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Calcium in PDB 7skm: Complex Between S. Aureus Aureolysin and Wt Impi.

Enzymatic activity of Complex Between S. Aureus Aureolysin and Wt Impi.

All present enzymatic activity of Complex Between S. Aureus Aureolysin and Wt Impi.:
3.4.24.29;

Protein crystallography data

The structure of Complex Between S. Aureus Aureolysin and Wt Impi., PDB code: 7skm was solved by S.R.Mendes, U.Eckhard, A.Rodriguez-Banqueri, T.Guevara, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.69 / 1.85
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 68.14, 68.14, 166.18, 90, 90, 90
R / Rfree (%) 16.4 / 21.9

Other elements in 7skm:

The structure of Complex Between S. Aureus Aureolysin and Wt Impi. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex Between S. Aureus Aureolysin and Wt Impi. (pdb code 7skm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Complex Between S. Aureus Aureolysin and Wt Impi., PDB code: 7skm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7skm

Go back to Calcium Binding Sites List in 7skm
Calcium binding site 1 out of 6 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:43.1
occ:1.00
 OD1 A:ASP405 2.4 45.0 1.0
O A:THR399 2.4 42.7 1.0
O A:LYS402 2.4 51.0 1.0
O A:HOH702 2.4 38.8 1.0
O A:HOH721 2.4 41.4 1.0
OG1 A:THR399 2.4 40.7 1.0
O A:TYR398 2.4 41.6 1.0
C A:THR399 3.3 44.2 1.0
C A:LYS402 3.4 53.6 1.0
C A:TYR398 3.4 39.1 1.0
CG A:ASP405 3.4 44.5 1.0
CB A:THR399 3.5 39.5 1.0
CA A:THR399 3.6 40.9 1.0
OD2 A:ASP405 3.8 44.5 1.0
N A:THR399 3.9 40.4 1.0
N A:GLU403 4.1 54.5 1.0
CB A:LYS402 4.2 53.6 1.0
CA A:LYS402 4.3 55.3 1.0
CA A:GLU403 4.3 53.8 1.0
O A:ASP405 4.4 39.2 1.0
N A:PRO400 4.5 45.6 1.0
O A:GLU395 4.5 35.3 1.0
OE2 A:GLU403 4.6 64.1 1.0
CA A:TYR398 4.6 36.6 1.0
N A:LYS402 4.7 57.5 1.0
C A:GLU403 4.7 51.9 1.0
CG2 A:THR399 4.7 40.0 1.0
CB A:ASP405 4.8 45.4 1.0
N A:ASP405 4.8 46.8 1.0
CB A:TYR398 4.9 37.1 1.0
C A:ASP405 4.9 42.5 1.0
CG A:LYS402 4.9 52.4 1.0
CD2 A:TYR398 5.0 38.8 1.0
CA A:PRO400 5.0 48.1 1.0

Calcium binding site 2 out of 6 in 7skm

Go back to Calcium Binding Sites List in 7skm
Calcium binding site 2 out of 6 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:34.1
occ:1.00
 OE2 A:GLU395 2.4 34.1 1.0
OD1 A:ASP390 2.4 33.1 1.0
OE2 A:GLU389 2.4 37.6 1.0
O A:HOH749 2.4 25.0 1.0
O A:HOH740 2.4 34.9 1.0
OD1 A:ASP387 2.4 32.0 1.0
OD2 A:ASP387 2.4 30.8 1.0
CG A:ASP387 2.8 29.6 1.0
CD A:GLU389 3.3 41.3 1.0
CG A:ASP390 3.4 32.1 1.0
CG A:GLU389 3.5 38.6 1.0
CD A:GLU395 3.5 32.1 1.0
CA A:CA603 3.6 32.1 1.0
OD2 A:ASP390 4.0 31.9 1.0
CG A:GLU395 4.2 34.7 1.0
CB A:ASP387 4.3 28.7 1.0
OD1 A:ASP396 4.4 41.5 1.0
OE1 A:GLU395 4.5 33.9 1.0
OE1 A:GLU389 4.5 41.5 1.0
CB A:ASP390 4.6 33.0 1.0
OD1 A:ASN347 4.6 34.1 1.0
OD2 A:ASP396 4.7 38.3 1.0
O A:HOH759 4.8 33.6 1.0
CG A:ASP396 4.8 37.8 1.0
O A:ASP387 4.9 31.2 1.0
O A:HOH772 4.9 30.3 1.0
O A:HOH782 4.9 39.0 1.0
O A:HOH862 5.0 36.8 1.0
CB A:GLU389 5.0 37.1 1.0

