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Sodium in PDB 1jtt: 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: 1jtt 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) 100.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.220, 72.840, 38.660, 90.00, 106.94, 90.00
R / Rfree (%) 16.4 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Degenerate Interfaces in Antigen-Antibody Complexes (pdb code 1jtt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Degenerate Interfaces in Antigen-Antibody Complexes, PDB code: 1jtt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 1jtt

Go back to Sodium Binding Sites List in 1jtt
Sodium binding site 1 out of 6 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:Na301

b:25.3
occ:1.00
 O A:GLY119 2.3 15.1 1.0
O A:HOH507 2.3 28.8 1.0
O A:HOH467 2.4 17.4 1.0
OD1 A:ASP99 2.5 15.6 1.0
OD2 A:ASP121 2.5 18.7 1.0
CG A:ASP99 3.2 14.2 1.0
OG1 A:THR101 3.2 16.6 1.0
C A:GLY119 3.4 17.9 1.0
CG A:ASP121 3.6 18.3 1.0
OD2 A:ASP99 3.7 12.1 1.0
CA A:GLY119 3.9 16.8 1.0
N A:SER100 3.9 16.6 1.0
CB A:ASP121 3.9 17.7 1.0
N A:THR101 4.0 16.7 1.0
CA A:ASP99 4.0 13.4 1.0
CB A:THR101 4.1 14.6 1.0
N A:ASP121 4.1 18.0 1.0
CB A:ASP99 4.2 13.6 1.0
OH A:TYR103 4.3 12.8 1.0
C A:ASP99 4.3 16.1 1.0
N A:TYR120 4.5 15.4 1.0
CA A:THR101 4.7 16.4 1.0
OD1 A:ASP121 4.7 19.5 1.0
CA A:ASP121 4.7 18.4 1.0
O A:HOH489 4.8 37.0 1.0
CA A:SER100 4.8 17.5 1.0
CA A:TYR120 4.8 16.7 1.0
C A:SER100 4.9 16.6 1.0
C A:TYR120 4.9 16.8 1.0

Sodium binding site 2 out of 6 in 1jtt

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Sodium binding site 2 out of 6 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
A:Na306

b:52.1
occ:1.00
 O A:HOH415 2.4 37.9 1.0
OD1 A:ASN77 2.6 33.0 1.0
OD1 A:ASN74 2.7 41.0 1.0
O A:ASN74 2.8 23.9 1.0
O A:HOH479 3.2 29.7 1.0
O A:HOH480 3.3 38.8 1.0
CG A:ASN74 3.5 37.5 1.0
CG A:ASN77 3.6 30.5 1.0
C A:ASN74 3.6 26.3 1.0
O A:HOH490 3.7 37.6 1.0
O A:GLY30 3.7 21.8 0.5
CA A:ASN74 3.9 27.9 1.0
CE A:MET53 4.1 14.7 1.0
O A:GLY30 4.1 20.2 0.5
C A:GLY30 4.2 21.4 0.5
ND2 A:ASN74 4.2 39.0 1.0
ND2 A:ASN77 4.2 32.6 1.0
CB A:ASN74 4.3 31.4 1.0
CB A:MET53 4.4 14.8 1.0
CA A:ASN77 4.4 23.2 1.0
C A:GLY30 4.5 20.2 0.5
O A:PRO31 4.6 12.0 1.0
CB A:ASN77 4.6 22.5 1.0
N A:ASN77 4.7 20.8 1.0
O A:HOH414 4.7 39.1 1.0
N A:PRO31 4.7 18.9 1.0
O A:ILE29 4.7 24.0 0.5
CD A:PRO31 4.7 19.5 1.0
CG A:MET53 4.8 13.7 1.0
N A:ALA75 4.8 25.4 1.0
CA A:GLY30 4.9 21.8 0.5

Sodium binding site 3 out of 6 in 1jtt

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Sodium binding site 3 out of 6 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
A:Na307

b:31.3
occ:1.00
 O A:GLY42 2.8 25.7 1.0
C A:GLY42 3.6 24.2 1.0
CA A:GLY42 3.6 21.2 1.0
N A:LYS43 4.8 24.4 1.0
O A:HOH461 5.0 39.3 1.0

