Atomistry » Sodium » PDB 1jb7-1k73 » 1jtp
Atomistry »
  Sodium »
    PDB 1jb7-1k73 »
      1jtp »

Sodium in PDB 1jtp: Degenerate Interfaces in Antigen-Antibody Complexes

Enzymatic activity of Degenerate Interfaces in Antigen-Antibody Complexes

All present enzymatic activity of Degenerate Interfaces in Antigen-Antibody Complexes:
3.2.1.17;

Protein crystallography data

The structure of Degenerate Interfaces in Antigen-Antibody Complexes, PDB code: 1jtp was solved by K.Decanniere, T.R.Transue, A.Desmyter, D.Maes, S.Muyldermans, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.123, 69.375, 113.231, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Degenerate Interfaces in Antigen-Antibody Complexes (pdb code 1jtp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Degenerate Interfaces in Antigen-Antibody Complexes, PDB code: 1jtp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 1jtp

Go back to Sodium Binding Sites List in 1jtp
Sodium binding site 1 out of 5 in the Degenerate Interfaces in Antigen-Antibody Complexes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Degenerate Interfaces in Antigen-Antibody Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:16.8
occ:1.00
 O A:GLY119 2.3 15.6 1.0
OD1 A:ASP99 2.4 12.4 1.0
O A:HOH537 2.4 31.7 1.0
OD2 A:ASP121 2.4 19.9 1.0
O A:HOH510 2.5 15.4 1.0
OG1 A:THR101 3.0 16.2 1.0
CG A:ASP99 3.2 19.2 1.0
C A:GLY119 3.4 15.2 1.0
CG A:ASP121 3.5 16.2 1.0
CA A:GLY119 3.8 14.3 1.0
OD2 A:ASP99 3.8 15.9 1.0
CB A:THR101 3.8 13.3 1.0
N A:THR101 3.9 13.9 1.0
N A:SER100 4.0 14.9 1.0
CB A:ASP121 4.0 16.0 1.0
CA A:ASP99 4.1 13.1 1.0
CB A:ASP99 4.2 11.2 1.0
N A:ASP121 4.2 12.1 1.0
OH A:TYR103 4.3 9.4 1.0
C A:ASP99 4.3 12.1 1.0
CA A:THR101 4.5 12.8 1.0
OD1 A:ASP121 4.5 20.5 1.0
N A:TYR120 4.5 12.3 1.0
O A:HOH575 4.6 27.6 1.0
OD1 L:ASN103 4.8 34.7 1.0
C A:SER100 4.8 15.4 1.0
CA A:ASP121 4.8 13.4 1.0
O A:HOH574 4.8 30.7 1.0
CA A:SER100 4.9 14.5 1.0
CA A:TYR120 4.9 11.1 1.0
C A:TYR120 5.0 12.4 1.0

Sodium binding site 2 out of 5 in 1jtp

Go back to Sodium Binding Sites List in 1jtp
Sodium binding site 2 out of 5 in the Degenerate Interfaces in Antigen-Antibody Complexes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Degenerate Interfaces in Antigen-Antibody Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:17.7
occ:1.00
 O B:GLY119 2.3 12.3 1.0
OD1 B:ASP99 2.3 10.3 1.0
O B:HOH511 2.4 13.5 1.0
OD2 B:ASP121 2.5 17.5 1.0
O M:HOH559 2.5 25.7 1.0
OG1 B:THR101 3.0 16.9 1.0
CG B:ASP99 3.2 11.8 1.0
C B:GLY119 3.3 13.8 1.0
CG B:ASP121 3.5 15.1 1.0
OD2 B:ASP99 3.7 12.4 1.0
N B:THR101 3.8 12.1 1.0
N B:SER100 3.8 10.7 1.0
CB B:THR101 3.8 12.2 1.0
CA B:GLY119 3.9 15.7 1.0
CB B:ASP121 4.0 14.6 1.0
CA B:ASP99 4.0 14.6 1.0
CB B:ASP99 4.2 15.0 1.0
O M:HOH557 4.2 33.2 1.0
OH B:TYR103 4.2 13.3 1.0
N B:ASP121 4.2 15.5 1.0
C B:ASP99 4.3 12.4 1.0
CA B:THR101 4.4 13.2 1.0
N B:TYR120 4.5 10.8 1.0
OD1 B:ASP121 4.6 14.5 1.0
C B:SER100 4.7 13.0 1.0
ND2 M:ASN103 4.7 44.3 1.0
CA B:SER100 4.7 14.1 1.0
CA B:ASP121 4.8 15.3 1.0
O1 M:FMT404 4.9 49.9 1.0
CA B:TYR120 4.9 12.0 1.0
C B:TYR120 4.9 14.8 1.0