Calcium binding site 3 out of 6 in 7skm

Go back to Calcium Binding Sites List in 7skm
Calcium binding site 3 out of 6 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:32.1
occ:1.00
 OE2 A:GLU395 2.4 34.1 1.0
OD2 A:ASP387 2.4 30.8 1.0
O A:HOH772 2.4 30.3 1.0
OD2 A:ASP348 2.4 30.4 1.0
O A:LEU392 2.4 32.8 1.0
OE1 A:GLU395 2.4 33.9 1.0
OD2 A:ASP390 2.4 31.9 1.0
CD A:GLU395 2.7 32.1 1.0
CG A:ASP390 3.2 32.1 1.0
OD1 A:ASP390 3.2 33.1 1.0
CG A:ASP348 3.4 30.4 1.0
C A:LEU392 3.4 30.3 1.0
CG A:ASP387 3.5 29.6 1.0
CA A:CA602 3.6 34.1 1.0
CB A:ASP348 3.9 29.8 1.0
N A:LEU392 4.2 33.6 1.0
CG A:GLU395 4.2 34.7 1.0
CA A:LEU392 4.3 34.0 1.0
OD1 A:ASP348 4.3 27.9 1.0
N A:MET393 4.4 30.2 1.0
CA A:MET393 4.4 31.1 1.0
O A:HOH759 4.4 33.6 1.0
OD1 A:ASP387 4.4 32.0 1.0
CB A:ASP387 4.4 28.7 1.0
O A:ASP387 4.5 31.2 1.0
CB A:LEU392 4.6 33.0 1.0
N A:GLY394 4.6 33.0 1.0
O A:HOH749 4.6 25.0 1.0
CB A:ASP390 4.6 33.0 1.0
O A:ASP390 4.7 34.7 1.0
C A:MET393 4.9 32.3 1.0
N A:GLU395 5.0 35.0 1.0
C A:ASP390 5.0 34.1 1.0

Calcium binding site 4 out of 6 in 7skm

Go back to Calcium Binding Sites List in 7skm
Calcium binding site 4 out of 6 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:54.6
occ:1.00
 O C:THR399 2.4 53.2 1.0
OD1 C:ASP405 2.4 57.5 1.0
O C:TYR398 2.4 49.9 1.0
O C:HOH701 2.4 48.2 1.0
O C:LYS402 2.4 62.6 1.0
O C:HOH709 2.4 47.4 1.0
OG1 C:THR399 2.4 55.4 1.0
C C:THR399 3.3 54.5 1.0
C C:TYR398 3.4 49.2 1.0
C C:LYS402 3.4 65.3 1.0
CG C:ASP405 3.4 55.9 1.0
CB C:THR399 3.5 55.5 1.0
CA C:THR399 3.7 53.7 1.0
OD2 C:ASP405 3.8 56.3 1.0
N C:THR399 3.8 50.9 1.0
N C:GLU403 4.2 66.9 1.0
CA C:GLU403 4.3 69.2 1.0
CA C:LYS402 4.3 65.0 1.0
CB C:LYS402 4.3 64.1 1.0
O C:ASP405 4.4 45.9 1.0
O C:GLU395 4.4 43.9 1.0
N C:PRO400 4.5 56.8 1.0
CA C:TYR398 4.6 46.6 1.0
OE2 C:GLU403 4.6 82.7 1.0
N C:LYS402 4.7 64.8 1.0
C C:GLU403 4.7 68.5 1.0
CB C:ASP405 4.8 56.5 1.0
CG2 C:THR399 4.8 57.1 1.0
N C:ASP405 4.8 59.4 1.0
CB C:TYR398 4.9 46.8 1.0
C C:ASP405 4.9 49.4 1.0

