Sodium in PDB 2izc: Apostreptavidin pH 2.0 I222 Complex

The structure of Apostreptavidin pH 2.0 I222 Complex, PDB code: 2izc was solved by B.A.Katz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.50 / 1.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.850, 105.630, 48.140, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.1

The structure of Apostreptavidin pH 2.0 I222 Complex also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Apostreptavidin pH 2.0 I222 Complex (pdb code 2izc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Apostreptavidin pH 2.0 I222 Complex, PDB code: 2izc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Apostreptavidin pH 2.0 I222 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apostreptavidin pH 2.0 I222 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:49.1 occ:1.00 O B:HOH507 2.5 39.9 1.0 H2 B:HOH507 3.0 37.4 1.0 H1 B:HOH507 3.2 39.1 1.0 CL B:CL509 3.4 36.6 0.8 HZ2 B:TRP92 3.7 16.4 1.0 CE2 B:TRP108 3.8 14.8 1.0 HG22 B:THR90 3.8 16.9 1.0 CZ2 B:TRP108 3.9 19.8 1.0 NE1 B:TRP108 4.0 17.7 1.0 CD2 B:TRP108 4.1 12.0 1.0 OD2 B:ASP128 4.1 22.4 1.0 HZ2 B:TRP108 4.2 18.7 1.0 HD11 B:LEU110 4.2 16.9 0.4 HE1 B:TRP108 4.2 16.0 1.0 HG23 B:VAL47 4.3 38.8 1.0 HD11 B:LEU25 4.4 32.1 1.0 HE1 B:TRP92 4.4 16.5 1.0 CZ2 B:TRP92 4.4 15.1 1.0 CH2 B:TRP108 4.4 16.4 1.0 CD1 B:TRP108 4.5 17.3 1.0 CG B:TRP108 4.5 14.8 1.0 CE3 B:TRP108 4.6 14.8 1.0 HG21 B:VAL47 4.6 39.0 1.0 HD13 B:LEU25 4.6 31.1 1.0 HG1 B:THR90 4.7 22.5 1.0 HG22 B:VAL47 4.7 38.4 1.0 HD23 B:LEU110 4.7 20.1 0.7 CZ3 B:TRP108 4.7 18.0 1.0 HH B:TYR43 4.7 20.2 1.0 HZ2 B:TRP79 4.8 23.9 1.0 CG2 B:THR90 4.8 16.5 1.0 CG2 B:VAL47 4.8 38.2 1.0 HD12 B:LEU25 4.8 31.4 1.0 OD1 B:ASP128 4.8 29.4 1.0 O B:HOH867 4.8 31.4 1.0 CD1 B:LEU25 4.9 31.3 1.0 CG B:ASP128 4.9 25.0 1.0 HG21 B:THR90 4.9 17.4 1.0 CE2 B:TRP92 4.9 17.7 1.0 NE1 B:TRP92 4.9 16.7 1.0 H2 B:HOH867 5.0 33.6 1.0 HH2 B:TRP108 5.0 16.6 1.0

Sodium binding site 2 out of 2 in the Apostreptavidin pH 2.0 I222 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apostreptavidin pH 2.0 I222 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na508 b:35.8 occ:1.00 CL D:CL505 2.7 72.6 1.1 O D:HOH501 3.0 41.4 1.0 OD2 D:ASP128 3.3 32.5 1.0 HZ2 D:TRP92 3.5 14.7 1.0 H1 D:HOH501 3.6 42.0 1.0 H2 D:HOH501 3.6 42.1 1.0 CE2 D:TRP108 3.7 15.2 1.0 HE1 D:TRP92 3.7 17.1 1.0 NE1 D:TRP108 3.7 15.9 1.0 HE1 D:TRP108 3.9 13.8 1.0 HG22 D:THR90 3.9 15.9 1.0 HD11 D:LEU25 4.0 44.9 1.0 CZ2 D:TRP108 4.1 16.3 1.0 HH D:TYR43 4.1 25.6 1.0 CD2 D:TRP108 4.1 13.7 1.0 CD1 D:TRP108 4.1 16.2 1.0 CZ2 D:TRP92 4.2 16.6 1.0 CG D:ASP128 4.2 29.4 1.0 HZ2 D:TRP108 4.3 13.4 1.0 NE1 D:TRP92 4.3 17.3 1.0 CG D:TRP108 4.3 13.8 1.0 HD13 D:LEU25 4.4 44.6 1.0 HD22 D:ASN23 4.4 37.6 1.0 OD1 D:ASP128 4.5 40.7 1.0 CE2 D:TRP92 4.5 18.7 1.0 HD1 D:TRP108 4.7 13.8 1.0 CD1 D:LEU25 4.7 46.8 1.0 OH D:TYR43 4.7 26.2 1.0 CH2 D:TRP108 4.7 15.1 1.0 CE3 D:TRP108 4.8 13.5 1.0 HG1 D:THR90 4.8 15.7 1.0 CG2 D:THR90 4.9 15.9 1.0 HD21 D:ASN23 4.9 37.7 1.0 HG22 D:VAL47 4.9 53.6 0.8

B.A.Katz, B.A.Katz. N/A N/A.
ISSN: ISSN 0022-2836
PubMed: 9405158
DOI: 10.1006/JMBI.1997.1444