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Magnesium 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
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State, PDB code: 8yib:

Magnesium binding site 1 out of 1 in 8yib

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg411

b:101.4
occ:1.00
 O A:HOH533 2.7 68.3 1.0
O A:ASP23 3.1 90.3 1.0
O A:ASN201 3.1 62.4 1.0
CB A:ASN201 3.6 64.2 1.0
C A:ASN201 3.8 65.3 1.0
CG2 A:ILE202 3.9 56.6 1.0
O A:ALA25 4.3 65.1 1.0
C A:ASP23 4.3 86.1 1.0
CA A:ASN201 4.3 66.3 1.0
N A:ILE202 4.7 60.6 1.0
CA A:ASN24 4.8 56.9 1.0
CG A:ASN201 4.8 88.8 1.0
CB A:ILE202 5.0 71.0 1.0
CA A:ILE202 5.0 58.7 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: Fri Aug 15 21:29:29 2025

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