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Calcium in PDB 7skl: Complex Between S. Aureus Aureolysin and Impi Mutant I57I

Enzymatic activity of Complex Between S. Aureus Aureolysin and Impi Mutant I57I

All present enzymatic activity of Complex Between S. Aureus Aureolysin and Impi Mutant I57I:
3.4.24.29;

Protein crystallography data

The structure of Complex Between S. Aureus Aureolysin and Impi Mutant I57I, PDB code: 7skl 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) 68.08 / 1.60
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 68.08, 68.08, 166.69, 90, 90, 90
R / Rfree (%) 15.8 / 18.8

Other elements in 7skl:

The structure of Complex Between S. Aureus Aureolysin and Impi Mutant I57I 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 Impi Mutant I57I (pdb code 7skl). 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 Impi Mutant I57I, PDB code: 7skl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7skl

Go back to Calcium Binding Sites List in 7skl
Calcium binding site 1 out of 6 in the Complex Between S. Aureus Aureolysin and Impi Mutant I57I


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 Impi Mutant I57I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:44.5
occ:1.00
 O A:TYR398 2.4 37.6 1.0
OG1 A:THR399 2.4 38.8 1.0
O A:HOH736 2.4 45.1 1.0
O A:THR399 2.4 40.9 1.0
O A:LYS402 2.4 50.1 1.0
O A:HOH708 2.4 39.1 1.0
OD1 A:ASP405 2.4 46.3 1.0
C A:THR399 3.4 39.5 1.0
C A:TYR398 3.4 34.8 1.0
CG A:ASP405 3.4 43.7 1.0
C A:LYS402 3.5 53.7 1.0
CB A:THR399 3.6 36.6 1.0
CA A:THR399 3.8 37.3 1.0
OD2 A:ASP405 3.8 45.2 1.0
N A:THR399 4.0 34.2 1.0
CA A:LYS402 4.3 51.9 1.0
O A:GLU395 4.4 31.3 1.0
N A:LYS402 4.4 53.6 1.0
CB A:LYS402 4.4 51.8 1.0
N A:PRO400 4.5 42.2 1.0
O A:ASP405 4.5 43.1 1.0
N A:GLU403 4.5 54.5 1.0
CA A:TYR398 4.6 32.8 1.0
CD2 A:TYR398 4.7 34.5 1.0
CG2 A:THR399 4.8 37.1 1.0
CB A:ASP405 4.8 44.8 1.0
CB A:TYR398 4.8 32.3 1.0
CA A:GLU403 4.8 56.5 1.0
N A:ASP405 4.9 41.7 1.0
C A:GLU403 4.9 54.4 1.0
CA A:PRO400 5.0 45.6 1.0
C A:ASP405 5.0 40.6 1.0

Calcium binding site 2 out of 6 in 7skl

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Calcium binding site 2 out of 6 in the Complex Between S. Aureus Aureolysin and Impi Mutant I57I


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 Impi Mutant I57I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:30.1
occ:1.00
 O A:HOH733 2.4 28.2 1.0
OD1 A:ASP390 2.4 32.3 1.0
O2 A:EDO606 2.4 32.9 1.0
OE2 A:GLU389 2.4 32.0 1.0
OD1 A:ASP387 2.4 30.8 1.0
OE2 A:GLU395 2.4 26.7 1.0
OD2 A:ASP387 2.4 28.7 1.0
CG A:ASP387 2.8 27.9 1.0
CD A:GLU389 3.3 34.4 1.0
C2 A:EDO606 3.5 36.7 1.0
CG A:ASP390 3.5 29.5 1.0
CD A:GLU395 3.5 27.2 1.0
CG A:GLU389 3.5 33.1 1.0
CA A:CA603 3.7 26.9 1.0
OD2 A:ASP390 4.0 31.4 1.0
CG A:GLU395 4.2 28.4 1.0
CB A:ASP387 4.3 27.3 1.0
OE1 A:GLU395 4.5 27.1 1.0
OD2 A:ASP396 4.5 32.4 1.0
OE1 A:GLU389 4.5 33.8 1.0
O A:HOH739 4.5 31.8 1.0
OD1 A:ASP396 4.6 32.1 1.0
OD1 A:ASN347 4.6 24.9 1.0
O A:HOH764 4.6 31.6 1.0
C1 A:EDO606 4.7 42.2 1.0
CB A:ASP390 4.7 30.5 1.0
CG A:ASP396 4.9 32.6 1.0
O A:ASP387 4.9 24.9 1.0
CB A:GLU389 4.9 33.3 1.0

