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Sodium in PDB 1oar: Fv Ige Spe-7 in Complex with Alizarin Red

Protein crystallography data

The structure of Fv Ige Spe-7 in Complex with Alizarin Red, PDB code: 1oar was solved by L.C.James, P.Roversi, D.Tawfik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.71 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.917, 78.882, 169.036, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.1

Other elements in 1oar:

The structure of Fv Ige Spe-7 in Complex with Alizarin Red also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Fv Ige Spe-7 in Complex with Alizarin Red (pdb code 1oar). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Fv Ige Spe-7 in Complex with Alizarin Red, PDB code: 1oar:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 1oar

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Sodium binding site 1 out of 6 in the Fv Ige Spe-7 in Complex with Alizarin Red


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fv Ige Spe-7 in Complex with Alizarin Red within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na903

b:39.1
occ:1.00
 O L:HOH2062 2.8 21.8 1.0
O L:GLY103 2.8 21.5 1.0
O L:GLN6 3.3 22.2 1.0
C L:GLY102 3.6 22.7 1.0
N L:GLY103 3.8 19.5 1.0
CA L:GLY102 3.8 18.0 1.0
C L:GLY103 3.8 22.0 1.0
CA L:SER8 3.9 18.3 1.0
O L:GLU7 3.9 21.1 1.0
O L:GLY102 3.9 22.3 1.0
C L:GLN6 4.0 22.9 1.0
N L:SER8 4.2 18.8 1.0
C L:GLU7 4.2 22.1 1.0
CB L:GLN6 4.2 20.5 1.0
N L:GLY102 4.3 17.9 1.0
CA L:GLY103 4.4 18.9 1.0
N L:GLN6 4.5 20.3 1.0
O L:HOH2011 4.5 46.7 1.0
CA L:GLN6 4.5 19.5 1.0
CB L:SER8 4.6 22.1 1.0
O L:HOH2012 4.7 32.1 1.0
C L:SER8 4.9 20.8 1.0
O L:SER8 4.9 20.2 1.0
N L:GLU7 4.9 19.1 1.0
N L:THR104 4.9 17.8 1.0

Sodium binding site 2 out of 6 in 1oar

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Sodium binding site 2 out of 6 in the Fv Ige Spe-7 in Complex with Alizarin Red


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fv Ige Spe-7 in Complex with Alizarin Red within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na903

b:0.3
occ:1.00
 O N:HOH2012 2.1 32.2 1.0
O N:HOH2010 2.2 46.8 1.0
CL N:CL913 3.3 65.2 1.0
OG N:SER8 3.9 31.2 1.0
O N:HOH2011 4.0 43.9 1.0
NA J:NA903 4.3 39.2 1.0
O N:SER8 4.3 20.1 1.0
O N:GLY102 4.3 22.2 1.0
O N:GLY103 4.4 21.5 1.0
O N:HOH2065 4.6 40.3 1.0
CA N:SER8 4.7 18.2 1.0
CB N:SER8 4.7 22.1 1.0
C N:SER8 4.9 20.7 1.0

Sodium binding site 3 out of 6 in 1oar

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Sodium binding site 3 out of 6 in the Fv Ige Spe-7 in Complex with Alizarin Red


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Fv Ige Spe-7 in Complex with Alizarin Red within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na903

b:39.2
occ:1.00
 O N:HOH2064 2.8 21.9 1.0
O N:GLY103 2.8 21.5 1.0
O N:GLN6 3.3 22.2 1.0
C N:GLY102 3.6 22.7 1.0
N N:GLY103 3.8 19.4 1.0
CA N:GLY102 3.8 18.0 1.0
C N:GLY103 3.9 22.0 1.0
CA N:SER8 3.9 18.2 1.0
O N:GLY102 3.9 22.2 1.0
O N:GLU7 3.9 21.0 1.0
C N:GLN6 4.1 22.9 1.0
N N:SER8 4.2 18.8 1.0
C N:GLU7 4.2 22.0 1.0
CB N:GLN6 4.2 20.5 1.0
N N:GLY102 4.3 17.9 1.0
NA I:NA903 4.3 0.3 1.0
CA N:GLY103 4.4 18.9 1.0
O N:HOH2010 4.5 46.8 1.0
N N:GLN6 4.5 20.2 1.0
CA N:GLN6 4.5 19.5 1.0
CB N:SER8 4.6 22.1 1.0
O N:HOH2012 4.7 32.2 1.0
C N:SER8 4.9 20.7 1.0
O N:SER8 4.9 20.1 1.0
N N:GLU7 4.9 19.1 1.0
N N:THR104 4.9 17.8 1.0

