Atomistry » Sodium » PDB 1oar-1ph6 » 1oar
Atomistry »
  Sodium »
    PDB 1oar-1ph6 »
      1oar »

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

Go back to Sodium Binding Sites List in 1oar
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

Go back to Sodium Binding Sites List in 1oar
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

Go back to Sodium Binding Sites List in 1oar
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

Go back to Sodium Binding Sites List in 1oar
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

Go back to Sodium Binding Sites List in 1oar
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

Go back to Sodium Binding Sites List in 1oar
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy