Sodium in PDB 4asl: Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac)

The structure of Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac), PDB code: 4asl was solved by M.Maestre-Reyna, R.Diderrich, M.S.Veelders, G.Eulenburg, V.Kalugin, S.Brueckner, P.Keller, S.Rupp, H.-U.Moesch, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.24
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	74.600, 103.900, 69.400, 89.90, 90.00, 89.90
R / Rfree (%)	11.7 / 15.5

The structure of Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac) (pdb code 4asl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac), PDB code: 4asl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:38.8 occ:1.00 OD1 A:ASP69 2.1 30.8 1.0 O A:HOH648 2.3 26.6 1.0 O A:HOH579 2.7 14.9 1.0 O A:HOH553 3.1 49.1 1.0 CG A:ASP69 3.2 27.0 1.0 CA A:ASP69 3.7 20.3 1.0 ND2 A:ASN140 3.7 12.4 1.0 O A:HOH644 3.9 26.2 1.0 N A:ASP69 3.9 18.2 1.0 O A:HOH794 3.9 32.1 1.0 CB A:ASP69 4.0 25.4 1.0 O A:HOH555 4.0 17.8 1.0 CB A:SER67 4.1 11.7 0.5 NH2 A:ARG97 4.1 24.2 0.3 OD2 A:ASP69 4.2 34.6 1.0 C A:TYR68 4.3 12.5 1.0 NH1 A:ARG97 4.3 24.5 0.3 OG A:SER67 4.3 13.0 0.5 CB A:SER67 4.4 14.6 0.5 O A:TYR68 4.4 13.1 1.0 O A:HOH710 4.4 89.8 1.0 N A:TYR68 4.5 12.3 1.0 CZ A:ARG97 4.7 25.4 0.3 O A:HOH729 4.8 51.4 1.0 OG1 A:THR137 4.8 12.8 1.0 CG A:ASN140 4.9 10.6 1.0 C A:ASP69 5.0 20.2 1.0 O A:HOH590 5.0 20.9 1.0 CA A:SER67 5.0 13.2 0.5 CA A:SER67 5.0 11.8 0.5

Sodium binding site 2 out of 5 in the Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:49.1 occ:0.50 O A:HOH737 2.3 48.6 1.0 OE2 A:GLU206 2.5 33.8 1.0 CD A:GLU206 3.2 31.0 1.0 O A:HOH424 3.2 48.1 1.0 CE A:LYS204 3.5 34.2 0.7 CG A:GLU206 3.5 28.8 1.0 O A:HOH410 3.9 49.1 1.0 NZ A:LYS204 4.0 35.6 0.7 OE1 A:GLU206 4.2 31.5 1.0 O A:HOH678 4.4 52.9 1.0 CD A:LYS204 4.5 31.8 0.7 CB A:GLU206 4.7 25.0 1.0 O A:HOH601 4.8 39.5 1.0

Sodium binding site 3 out of 5 in the Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:30.1 occ:0.30 OH A:TYR66 2.1 13.3 1.0 O A:HOH517 2.1 15.4 1.0 O3 A:GOL309 2.3 20.8 0.3 OE1 A:GLU64 2.5 12.9 1.0 C3 A:GOL309 3.2 18.3 0.3 CZ A:TYR66 3.4 10.9 1.0 CD A:GLU64 3.5 11.4 1.0 CE2 A:TYR93 3.6 12.8 1.0 OH A:TYR93 3.7 13.7 1.0 OE2 A:GLU64 4.0 13.3 1.0 CE1 A:TYR66 4.1 12.0 1.0 CZ A:TYR93 4.2 12.0 1.0 CE2 A:TYR66 4.2 11.9 1.0 O A:HOH509 4.3 13.0 1.0 C2 A:GOL309 4.6 17.7 0.3 CG A:GLU64 4.7 10.1 1.0 O A:HOH417 4.7 24.1 1.0 CG A:LYS94 4.7 15.6 1.0 CD2 A:TYR93 4.8 12.4 1.0 O2 A:GOL309 4.8 16.9 0.3 CD2 A:LEU144 4.9 16.9 1.0 CB A:GLU64 5.0 9.3 1.0

Sodium binding site 4 out of 5 in the Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:54.9 occ:0.50 OD2 A:ASP53 2.7 34.7 0.7 O A:HOH689 2.7 49.7 1.0 OD2 A:ASP53 3.0 20.4 0.3 CG A:ASP53 3.7 31.2 0.7 CG A:ASP53 3.8 20.2 0.3 O A:HOH685 3.8 44.6 1.0 CB A:ASP53 3.9 30.6 0.7 O A:HOH623 3.9 68.8 1.0 O A:HOH753 4.0 60.6 1.0 CB A:ASP53 4.1 19.0 0.3 CG2 A:ILE54 4.8 26.0 0.3 OD1 A:ASP53 4.8 22.3 0.3 OD1 A:ASP53 4.8 30.0 0.7 O A:HOH682 5.0 41.1 1.0

Sodium binding site 5 out of 5 in the Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of EPA1A in Complex with the T-Antigen (Gal-B1-3- Galnac) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:59.5 occ:0.50 O A:HOH598 2.4 28.6 1.0 OD1 A:ASN243 3.6 32.7 1.0 CA A:ASN243 4.2 21.1 1.0 CG A:ASN243 4.5 29.1 1.0 O A:GLU242 4.6 26.7 1.0 CB A:ASN243 4.6 25.1 1.0 O A:HOH444 4.7 18.0 0.5 N A:THR244 4.8 15.2 1.0 N A:ASN243 5.0 21.5 1.0

M.Maestre-Reyna, R.Diderrich, M.S.Veelders, G.Eulenburg, V.Kalugin, S.Bruckner, P.Keller, S.Rupp, H.Mosch, L.-O.Essen. Structural Basis For Promiscuity and Specificity During Candida Glabrata Invasion of Host Epithelia. Proc.Natl.Acad.Sci.Usa V. 109 16864 2012.
ISSN: ISSN 0027-8424
PubMed: 23035251
DOI: 10.1073/PNAS.1207653109