Calcium binding site 3 out of 6 in 7skl

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Calcium binding site 3 out of 6 in the Complex Between S. Aureus Aureolysin and Impi Mutant I57I


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 Impi Mutant I57I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:26.9
occ:1.00
 OD2 A:ASP348 2.3 25.6 1.0
OD2 A:ASP387 2.4 28.7 1.0
O A:LEU392 2.4 27.7 1.0
O A:HOH785 2.4 28.1 1.0
OE2 A:GLU395 2.4 26.7 1.0
OE1 A:GLU395 2.4 27.1 1.0
OD2 A:ASP390 2.4 31.4 1.0
CD A:GLU395 2.7 27.2 1.0
CG A:ASP390 3.2 29.5 1.0
CG A:ASP348 3.3 25.4 1.0
OD1 A:ASP390 3.3 32.3 1.0
C A:LEU392 3.4 27.1 1.0
CG A:ASP387 3.4 27.9 1.0
CA A:CA602 3.7 30.1 1.0
CB A:ASP348 3.9 24.3 1.0
CB A:ASP387 4.2 27.3 1.0
O A:HOH739 4.2 31.8 1.0
N A:LEU392 4.2 28.4 1.0
CG A:GLU395 4.2 28.4 1.0
CA A:LEU392 4.3 27.6 1.0
OD1 A:ASP348 4.3 24.9 1.0
OD1 A:ASP387 4.3 30.8 1.0
N A:MET393 4.3 27.3 1.0
CA A:MET393 4.3 28.4 1.0
N A:GLY394 4.4 28.0 1.0
CB A:LEU392 4.5 28.2 1.0
O A:HOH830 4.5 54.7 1.0
O A:ASP387 4.6 24.9 1.0
O A:ASP390 4.6 29.0 1.0
O A:HOH733 4.6 28.2 1.0
CB A:ASP390 4.7 30.5 1.0
C A:MET393 4.8 25.3 1.0
C A:ASP390 4.9 28.7 1.0

Calcium binding site 4 out of 6 in 7skl

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Calcium binding site 4 out of 6 in the Complex Between S. Aureus Aureolysin and Impi Mutant I57I


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 Impi Mutant I57I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:47.2
occ:1.00
 O C:THR399 2.4 52.4 1.0
O C:TYR398 2.4 43.9 1.0
O C:HOH703 2.4 46.4 1.0
O C:LYS402 2.4 57.3 1.0
OD1 C:ASP405 2.4 47.0 1.0
OG1 C:THR399 2.4 45.7 1.0
C C:THR399 3.4 52.8 1.0
C C:TYR398 3.4 46.1 1.0
C C:LYS402 3.5 61.9 1.0
CG C:ASP405 3.5 46.5 1.0
CB C:THR399 3.6 48.7 1.0
CA C:THR399 3.8 49.4 1.0
OD2 C:ASP405 3.9 46.2 1.0
N C:THR399 4.0 48.1 1.0
CA C:LYS402 4.2 63.0 1.0
CB C:LYS402 4.2 66.4 1.0
N C:LYS402 4.3 65.0 1.0
O C:ASP405 4.3 40.6 1.0
O C:GLU395 4.4 32.9 1.0
N C:GLU403 4.4 62.5 1.0
N C:PRO400 4.5 56.3 1.0
CA C:TYR398 4.7 43.5 1.0
CA C:GLU403 4.7 66.6 1.0
CG2 C:THR399 4.8 48.0 1.0
CB C:ASP405 4.8 46.2 1.0
CD2 C:TYR398 4.9 43.3 1.0
C C:ASP405 4.9 42.4 1.0
O C:HOH746 5.0 38.4 1.0
N C:ASP405 5.0 50.7 1.0
CB C:TYR398 5.0 42.5 1.0

