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Calcium 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
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Selenomethionine Variant of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen, PDB code: 4yu5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4yu5

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Calcium binding site 1 out of 8 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 Calcium with other atoms in the Ca 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:Ca1002

b:52.1
occ:1.00
OD1 A:ASP724 2.3 55.4 1.0
O A:GLN721 2.3 46.4 1.0
O A:HIS701 2.4 56.3 1.0
OD2 A:ASP699 2.5 51.5 1.0
OD1 A:ASP699 2.8 47.4 1.0
CG A:ASP699 3.0 47.3 1.0
CG A:ASP724 3.2 53.1 1.0
OD2 A:ASP724 3.3 61.2 1.0
C A:GLN721 3.4 46.8 1.0
C A:HIS701 3.6 53.9 1.0
CB A:HIS701 3.9 44.5 1.0
CA A:GLN721 4.1 45.9 1.0
CA A:HIS701 4.2 45.7 1.0
OE1 A:GLN721 4.3 65.0 1.0
O A:GLU703 4.3 54.6 1.0
CB A:ASP699 4.5 42.0 1.0
N A:ILE722 4.5 41.2 1.0
CB A:ASP724 4.6 38.0 1.0
N A:PRO702 4.6 51.0 1.0
N A:HIS701 4.7 45.4 1.0
CB A:GLN721 4.7 47.6 1.0
CA A:ILE722 4.7 39.7 1.0
CA A:PRO702 4.8 51.1 1.0
N A:ASP724 4.8 39.4 1.0

Calcium binding site 2 out of 8 in 4yu5

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Calcium binding site 2 out of 8 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 Calcium with other atoms in the Ca 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
A:Ca1003

b:87.8
occ:1.00
OD1 A:ASP305 2.3 81.7 1.0
O A:PHE290 2.3 79.9 1.0
O A:VAL307 2.4 58.9 1.0
OD1 A:ASP309 2.4 62.2 1.0
OD1 A:ASP288 2.5 75.1 1.0
CG A:ASP305 3.1 80.4 1.0
OD2 A:ASP305 3.5 88.7 1.0
C A:VAL307 3.5 58.3 1.0
C A:PHE290 3.5 80.6 1.0
CG A:ASP288 3.6 75.7 1.0
CG A:ASP309 3.7 64.1 1.0
N A:PHE290 4.1 73.6 1.0
N A:VAL307 4.1 60.4 1.0
N A:ASP305 4.1 68.0 1.0
CA A:VAL307 4.2 56.3 1.0
CA A:ASP288 4.2 60.5 1.0
CB A:ASP288 4.2 63.4 1.0
CB A:ASP305 4.3 67.4 1.0
N A:ASP309 4.3 56.5 1.0
N A:GLN289 4.4 66.0 1.0
CB A:VAL307 4.4 57.6 1.0
CA A:ASP309 4.4 56.2 1.0
CA A:PHE290 4.4 75.0 1.0
OD2 A:ASP309 4.5 69.9 1.0
N A:ASP291 4.5 80.7 1.0
C A:ILE308 4.5 58.6 1.0
OD2 A:ASP288 4.6 84.8 1.0
N A:ILE308 4.6 52.1 1.0
C A:ASP288 4.6 68.6 1.0
CB A:ASP309 4.6 58.3 1.0
CA A:ASP305 4.6 67.2 1.0
CA A:ASP291 4.7 82.4 1.0
N A:GLY306 4.8 65.1 1.0
O A:ILE308 4.9 60.1 1.0
CA A:ILE308 5.0 49.3 1.0
C A:ASP305 5.0 71.5 1.0