Calcium binding site 5 out of 6 in 7skm

Go back to Calcium Binding Sites List in 7skm
Calcium binding site 5 out of 6 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:43.1
occ:1.00
 OE2 C:GLU395 2.4 39.9 1.0
OD1 C:ASP390 2.4 43.7 1.0
OE2 C:GLU389 2.4 47.8 1.0
O C:HOH741 2.4 39.0 1.0
OD1 C:ASP387 2.4 41.5 1.0
OD2 C:ASP387 2.4 38.2 1.0
CG C:ASP387 2.7 38.1 1.0
CD C:GLU389 3.3 52.1 1.0
CG C:ASP390 3.4 41.4 1.0
CG C:GLU389 3.4 48.6 1.0
CD C:GLU395 3.6 38.8 1.0
CA C:CA603 3.7 36.4 1.0
OD2 C:ASP390 3.9 40.0 1.0
CG C:GLU395 4.2 36.4 1.0
OD1 C:ASP396 4.2 52.2 1.0
CB C:ASP387 4.3 38.0 1.0
O C:HOH740 4.5 29.3 1.0
OE1 C:GLU389 4.5 50.7 1.0
CB C:ASP390 4.5 43.6 1.0
OE1 C:GLU395 4.5 35.9 1.0
OD1 C:ASN347 4.6 32.7 1.0
O C:HOH730 4.7 27.5 0.5
OD2 C:ASP396 4.7 50.2 1.0
O C:HOH707 4.8 33.0 1.0
CG C:ASP396 4.8 48.3 1.0
O C:ASP387 4.9 38.4 1.0
CB C:GLU389 4.9 46.7 1.0

Calcium binding site 6 out of 6 in 7skm

Go back to Calcium Binding Sites List in 7skm
Calcium binding site 6 out of 6 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:36.4
occ:1.00
 O C:LEU392 2.4 37.2 1.0
OD2 C:ASP387 2.4 38.2 1.0
O C:HOH707 2.4 33.0 1.0
OE2 C:GLU395 2.4 39.9 1.0
OD2 C:ASP348 2.4 37.2 1.0
OD2 C:ASP390 2.4 40.0 1.0
OE1 C:GLU395 2.4 35.9 1.0
CD C:GLU395 2.7 38.8 1.0
OD1 C:ASP390 3.1 43.7 1.0
CG C:ASP390 3.1 41.4 1.0
CG C:ASP348 3.4 36.7 1.0
C C:LEU392 3.4 38.0 1.0
CG C:ASP387 3.6 38.1 1.0
CA C:CA602 3.7 43.1 1.0
CB C:ASP348 3.9 36.4 1.0
N C:LEU392 4.2 38.8 1.0
CA C:LEU392 4.2 37.7 1.0
O C:HOH740 4.3 29.3 1.0
CG C:GLU395 4.3 36.4 1.0
CB C:ASP387 4.4 38.0 1.0
OD1 C:ASP348 4.4 37.5 1.0
N C:MET393 4.4 36.8 1.0
O C:ASP387 4.4 38.4 1.0
CA C:MET393 4.4 39.0 1.0
OD1 C:ASP387 4.5 41.5 1.0
CB C:LEU392 4.5 38.4 1.0
O C:ASP390 4.6 37.8 1.0
CB C:ASP390 4.6 43.6 1.0
N C:GLY394 4.6 39.0 1.0
O C:HOH741 4.7 39.0 1.0
C C:ASP390 4.8 42.3 1.0
C C:MET393 4.9 36.6 1.0

Reference:

S.R.Mendes, U.Eckhard, A.Rodriguez-Banqueri, T.Guevara, P.Czermak, E.Marcos, A.Vilcinskas. An Engineered Protein-Based Submicromolar Competitive Inhibitor of the Staphylococcus Aureus Virulence Factor Aureolysin Comput Struct Biotechnol J V. 20 534 2022.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2022.01.001
Page generated: Fri Jul 19 04:09:23 2024

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