C:TYR292 4.2 184.0 1.0
CG C:HIS232 4.2 170.4 1.0
CG C:HIS238 4.2 179.4 1.0
OH C:TYR292 4.4 186.1 1.0
CA C:CYS23 4.4 184.4 1.0
CB C:ALA25 4.7 180.9 1.0
CZ C:TYR292 4.8 186.0 1.0
C C:CYS23 5.0 185.2 1.0
CA C:ALA229 5.0 173.8 1.0

Zinc binding site 4 out of 14 in 8cdb

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Zinc binding site 4 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:156.1
occ:1.00
 NE2 D:HIS238 2.1 157.5 1.0
SG D:CYS23 2.1 158.8 1.0
NE2 D:HIS228 2.1 166.1 1.0
NE2 D:HIS232 2.1 157.4 1.0
CB D:CYS23 2.8 161.3 1.0
CE1 D:HIS238 3.0 158.2 1.0
CD2 D:HIS228 3.0 166.0 1.0
CE1 D:HIS232 3.1 156.3 1.0
CE1 D:HIS228 3.1 165.8 1.0
CD2 D:HIS232 3.1 156.9 1.0
CD2 D:HIS238 3.2 156.5 1.0
ND1 D:HIS238 4.1 157.7 1.0
ND1 D:HIS228 4.2 165.4 1.0
CG D:HIS228 4.2 165.5 1.0
ND1 D:HIS232 4.2 155.2 1.0
CE1 D:TYR292 4.2 168.5 1.0
CG D:HIS232 4.2 155.6 1.0
CG D:HIS238 4.3 156.6 1.0
CA D:CYS23 4.3 163.8 1.0
OH D:TYR292 4.3 169.5 1.0
CB D:ALA25 4.6 160.1 1.0
CZ D:TYR292 4.8 170.1 1.0
C D:CYS23 4.9 163.9 1.0
O D:CYS23 5.0 163.6 1.0

Zinc binding site 5 out of 14 in 8cdb

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Zinc binding site 5 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:152.7
occ:1.00
 NE2 E:HIS238 2.1 161.6 1.0
NE2 E:HIS232 2.1 153.7 1.0
NE2 E:HIS228 2.1 160.6 1.0
SG E:CYS23 2.1 166.5 1.0
CB E:CYS23 2.9 168.9 1.0
CE1 E:HIS238 3.0 162.4 1.0
CD2 E:HIS228 3.0 160.2 1.0
CE1 E:HIS232 3.0 152.9 1.0
CE1 E:HIS228 3.1 160.5 1.0
CD2 E:HIS232 3.1 153.0 1.0
CD2 E:HIS238 3.1 160.9 1.0
ND1 E:HIS228 4.1 160.1 1.0
CG E:HIS228 4.1 159.9 1.0
ND1 E:HIS238 4.1 162.3 1.0
ND1 E:HIS232 4.2 151.7 1.0
CE1 E:TYR292 4.2 168.1 1.0
CG E:HIS232 4.2 151.8 1.0
CG E:HIS238 4.2 161.3 1.0
OH E:TYR292 4.4 168.8 1.0
CA E:CYS23 4.4 170.8 1.0
CB E:ALA25 4.7 167.4 1.0
CZ E:TYR292 4.8 169.4 1.0
CA E:ALA229 5.0 155.5 1.0

Zinc binding site 6 out of 14 in 8cdb

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Zinc binding site 6 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:141.0
occ:1.00
 NE2 F:HIS238 2.1 161.6 1.0
NE2 F:HIS228 2.1 162.2 1.0
SG F:CYS23 2.1 162.6 1.0
NE2 F:HIS232 2.1 158.8 1.0
CB F:CYS23 2.9 164.0 1.0
CE1 F:HIS238 3.0 162.3 1.0
CD2 F:HIS228 3.0 162.5 1.0
CE1 F:HIS232 3.1 157.6 1.0
CE1 F:HIS228 3.1 161.2 1.0
CD2 F:HIS232 3.1 159.1 1.0
CD2 F:HIS238 3.2 160.2 1.0
ND1 F:HIS228 4.1 160.8 1.0
ND1 F:HIS238 4.1 161.4 1.0
CG F:HIS228 4.1 161.6 1.0
CE1 F:TYR292 4.2 166.2 1.0
ND1 F:HIS232 4.2 157.3 1.0
CG F:HIS238 4.2 160.1 1.0
CG F:HIS232 4.2 158.2 1.0
OH F:TYR292 4.3 167.9 1.0
CA F:CYS23 4.4 166.3 1.0
CB F:ALA25 4.7 159.1 1.0
CZ F:TYR292 4.8 167.6 1.0
C F:CYS23 4.9 166.8 1.0
CA F:ALA229 5.0 159.5 1.0

Zinc binding site 7 out of 14 in 8cdb

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Zinc binding site 7 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:159.5
occ:1.00
 NE2 G:HIS238 2.1 154.4 1.0
SG G:CYS23 2.1 150.8 1.0
NE2 G:HIS228 2.1 154.6 1.0
NE2 G:HIS232 2.1 152.8 1.0
CB G:CYS23 2.9 152.7 1.0
CE1 G:HIS238 3.0 155.7 1.0
CD2 G:HIS228 3.0 153.4 1.0
CE1 G:HIS232 3.1 153.4 1.0
CE1 G:HIS228 3.1 155.2 1.0
CD2 G:HIS232 3.1 151.7 1.0
CD2 G:HIS238 3.2 154.7 1.0
ND1 G:HIS238 4.1 156.8 1.0
CG G:HIS228 4.1 153.3 1.0
ND1 G:HIS228 4.1 154.4 1.0
CE1 G:TYR292 4.2 158.5 1.0
ND1 G:HIS232 4.2 152.7 1.0
CG G:HIS232 4.2 151.6 1.0
CG G:HIS238 4.2 156.2 1.0
OH G:TYR292 4.3 159.6 1.0
CA G:CYS23 4.4 153.5 1.0
CB G:ALA25 4.6 151.8 1.0
CZ G:TYR292 4.8 159.8 1.0
C G:CYS23 4.9 154.2 1.0
O G:CYS23 5.0 155.3 1.0