Calcium binding site 3 out of 8 in 4yu5

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Calcium binding site 3 out of 8 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 Calcium with other atoms in the Ca binding site number 3 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:Ca1004

b:67.0
occ:1.00
OE1 A:GLN320 2.1 62.2 1.0
O A:ASP329 2.3 68.3 1.0
O A:GLY251 2.3 70.2 1.0
OD1 A:ASP259 2.3 61.4 1.0
OD1 A:ASP253 2.4 88.2 1.0
O A:ALA331 2.5 66.2 1.0
CD A:GLN320 3.3 76.2 1.0
CG A:ASP253 3.3 87.5 1.0
C A:GLY251 3.4 71.7 1.0
C A:ASP329 3.5 69.8 1.0
CG A:ASP259 3.5 62.7 1.0
C A:ALA331 3.7 64.6 1.0
OD2 A:ASP253 3.7 91.2 1.0
N A:ASP259 3.9 70.9 1.0
CA A:GLY251 3.9 67.1 1.0
C A:ASP330 3.9 68.6 1.0
N A:ALA331 4.0 63.7 1.0
NE2 A:GLN320 4.1 77.4 1.0
CA A:ASP330 4.2 67.1 1.0
CA A:ASP259 4.2 69.3 1.0
O A:ASP330 4.2 69.2 1.0
CG A:GLN320 4.3 57.3 1.0
N A:ASP330 4.3 67.0 1.0
CB A:ASP259 4.3 67.8 1.0
N A:ASP253 4.4 74.9 1.0
OD2 A:ASP259 4.4 64.5 1.0
CB A:GLN320 4.5 59.7 1.0
CA A:ALA331 4.5 61.5 1.0
N A:ALA252 4.5 69.1 1.0
CA A:ASP329 4.5 68.0 1.0
N A:ILE332 4.6 58.2 1.0
CB A:ASP253 4.6 76.6 1.0
CA A:ILE332 4.6 56.2 1.0
C A:ALA252 4.6 77.9 1.0
CB A:HIS258 4.8 69.7 1.0
N A:TRP333 4.8 57.6 1.0
CA A:ALA252 4.8 70.3 1.0
CA A:ASP253 4.9 75.2 1.0
C A:HIS258 4.9 76.1 1.0
C A:ILE332 5.0 62.2 1.0

Calcium binding site 4 out of 8 in 4yu5

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Calcium binding site 4 out of 8 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 Calcium with other atoms in the Ca binding site number 4 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:Ca1005

b:0.8
occ:1.00
O A:VAL598 2.1 0.9 1.0
OD1 A:ASP536 2.4 0.8 1.0
OD1 A:ASP595 2.7 0.1 1.0
OE1 A:GLU532 2.8 0.6 1.0
C A:VAL598 3.3 0.5 1.0
O A:ASP595 3.3 0.7 1.0
CG A:ASP536 3.4 0.2 1.0
OD2 A:ASP536 3.6 0.2 1.0
CG A:ASP595 3.6 0.3 1.0
N A:VAL598 3.6 0.4 1.0
OD1 A:ASP502 3.8 0.7 1.0
N A:ASP595 3.9 0.7 1.0
C A:ALA597 4.0 0.5 1.0
CA A:VAL598 4.0 0.2 1.0
C A:ASP595 4.1 0.7 1.0
CD A:GLU532 4.1 1.0 1.0
N A:ALA597 4.2 0.9 1.0
OD2 A:ASP595 4.3 0.8 1.0
CB A:THR594 4.3 99.0 1.0
N A:THR599 4.3 0.8 1.0
CA A:ASP595 4.3 0.8 1.0
CA A:ALA597 4.4 0.2 1.0
CB A:ASP595 4.5 0.8 1.0
CB A:ALA597 4.5 0.3 1.0
O A:ALA597 4.6 0.1 1.0
CG2 A:THR594 4.6 93.8 1.0
CB A:GLU532 4.6 0.7 1.0
CA A:THR599 4.6 99.9 1.0
CB A:VAL598 4.7 0.4 1.0
C A:THR594 4.7 0.8 1.0
CB A:ASP536 4.7 95.0 1.0
CA A:THR594 4.8 90.5 1.0
OE2 A:GLU532 4.9 0.1 1.0
CG A:GLU532 5.0 0.0 1.0

