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Sodium in PDB 4yu6: Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen

Protein crystallography data

The structure of Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen, PDB code: 4yu6 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) 47.67 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.980, 108.870, 100.410, 90.00, 119.07, 90.00
R / Rfree (%) 17.1 / 21.1

Other elements in 4yu6:

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

Potassium (K) 2 atoms
Zinc (Zn) 2 atoms
Calcium (Ca) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen (pdb code 4yu6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen, PDB code: 4yu6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4yu6

Go back to Sodium Binding Sites List in 4yu6
Sodium binding site 1 out of 2 in the Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:70.0
occ:1.00
O A:HIS494 2.4 57.5 1.0
O A:ASP621 2.5 67.8 1.0
OD1 A:ASP606 2.6 64.6 1.0
OD2 A:ASP606 2.7 74.3 1.0
CG A:ASP606 3.0 65.2 1.0
O A:PHE491 3.2 90.7 1.0
OE2 A:GLU623 3.3 88.0 1.0
C A:HIS494 3.7 56.6 1.0
C A:ASP621 3.7 67.9 1.0
CE1 A:HIS607 4.0 70.5 1.0
NE2 A:HIS607 4.0 70.1 1.0
CB A:ASP621 4.2 68.0 1.0
CA A:ASP621 4.3 64.2 1.0
CD A:GLU623 4.3 99.7 1.0
C A:PHE491 4.3 92.3 1.0
CA A:GLY492 4.3 86.5 1.0
N A:HIS494 4.4 61.3 1.0
CG A:GLU623 4.4 81.2 1.0
CB A:ASP606 4.5 52.4 1.0
CA A:HIS494 4.6 56.9 1.0
N A:ALA495 4.6 50.6 1.0
ND1 A:HIS607 4.7 69.7 1.0
C A:GLY492 4.7 85.9 1.0
CD2 A:HIS607 4.8 68.4 1.0
CA A:ALA495 4.8 47.7 1.0
N A:ALA622 4.8 62.8 1.0
N A:GLY492 4.8 88.5 1.0
CB A:ALA622 4.9 60.2 1.0
CB A:PRO489 4.9 65.2 1.0

Sodium binding site 2 out of 2 in 4yu6

Go back to Sodium Binding Sites List in 4yu6
Sodium binding site 2 out of 2 in the Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bacillus Anthracis Immune Inhibitor A2 Peptidase Zymogen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1010

b:64.6
occ:1.00
OD1 A:ASP637 2.3 71.4 1.0
O A:THR639 2.7 55.2 1.0
N A:ASP637 3.3 53.2 1.0
CG A:ASP637 3.4 72.9 1.0
CA A:SER636 3.7 46.8 1.0
C A:THR639 3.9 55.4 1.0
OG A:SER636 3.9 62.5 1.0
C A:SER636 4.0 53.8 1.0
O A:VAL635 4.1 51.3 1.0
CB A:ASP637 4.1 59.8 1.0
CA A:ASP637 4.2 55.5 1.0
OD2 A:ASP637 4.3 83.2 1.0
CB A:SER636 4.3 49.2 1.0
OG1 A:THR639 4.4 60.1 1.0
N A:THR639 4.5 50.1 1.0
CA A:THR639 4.7 50.7 1.0
N A:GLY638 4.7 53.1 1.0
N A:SER636 4.7 47.5 1.0
N A:GLU640 4.8 51.8 1.0
C A:ASP637 4.8 59.0 1.0
C A:VAL635 4.9 52.2 1.0
CA A:GLU640 5.0 51.2 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: Tue Dec 15 10:04:37 2020

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