Sodium binding site 4 out of 6 in 1oar

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Sodium binding site 4 out of 6 in the Fv Ige Spe-7 in Complex with Alizarin Red


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Fv Ige Spe-7 in Complex with Alizarin Red within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na901

b:71.4
occ:1.00
 O L:HOH2035 2.3 33.8 1.0
CL L:CL913 2.7 65.2 1.0
O H:HOH2026 3.1 32.8 1.0
O H:HOH2021 3.6 39.5 1.0
CZ L:PHE89 3.7 21.4 1.0
CD1 L:ILE87 4.2 28.0 1.0
CE1 L:PHE89 4.3 22.5 1.0
CG2 L:ILE87 4.4 20.1 1.0
O L:GLY102 4.6 22.3 1.0
CE2 L:PHE89 4.6 23.4 1.0
OE1 L:GLU40 4.6 25.9 1.0
O L:HOH2063 4.7 40.2 1.0
CA H:GLY44 4.7 31.3 1.0

Sodium binding site 5 out of 6 in 1oar

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Sodium binding site 5 out of 6 in the Fv Ige Spe-7 in Complex with Alizarin Red


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Fv Ige Spe-7 in Complex with Alizarin Red within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na903

b:49.4
occ:1.00
 OG1 M:THR19 2.7 34.6 1.0
O M:HOH2007 2.9 80.9 1.0
O J:TYR102 3.0 35.3 1.0
N M:THR19 3.3 29.9 1.0
CB M:THR19 3.3 35.9 1.0
C J:TYR102 3.3 35.5 1.0
CL M:CL913 3.3 49.6 1.0
CG2 M:THR17 3.5 35.4 1.0
C M:VAL18 3.5 32.4 1.0
CA J:GLY103 3.6 31.4 1.0
N J:GLY103 3.6 31.8 1.0
CA M:VAL18 3.8 28.7 1.0
O M:THR17 3.8 33.4 1.0
CA M:THR19 3.9 30.2 1.0
C M:THR17 3.9 33.8 1.0
N M:VAL18 3.9 29.4 1.0
CB J:TYR102 4.0 33.9 1.0
O M:VAL18 4.1 31.5 1.0
CA J:TYR102 4.3 31.7 1.0
CB M:THR17 4.4 37.8 1.0
CG2 M:THR76 4.6 37.3 1.0
CG2 M:THR19 4.7 33.5 1.0
CA M:THR17 4.8 30.9 1.0
C J:GLY103 4.8 34.6 1.0

Sodium binding site 6 out of 6 in 1oar

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Sodium binding site 6 out of 6 in the Fv Ige Spe-7 in Complex with Alizarin Red


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Fv Ige Spe-7 in Complex with Alizarin Red within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na901

b:71.4
occ:1.00
 O N:HOH2034 2.3 33.7 1.0
CL N:CL913 2.7 65.2 1.0
O J:HOH2024 3.1 32.9 1.0
O J:HOH2019 3.6 39.5 1.0
CZ N:PHE89 3.7 21.4 1.0
CD1 N:ILE87 4.2 28.0 1.0
CE1 N:PHE89 4.3 22.4 1.0
CG2 N:ILE87 4.4 20.1 1.0
O N:GLY102 4.6 22.2 1.0
CE2 N:PHE89 4.6 23.4 1.0
OE1 N:GLU40 4.6 25.8 1.0
CA J:GLY44 4.7 31.4 1.0
O N:HOH2065 4.7 40.3 1.0

Reference:

L.C.James, P.Roversi, D.Tawfik. Antibody Multispecificity Mediated By Conformational Diversity Science V. 299 1362 2003.
ISSN: ISSN 0036-8075
PubMed: 12610298
DOI: 10.1126/SCIENCE.1079731
Page generated: Sun Oct 6 21:11:05 2024

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