Calcium binding site 5 out of 8 in 4yu5

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Calcium binding site 5 out of 8 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 Calcium with other atoms in the Ca binding site number 5 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:Ca1002

b:61.8
occ:1.00
O B:HIS701 2.3 54.4 1.0
OD2 B:ASP699 2.3 59.8 1.0
OD1 B:ASP724 2.4 56.8 1.0
O B:GLN721 2.4 53.9 1.0
OD1 B:ASP699 2.7 54.1 1.0
CG B:ASP699 2.9 54.8 1.0
CG B:ASP724 3.3 57.8 1.0
C B:HIS701 3.4 54.6 1.0
OD2 B:ASP724 3.5 66.1 1.0
C B:GLN721 3.5 56.4 1.0
CB B:HIS701 3.8 47.6 1.0
CA B:HIS701 4.1 47.7 1.0
CA B:GLN721 4.2 59.8 1.0
O B:GLU703 4.3 73.1 1.0
OE1 B:GLN721 4.3 73.5 1.0
CB B:ASP699 4.3 47.2 1.0
N B:PRO702 4.5 53.5 1.0
N B:ILE722 4.5 50.5 1.0
N B:HIS701 4.6 46.8 1.0
CA B:PRO702 4.6 54.9 1.0
CB B:ASP724 4.7 44.8 1.0
CA B:ILE722 4.7 48.4 1.0
CB B:GLN721 4.7 61.6 1.0
N B:ASP724 4.9 44.1 1.0
C B:PRO702 5.0 64.2 1.0

Calcium binding site 6 out of 8 in 4yu5

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Calcium binding site 6 out of 8 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 Calcium with other atoms in the Ca binding site number 6 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:Ca1003

b:0.1
occ:1.00
OD1 B:ASP305 2.3 0.3 1.0
O B:PHE290 2.3 0.4 1.0
O B:VAL307 2.4 88.0 1.0
OD1 B:ASP309 2.5 90.8 1.0
OD1 B:ASP288 2.5 0.9 1.0
CG B:ASP305 3.1 0.1 1.0
OD2 B:ASP305 3.5 0.0 1.0
C B:VAL307 3.5 90.7 1.0
C B:PHE290 3.5 0.4 1.0
CG B:ASP288 3.6 0.6 1.0
CG B:ASP309 3.7 89.4 1.0
N B:PHE290 4.1 0.0 1.0
N B:VAL307 4.1 93.4 1.0
N B:ASP305 4.1 0.5 1.0
CA B:VAL307 4.2 90.2 1.0
CA B:ASP288 4.2 92.9 1.0
CB B:ASP288 4.2 97.4 1.0
N B:ASP309 4.3 83.3 1.0
CB B:ASP305 4.3 0.3 1.0
N B:GLN289 4.4 94.7 1.0
CB B:VAL307 4.4 92.5 1.0
CA B:ASP309 4.4 80.7 1.0
CA B:PHE290 4.4 0.1 1.0
N B:ASP291 4.5 0.7 1.0
OD2 B:ASP309 4.5 97.3 1.0
C B:ILE308 4.5 86.9 1.0
N B:ILE308 4.6 86.7 1.0
OD2 B:ASP288 4.6 0.5 1.0
C B:ASP288 4.6 99.1 1.0
CB B:ASP309 4.6 81.4 1.0
CA B:ASP291 4.7 0.3 1.0
CA B:ASP305 4.7 0.5 1.0
N B:GLY306 4.8 0.8 1.0
O B:ILE308 4.9 85.8 1.0
CA B:ILE308 4.9 84.0 1.0