Calcium binding site 5 out of 6 in 7skl

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Calcium binding site 5 out of 6 in the Complex Between S. Aureus Aureolysin and Impi Mutant I57I


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 Impi Mutant I57I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:35.2
occ:1.00
 OD1 C:ASP390 2.4 35.6 1.0
OD1 C:ASP387 2.4 36.3 1.0
O C:HOH708 2.4 39.1 1.0
OE2 C:GLU389 2.4 37.8 1.0
OE2 C:GLU395 2.4 32.8 1.0
OD2 C:ASP387 2.4 33.5 1.0
CG C:ASP387 2.7 36.0 1.0
CD C:GLU389 3.4 38.9 1.0
CG C:ASP390 3.5 34.0 1.0
CG C:GLU389 3.5 38.8 1.0
CD C:GLU395 3.6 32.1 1.0
CA C:CA603 3.7 31.4 1.0
OD2 C:ASP390 4.0 31.6 1.0
CG C:GLU395 4.2 31.7 1.0
CB C:ASP387 4.2 33.5 1.0
O C:HOH743 4.3 33.3 1.0
OD2 C:ASP396 4.4 39.7 1.0
O C:HOH702 4.4 38.3 1.0
OD1 C:ASP396 4.4 42.4 1.0
OD1 C:ASN347 4.4 25.7 1.0
OE1 C:GLU395 4.5 32.1 1.0
OE1 C:GLU389 4.5 39.5 1.0
CG C:ASP396 4.7 40.3 1.0
CB C:ASP390 4.7 34.7 1.0
O C:HOH728 4.9 32.6 1.0
O C:ASP387 4.9 30.6 1.0

Calcium binding site 6 out of 6 in 7skl

Go back to Calcium Binding Sites List in 7skl
Calcium binding site 6 out of 6 in the Complex Between S. Aureus Aureolysin and Impi Mutant I57I


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 Impi Mutant I57I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:31.4
occ:1.00
 OD2 C:ASP348 2.4 32.0 1.0
O C:LEU392 2.4 33.0 1.0
OD2 C:ASP390 2.4 31.6 1.0
OE2 C:GLU395 2.4 32.8 1.0
OD2 C:ASP387 2.4 33.5 1.0
O C:HOH728 2.4 32.6 1.0
OE1 C:GLU395 2.4 32.1 1.0
CD C:GLU395 2.7 32.1 1.0
CG C:ASP390 3.2 34.0 1.0
CG C:ASP348 3.3 28.8 1.0
OD1 C:ASP390 3.4 35.6 1.0
C C:LEU392 3.4 29.1 1.0
CG C:ASP387 3.6 36.0 1.0
CA C:CA602 3.7 35.2 1.0
CB C:ASP348 3.9 29.6 1.0
O C:HOH743 4.1 33.3 1.0
N C:LEU392 4.2 32.4 1.0
CG C:GLU395 4.2 31.7 1.0
CA C:LEU392 4.2 32.4 1.0
OD1 C:ASP348 4.3 29.5 1.0
N C:MET393 4.3 30.4 1.0
CB C:ASP387 4.3 33.5 1.0
OD1 C:ASP387 4.4 36.3 1.0
O C:ASP387 4.4 30.6 1.0
CB C:LEU392 4.5 31.3 1.0
CA C:MET393 4.5 30.0 1.0
N C:GLY394 4.5 30.4 1.0
O C:ASP390 4.6 31.9 1.0
CB C:ASP390 4.6 34.7 1.0
C C:ASP390 4.8 32.2 1.0
C C:MET393 5.0 30.6 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: Thu Jul 10 01:03:34 2025

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