Zinc binding site 8 out of 14 in 8cdb

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Zinc binding site 8 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn401

b:136.1
occ:1.00
 NE2 H:HIS232 2.1 136.1 1.0
NE2 H:HIS238 2.1 140.0 1.0
NE2 H:HIS228 2.1 140.8 1.0
SG H:CYS23 2.1 142.3 1.0
CB H:CYS23 2.9 142.0 1.0
CE1 H:HIS238 3.0 140.5 1.0
CD2 H:HIS228 3.0 140.7 1.0
CE1 H:HIS232 3.1 136.5 1.0
CE1 H:HIS228 3.1 141.7 1.0
CD2 H:HIS232 3.1 136.4 1.0
CD2 H:HIS238 3.2 140.9 1.0
CG H:HIS228 4.1 140.7 1.0
ND1 H:HIS228 4.1 141.4 1.0
ND1 H:HIS238 4.1 141.7 1.0
ND1 H:HIS232 4.2 137.1 1.0
CE1 H:TYR292 4.2 145.9 1.0
CG H:HIS232 4.2 137.0 1.0
CG H:HIS238 4.3 142.0 1.0
CA H:CYS23 4.4 141.9 1.0
OH H:TYR292 4.4 145.6 1.0
CB H:ALA25 4.6 145.3 1.0
CZ H:TYR292 4.8 146.2 1.0
C H:CYS23 5.0 142.0 1.0
CA H:ALA229 5.0 137.9 1.0

Zinc binding site 9 out of 14 in 8cdb

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Zinc binding site 9 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn401

b:142.4
occ:1.00
 NE2 I:HIS228 2.1 160.1 1.0
SG I:CYS23 2.1 165.1 1.0
NE2 I:HIS232 2.1 159.6 1.0
NE2 I:HIS238 2.1 155.4 1.0
CB I:CYS23 2.9 166.1 1.0
CD2 I:HIS228 3.0 159.9 1.0
CE1 I:HIS238 3.0 156.4 1.0
CE1 I:HIS228 3.0 159.4 1.0
CE1 I:HIS232 3.1 159.3 1.0
CD2 I:HIS232 3.1 159.9 1.0
CD2 I:HIS238 3.2 154.6 1.0
ND1 I:HIS228 4.1 158.7 1.0
CG I:HIS228 4.1 159.0 1.0
ND1 I:HIS238 4.2 156.3 1.0
ND1 I:HIS232 4.2 159.4 1.0
CE1 I:TYR292 4.2 165.2 1.0
CG I:HIS232 4.2 159.8 1.0
CG I:HIS238 4.3 155.1 1.0
OH I:TYR292 4.4 167.0 1.0
CA I:CYS23 4.4 167.8 1.0
CB I:ALA25 4.7 163.7 1.0
CZ I:TYR292 4.8 166.6 1.0
CA I:ALA229 4.9 161.3 1.0

Zinc binding site 10 out of 14 in 8cdb

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Zinc binding site 10 out of 14 in the Proulilysin E229A Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Proulilysin E229A Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn401

b:142.9
occ:1.00
 NE2 J:HIS238 2.1 152.6 1.0
NE2 J:HIS232 2.1 143.5 1.0
NE2 J:HIS228 2.1 154.4 1.0
SG J:CYS23 2.1 156.3 1.0
CB J:CYS23 2.9 156.3 1.0
CE1 J:HIS238 3.0 153.7 1.0
CD2 J:HIS228 3.0 154.3 1.0
CE1 J:HIS232 3.0 143.4 1.0
CE1 J:HIS228 3.1 153.3 1.0
CD2 J:HIS232 3.1 144.5 1.0
CD2 J:HIS238 3.2 151.7 1.0
ND1 J:HIS228 4.1 152.5 1.0
ND1 J:HIS238 4.1 153.5 1.0
CG J:HIS228 4.1 153.1 1.0
ND1 J:HIS232 4.2 144.2 1.0
CE1 J:TYR292 4.2 158.6 1.0
CG J:HIS232 4.2 144.9 1.0
CG J:HIS238 4.2 152.3 1.0
OH J:TYR292 4.4 161.0 1.0
CA J:CYS23 4.4 157.8 1.0
CB J:ALA25 4.6 158.9 1.0
CZ J:TYR292 4.8 159.9 1.0
C J:CYS23 5.0 159.3 1.0
CA J:ALA229 5.0 147.1 1.0

Reference:

A.Rodriguez-Banqueri, M.Moliner-Culubret, S.R.Mendes, T.Guevara, U.Eckhard, F.X.Gomis-Ruth. Structural Insights Into Latency of the Metallopeptidase Ulilysin (Lysarginase) and Its Unexpected Inhibition By A Sulfonyl-Fluoride Inhibitor of Serine Peptidases. Dalton Trans V. 52 3610 2023.
ISSN: ESSN 1477-9234
PubMed: 36857690
DOI: 10.1039/D3DT00458A
Page generated: Tue Apr 11 18:25:31 2023

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