Calcium binding site 7 out of 8 in 4yu5

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Calcium binding site 7 out of 8 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 Calcium with other atoms in the Ca binding site number 7 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:Ca1004

b:0.8
occ:1.00
OD1 B:ASP259 2.2 0.1 1.0
O B:GLY251 2.2 0.4 1.0
OD1 B:ASP253 2.4 0.3 1.0
O B:ASP329 2.4 0.8 1.0
O B:ALA331 2.5 99.6 1.0
OE1 B:GLN320 2.6 0.4 1.0
CG B:ASP253 3.3 0.0 1.0
CD B:GLN320 3.3 0.2 1.0
C B:GLY251 3.4 0.5 1.0
CG B:ASP259 3.4 0.7 1.0
OD2 B:ASP253 3.6 0.2 1.0
C B:ASP329 3.6 0.9 1.0
C B:ALA331 3.6 99.5 1.0
N B:ASP259 3.8 0.3 1.0
CG B:GLN320 3.9 0.1 1.0
CA B:GLY251 4.0 0.7 1.0
C B:ASP330 4.0 0.6 1.0
N B:ALA331 4.1 0.1 1.0
CA B:ASP259 4.2 0.7 1.0
OD2 B:ASP259 4.3 0.2 1.0
O B:ASP330 4.3 0.3 1.0
NE2 B:GLN320 4.3 0.0 1.0
CA B:ASP330 4.3 0.3 1.0
CB B:ASP259 4.3 0.3 1.0
N B:ASP330 4.4 0.8 1.0
CA B:ILE332 4.4 90.5 1.0
CB B:GLN320 4.4 96.2 1.0
N B:ALA252 4.5 0.5 1.0
N B:ILE332 4.5 92.8 1.0
N B:ASP253 4.5 0.1 1.0
CA B:ALA331 4.5 99.4 1.0
C B:ALA252 4.5 0.7 1.0
CB B:HIS258 4.6 0.3 1.0
N B:TRP333 4.6 89.5 1.0
CB B:ASP253 4.6 0.0 1.0
CA B:ASP329 4.7 0.3 1.0
CA B:ALA252 4.7 0.3 1.0
C B:HIS258 4.8 0.7 1.0
C B:ILE332 4.8 94.5 1.0
CA B:HIS258 4.9 0.8 1.0
CA B:ASP253 5.0 0.5 1.0
O B:ALA252 5.0 1.0 1.0

Calcium binding site 8 out of 8 in 4yu5

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Calcium binding site 8 out of 8 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 Calcium with other atoms in the Ca binding site number 8 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:Ca1005

b:0.5
occ:1.00
O B:VAL598 2.2 0.3 1.0
OD1 B:ASP595 2.4 1.0 1.0
OE1 B:GLU532 2.6 0.4 1.0
OD1 B:ASP536 2.7 0.2 1.0
C B:VAL598 3.3 0.8 1.0
N B:VAL598 3.3 0.9 1.0
CG B:ASP595 3.3 0.9 1.0
O B:ASP595 3.3 0.2 1.0
C B:ALA597 3.7 0.7 1.0
CG B:ASP536 3.7 0.5 1.0
CA B:VAL598 3.8 0.4 1.0
OD1 B:ASP502 3.8 0.3 1.0
OD2 B:ASP595 3.9 0.5 1.0
CD B:GLU532 3.9 0.3 1.0
N B:ASP595 3.9 0.3 1.0
N B:ALA597 3.9 0.9 1.0
C B:ASP595 3.9 0.3 1.0
OD2 B:ASP536 4.0 0.9 1.0
CA B:ALA597 4.1 0.8 1.0
CB B:ALA597 4.1 0.4 1.0
CA B:ASP595 4.3 0.3 1.0
CB B:ASP595 4.3 0.9 1.0
O B:ALA597 4.4 0.8 1.0
CB B:VAL598 4.4 0.2 1.0
N B:THR599 4.4 0.1 1.0
OE2 B:GLU532 4.6 0.9 1.0
CB B:GLU532 4.6 86.7 1.0
CB B:THR594 4.7 98.5 1.0
C B:THR594 4.9 99.9 1.0
CG B:GLU532 4.9 99.2 1.0
C B:PRO596 4.9 0.7 1.0
CA B:THR599 4.9 0.9 1.0
CB B:CYS535 4.9 0.2 1.0
N B:PRO596 4.9 0.9 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: Sat Dec 12 05:14:02 2020

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