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Zinc in PDB 4yu5: Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen

Protein crystallography data

The structure of Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen, PDB code: 4yu5 was solved by J.L.Arolas, T.Goulas, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.46 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.610, 102.410, 242.880, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.7

Other elements in 4yu5:

The structure of Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen (pdb code 4yu5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen, PDB code: 4yu5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4yu5

Go back to Zinc Binding Sites List in 4yu5
Zinc binding site 1 out of 2 in the Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:55.0
occ:1.00
NE2 A:HIS379 2.0 45.4 1.0
OD1 A:ASP389 2.1 53.1 1.0
NE2 A:HIS383 2.2 46.2 1.0
N A:ASN50 2.3 67.9 1.0
CD2 A:HIS379 2.9 45.8 1.0
CG A:ASP389 3.0 54.0 1.0
CD2 A:HIS383 3.1 46.9 1.0
CE1 A:HIS379 3.2 44.4 1.0
OD2 A:ASP389 3.2 62.7 1.0
CE1 A:HIS383 3.2 46.5 1.0
CA A:ASN50 3.2 66.7 1.0
CB A:ASN50 4.0 65.8 1.0
OH A:TYR391 4.0 57.2 1.0
CG A:HIS379 4.1 42.9 1.0
ND1 A:HIS379 4.2 44.3 1.0
CG A:HIS383 4.3 46.3 1.0
ND1 A:HIS383 4.3 47.8 1.0
CB A:ASP389 4.4 46.6 1.0
CE2 A:TYR391 4.5 48.9 1.0
C A:ASN50 4.5 71.7 1.0
CZ A:TYR391 4.7 54.7 1.0
CE A:MSE408 4.9 44.5 1.0
ND2 A:ASN50 4.9 92.8 1.0
CA A:ASP389 4.9 45.4 1.0
CG A:ASN50 5.0 89.4 1.0

Zinc binding site 2 out of 2 in 4yu5

Go back to Zinc Binding Sites List in 4yu5
Zinc binding site 2 out of 2 in the Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:72.7
occ:1.00
OD1 B:ASP389 2.0 58.3 1.0
NE2 B:HIS383 2.2 63.8 1.0
NE2 B:HIS379 2.2 64.1 1.0
N B:ASN50 2.4 91.1 1.0
CG B:ASP389 2.9 61.9 1.0
CD2 B:HIS379 3.0 64.5 1.0
CD2 B:HIS383 3.1 65.1 1.0
OD2 B:ASP389 3.2 73.0 1.0
CE1 B:HIS383 3.2 63.7 1.0
CA B:ASN50 3.2 89.1 1.0
CE1 B:HIS379 3.4 62.0 1.0
NH1 B:ARG336 3.7 0.1 1.0
OH B:TYR391 3.9 67.4 1.0
CB B:ASN50 4.0 86.9 1.0
CG B:HIS379 4.2 60.7 1.0
CG B:HIS383 4.3 64.1 1.0
ND1 B:HIS383 4.3 65.2 1.0
CB B:ASP389 4.3 58.1 1.0
ND1 B:HIS379 4.4 61.1 1.0
CE2 B:TYR391 4.5 63.4 1.0
C B:ASN50 4.5 92.1 1.0
CZ B:TYR391 4.7 69.2 1.0
CZ B:ARG336 4.8 0.9 1.0
ND2 B:ASN50 4.9 0.1 1.0
CA B:ASP389 4.9 55.2 1.0
CG B:ASN50 5.0 0.4 1.0
CE B:MSE408 5.0 61.2 1.0

Reference:

J.L.Arolas, T.Goulas, A.P.Pomerantsev, S.H.Leppla, F.X.Gomis-Ruth. Structural Basis For Latency and Function of Immune Inhibitor A Metallopeptidase, A Modulator of the Bacillus Anthracis Secretome. Structure V. 24 25 2016.
ISSN: ISSN 0969-2126
PubMed: 26745529
DOI: 10.1016/J.STR.2015.10.015
Page generated: Sun Oct 27 11:27:44 2024

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