Sodium in PDB 8g1l: Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein)

The structure of Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein), PDB code: 8g1l was solved by J.J.Maciag, A.B.Herr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.77 / 1.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.664, 68.573, 109.272, 90, 90, 90
R / Rfree (%)	11.7 / 12.6

The structure of Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein) also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein) (pdb code 8g1l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein), PDB code: 8g1l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:8.3 occ:1.00 O A:GLN391 2.3 8.5 1.0 OE1 A:GLN579 2.4 9.1 1.0 O A:HOH971 2.4 9.0 1.0 O A:SER590 2.4 7.6 1.0 O A:ASN388 2.4 8.6 1.0 HB3 A:ASN388 3.2 8.3 1.0 O A:HOH936 3.3 22.0 1.0 C A:SER590 3.4 6.8 1.0 H A:GLN391 3.5 12.1 1.0 CD A:GLN579 3.5 7.3 1.0 C A:GLN391 3.5 8.6 1.0 C A:ASN388 3.6 7.8 1.0 HG21 A:THR397 3.7 9.1 1.0 HA A:PRO392 3.7 10.0 1.0 HE22 A:GLN579 3.8 9.4 1.0 HA A:SER590 3.8 8.5 1.0 HA3 A:GLY591 3.8 7.6 1.0 CB A:ASN388 3.9 6.9 1.0 HB2 A:ASN388 4.0 8.3 1.0 NE2 A:GLN579 4.1 7.9 1.0 CA A:SER590 4.2 7.1 1.0 N A:GLN391 4.2 10.1 1.0 CA A:ASN388 4.3 7.2 1.0 N A:GLY591 4.3 6.6 1.0 CA A:PRO392 4.3 8.3 1.0 HB3 A:GLN579 4.3 7.6 1.0 O A:ALA589 4.4 7.2 1.0 HA A:ASN388 4.4 8.7 1.0 N A:PRO392 4.4 8.0 1.0 HD3 A:PRO393 4.4 8.4 1.0 HA A:TYR389 4.4 11.0 1.0 HB3 A:GLN391 4.4 14.6 1.0 CA A:GLY591 4.5 6.3 1.0 CG2 A:THR397 4.5 7.6 1.0 CA A:GLN391 4.5 9.8 1.0 HG23 A:THR397 4.5 9.1 1.0 C A:PRO392 4.5 7.1 1.0 H A:GLY390 4.5 12.1 1.0 N A:TYR389 4.7 8.0 1.0 HG22 A:THR397 4.7 9.1 1.0 CG A:GLN579 4.8 6.7 1.0 HB2 A:GLN579 4.8 7.6 1.0 HB2 A:SER590 4.8 9.2 1.0 N A:GLY390 4.8 10.1 1.0 CB A:GLN579 4.9 6.3 1.0 N A:PRO393 4.9 7.0 1.0 CA A:TYR389 4.9 9.1 1.0 C A:GLY591 4.9 6.2 1.0 O A:PRO392 4.9 7.9 1.0 HE21 A:GLN579 4.9 9.4 1.0

Sodium binding site 2 out of 2 in the Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lectin Domain of Aap (Staphylococcus Epidermidis Accumulation Associated Protein) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:26.1 occ:1.00 H A:THR521 2.3 10.0 1.0 O A:HOH1124 2.6 32.1 1.0 O A:HOH1083 2.7 39.5 1.0 HB A:THR520 2.7 11.9 1.0 H A:ASN522 2.7 15.8 1.0 HB3 A:ASN522 3.0 27.6 1.0 N A:THR521 3.1 8.4 1.0 HA A:THR520 3.3 9.6 1.0 HD22 A:ASN522 3.4 32.0 1.0 N A:ASN522 3.4 13.1 1.0 CB A:THR520 3.5 9.9 1.0 O A:HOH1064 3.6 21.0 1.0 HG1 A:THR521 3.6 15.4 1.0 CA A:THR520 3.7 8.0 1.0 OG1 A:THR521 3.9 12.9 1.0 O A:HOH820 3.9 16.5 1.0 CB A:ASN522 3.9 23.0 1.0 C A:THR520 3.9 7.5 1.0 CA A:THR521 4.1 9.9 1.0 O A:HOH816 4.1 32.6 1.0 HG22 A:THR520 4.1 14.1 1.0 ND2 A:ASN522 4.2 26.7 1.0 C A:THR521 4.2 12.8 1.0 CA A:ASN522 4.3 16.8 1.0 CG2 A:THR520 4.3 11.7 1.0 O A:HOH1041 4.5 24.1 1.0 OG1 A:THR520 4.5 10.5 1.0 HB2 A:ASN522 4.5 27.6 1.0 HG21 A:THR520 4.6 14.1 1.0 CG A:ASN522 4.6 23.1 1.0 CB A:THR521 4.6 12.4 1.0 HA A:ASN522 4.6 20.2 1.0 HG1 A:THR520 4.7 12.7 1.0 HD21 A:ASN522 4.9 32.0 1.0 HA A:THR521 4.9 11.8 1.0

J.J.Maciag, A.B.Herr. Mechanistic Basis of Staphylococcal Interspecies Competition For Skin Colonization To Be Published.