Chlorine in PDB 8yib: Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State

Enzymatic activity of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State

All present enzymatic activity of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State:
3.1.1.3;

Protein crystallography data

The structure of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State, PDB code: 8yib was solved by J.Kitadokoro, S.Kamitani, K.Kitadokoro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.29 / 2.27
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.548, 132.548, 249.754, 90, 90, 90
R / Rfree (%) 19.7 / 22.1

Other elements in 8yib:

The structure of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 2 atoms
Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State (pdb code 8yib). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State, PDB code: 8yib:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8yib

Go back to Chlorine Binding Sites List in 8yib
Chlorine binding site 1 out of 4 in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl420

b:75.6
occ:1.00
 OH A:TYR70 3.7 56.6 1.0
ND1 A:HIS155 4.1 62.3 1.0
CE A:MET158 4.3 59.9 1.0
O A:TRP104 4.3 63.3 1.0
CE1 A:HIS155 4.4 55.8 1.0
CG A:HIS155 4.4 55.0 1.0
SD A:MET158 4.4 57.9 1.0
CZ A:TYR70 4.6 54.0 1.0
CE1 A:TYR70 4.7 50.5 1.0
CA A:GLU105 4.7 63.4 1.0
CB A:PRO149 4.8 58.8 1.0
CB A:HIS155 4.8 50.8 1.0
NE2 A:HIS155 4.9 69.3 1.0
CD2 A:HIS155 4.9 50.5 1.0
CD A:PRO106 4.9 60.3 1.0

Chlorine binding site 2 out of 4 in 8yib

Go back to Chlorine Binding Sites List in 8yib
Chlorine binding site 2 out of 4 in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl421

b:81.5
occ:1.00
 O A:HOH580 1.9 67.5 1.0
O A:ILE202 3.5 56.0 1.0
C A:ILE202 4.1 54.5 1.0
O A:MET195 4.2 50.5 1.0
NZ A:LYS212 4.2 95.0 1.0
CA A:ASP203 4.2 52.2 1.0
CD A:LYS212 4.3 79.2 1.0
N A:ASP203 4.3 49.9 1.0
CB A:ASP203 4.4 46.8 1.0
O A:SER200 4.4 52.0 1.0
CG2 A:THR207 4.6 44.5 1.0
OG A:SER200 4.7 55.5 1.0
O A:HOH576 4.8 71.8 1.0
CG A:ASP203 4.8 55.2 1.0
CB A:SER200 4.9 52.8 1.0
CE A:LYS212 4.9 80.0 1.0
N A:ILE202 4.9 60.6 1.0
CA A:GLY196 4.9 49.5 1.0
C A:SER200 5.0 52.6 1.0

Chlorine binding site 3 out of 4 in 8yib

Go back to Chlorine Binding Sites List in 8yib
Chlorine binding site 3 out of 4 in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl419

b:81.8
occ:1.00
 O B:ILE202 3.9 67.4 1.0
CD B:LYS212 4.0 97.7 1.0
CA B:ASP203 4.3 55.2 1.0
C B:ILE202 4.3 65.8 1.0
CB B:ASP203 4.3 55.5 1.0
CG2 B:THR207 4.4 51.5 1.0
CE B:LYS212 4.5 106.1 1.0
O B:MET195 4.5 56.9 1.0
O B:HOH527 4.5 51.1 1.0
N B:ASP203 4.5 56.0 1.0
NZ B:LYS212 4.6 112.6 1.0
O B:SER200 4.7 61.3 1.0
CG B:ASP203 4.7 67.9 1.0
OD2 B:ASP203 5.0 78.2 1.0

Chlorine binding site 4 out of 4 in 8yib

Go back to Chlorine Binding Sites List in 8yib
Chlorine binding site 4 out of 4 in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl420

b:95.0
occ:1.00
 OH B:TYR70 3.6 79.0 1.0
ND1 B:HIS155 4.2 95.3 1.0
CE B:MET158 4.2 76.1 1.0
O B:TRP104 4.2 83.6 1.0
CE1 B:HIS155 4.3 92.1 1.0
SD B:MET158 4.4 80.0 1.0
CB B:PRO149 4.5 67.6 1.0
CZ B:TYR70 4.6 83.6 1.0
CE1 B:TYR70 4.7 83.6 1.0
CA B:GLU105 4.8 97.4 1.0
CG B:HIS155 4.8 92.1 1.0
NE2 B:HIS155 4.9 103.9 1.0
CE B:LYS74 4.9 87.1 1.0
CD B:PRO106 5.0 72.6 1.0

Reference:

J.Kitadokoro, S.Kamitani, Y.Okuno, T.Hikima, M.Yamamoto, T.Hirokawa, K.Kitadokoro. Crystal Structure of Staphylococcus Aureus Lipase Complex with Unsaturated Petroselinic Acid. Febs Open Bio 2024.
ISSN: ESSN 2211-5463
PubMed: 38757397
DOI: 10.1002/2211-5463.13808
Page generated: Tue Jul 30 13:56:50 2024

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