Sodium binding site 3 out of 5 in 1jtp

Go back to Sodium Binding Sites List in 1jtp
Sodium binding site 3 out of 5 in the Degenerate Interfaces in Antigen-Antibody Complexes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Degenerate Interfaces in Antigen-Antibody Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na503

b:25.7
occ:1.00
 O L:SER60 2.3 18.0 1.0
O L:LYS73 2.4 24.8 1.0
OG L:SER72 2.4 23.6 1.0
O L:HOH568 2.5 27.9 1.0
O L:HOH515 2.5 17.4 1.0
O L:CYS64 2.6 16.1 1.0
CB L:SER72 3.1 26.2 1.0
C L:SER60 3.5 17.9 1.0
C L:LYS73 3.5 23.0 1.0
C L:CYS64 3.7 17.7 1.0
N L:LYS73 3.9 26.0 1.0
C L:SER72 3.9 30.7 1.0
CA L:ASN65 4.0 21.3 1.0
C L:ARG61 4.1 19.1 1.0
CA L:SER72 4.2 33.6 1.0
O L:ARG61 4.2 21.2 1.0
CA L:ARG61 4.2 20.4 1.0
N L:ASN65 4.3 20.2 1.0
O L:HOH542 4.3 27.9 1.0
CA L:SER60 4.3 17.7 1.0
N L:ARG61 4.4 19.9 1.0
CA L:LYS73 4.4 22.2 1.0
O L:SER72 4.4 31.9 1.0
N L:ASN74 4.4 23.0 1.0
OD1 L:ASN65 4.5 28.9 1.0
CA L:ASN74 4.5 21.5 1.0
N L:CYS64 4.6 14.9 1.0
N L:TRP62 4.6 14.2 1.0
CB L:ASN74 4.6 23.3 1.0
CB L:THR69 4.6 33.1 1.0
CB L:ASN65 4.7 24.7 1.0
CB L:SER60 4.8 17.0 1.0
CA L:CYS64 4.8 14.8 1.0
N L:ASP66 4.9 22.8 1.0
O L:THR69 4.9 38.0 1.0

Sodium binding site 4 out of 5 in 1jtp

Go back to Sodium Binding Sites List in 1jtp
Sodium binding site 4 out of 5 in the Degenerate Interfaces in Antigen-Antibody Complexes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Degenerate Interfaces in Antigen-Antibody Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na505

b:43.4
occ:1.00
 O L:HOH526 2.3 16.6 1.0
O1 L:FMT406 2.6 50.2 1.0
OE1 L:GLU35 2.7 12.9 1.0
O L:HOH551 2.8 33.0 1.0
O L:HOH550 3.0 34.9 1.0
CB A:SER105 3.5 20.6 1.0
CD L:GLU35 3.8 15.4 1.0
C L:FMT406 3.8 51.6 1.0
OD2 L:ASP52 3.9 27.8 1.0
OG A:SER105 4.0 25.7 1.0
O L:HOH576 4.0 42.2 1.0
CB L:GLN57 4.1 10.1 1.0
CG L:GLN57 4.2 11.5 1.0
OE2 L:GLU35 4.3 11.7 1.0
OE1 L:GLN57 4.4 10.2 1.0
O2 L:FMT406 4.6 49.6 1.0
O L:GLU35 4.7 9.5 1.0
CD L:GLN57 4.8 12.1 1.0
CA L:GLU35 4.9 11.5 1.0
CG L:ASP52 4.9 16.2 1.0
CA A:SER105 4.9 16.9 1.0

Sodium binding site 5 out of 5 in 1jtp

Go back to Sodium Binding Sites List in 1jtp
Sodium binding site 5 out of 5 in the Degenerate Interfaces in Antigen-Antibody Complexes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Degenerate Interfaces in Antigen-Antibody Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na504

b:20.5
occ:1.00
 O M:LYS73 2.3 21.3 1.0
O M:SER60 2.3 13.2 1.0
O M:CYS64 2.4 12.8 1.0
O M:HOH533 2.5 18.6 1.0
O M:HOH520 2.5 13.6 1.0
OG M:SER72 2.5 19.7 1.0
C M:LYS73 3.3 22.7 1.0
C M:SER60 3.4 16.7 1.0
CB M:SER72 3.6 22.1 1.0
C M:CYS64 3.6 16.1 1.0
CA M:ASN65 3.9 17.7 1.0
N M:LYS73 3.9 20.9 1.0
C M:SER72 4.0 25.1 1.0
C M:ARG61 4.0 13.3 1.0
O1 M:FMT403 4.1 25.4 1.0
O M:ARG61 4.1 15.2 1.0
CA M:ARG61 4.1 15.2 1.0
N M:ASN65 4.2 15.6 1.0
N M:ASN74 4.2 20.2 1.0
CA M:LYS73 4.2 20.1 1.0
N M:ARG61 4.2 13.6 1.0
O M:SER72 4.3 24.1 1.0
CA M:ASN74 4.4 17.1 1.0
CA M:SER60 4.4 13.2 1.0
N M:TRP62 4.4 11.0 1.0
CA M:SER72 4.4 22.5 1.0
CB M:ASN65 4.5 22.2 1.0
N M:CYS64 4.5 16.5 1.0
O2 M:FMT403 4.5 22.3 1.0
CB M:ASN74 4.6 18.1 1.0
OD1 M:ASN65 4.6 23.8 1.0
C M:FMT403 4.6 21.7 1.0
CA M:CYS64 4.7 15.5 1.0
CB M:SER60 4.9 16.1 1.0
N M:ASP66 4.9 15.9 1.0
OG1 M:THR69 4.9 19.1 1.0
C M:ASN65 4.9 18.7 1.0
C M:TRP62 5.0 16.7 1.0

Reference:

K.Decanniere, T.R.Transue, A.Desmyter, D.Maes, S.Muyldermans, L.Wyns. Degenerate Interfaces in Antigen-Antibody Complexes. J.Mol.Biol. V. 313 473 2001.
ISSN: ISSN 0022-2836
PubMed: 11676532
DOI: 10.1006/JMBI.2001.5075
Page generated: Sun Oct 6 18:59:24 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