Sodium binding site 4 out of 6 in 1jtt

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Sodium binding site 4 out of 6 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:Na302

b:16.7
occ:1.00
 O L:SER60 2.3 14.6 1.0
O L:ARG73 2.4 15.8 1.0
O L:HOH454 2.4 14.1 1.0
O L:HOH455 2.4 13.1 1.0
OG L:SER72 2.5 9.9 1.0
O L:CYS64 2.5 13.3 1.0
C L:ARG73 3.4 15.9 1.0
CB L:SER72 3.5 16.6 1.0
C L:SER60 3.5 13.4 1.0
C L:CYS64 3.5 11.5 1.0
CA L:ASN65 3.8 13.6 1.0
C L:SER72 3.9 19.3 1.0
N L:ARG73 4.0 18.1 1.0
O1 L:FMT402 4.0 17.6 1.0
N L:ASN65 4.1 13.1 1.0
O L:SER72 4.2 21.7 1.0
N L:ASN74 4.2 14.8 1.0
CA L:ARG73 4.3 15.8 1.0
C L:ARG61 4.3 16.3 1.0
CA L:SER60 4.3 12.4 1.0
CA L:SER72 4.3 16.9 1.0
O L:ARG61 4.4 17.4 1.0
N L:CYS64 4.4 11.6 1.0
CA L:ASN74 4.4 17.8 1.0
CA L:ARG61 4.4 16.3 1.0
N L:ARG61 4.4 13.1 1.0
O2 L:FMT402 4.5 17.6 1.0
CB L:SER60 4.6 11.2 1.0
CA L:CYS64 4.6 12.0 1.0
C L:FMT402 4.6 18.3 1.0
ND2 L:ASN65 4.6 11.3 1.0
CB L:ASN74 4.7 15.9 1.0
N L:TRP62 4.7 14.2 1.0
CB L:ASN65 4.7 13.2 1.0
OG1 L:THR69 4.7 13.7 1.0
N L:ASP66 4.8 12.8 1.0
O L:HOH453 4.8 10.9 1.0
C L:ASN65 4.8 13.2 1.0

Sodium binding site 5 out of 6 in 1jtt

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Sodium binding site 5 out of 6 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
L:Na304

b:36.3
occ:1.00
 O L:VAL99 2.3 30.7 1.0
O L:LYS96 2.5 12.6 1.0
CB L:SER100 2.6 34.4 1.0
OH L:TYR20 2.8 23.5 1.0
O2 L:FMT406 3.0 44.8 1.0
CA L:SER100 3.1 31.0 1.0
C L:VAL99 3.2 25.5 1.0
N L:SER100 3.5 29.5 1.0
CE2 L:TYR20 3.6 17.1 1.0
OG L:SER100 3.6 36.2 1.0
CZ L:TYR20 3.6 19.5 1.0
C L:LYS96 3.7 15.4 1.0
O1 L:FMT405 3.7 41.6 1.0
C L:FMT406 3.8 48.0 1.0
CD L:ARG21 4.2 26.0 1.0
CG2 L:VAL99 4.3 16.9 0.4
O L:LYS97 4.5 18.0 1.0
CA L:VAL99 4.5 23.6 1.0
CA L:LYS97 4.5 16.3 1.0
N L:LYS97 4.6 13.5 1.0
C L:SER100 4.6 32.6 1.0
CA L:LYS96 4.6 12.8 1.0
NE L:ARG21 4.7 27.9 1.0
C L:LYS97 4.7 17.5 1.0
O1 L:FMT406 4.7 48.2 1.0
N L:VAL99 4.8 20.4 1.0
CD2 L:TYR20 4.9 16.4 1.0
CB L:VAL99 4.9 21.2 0.4
CB L:VAL99 4.9 22.0 0.6
C L:FMT405 4.9 44.0 1.0
CE1 L:TYR20 5.0 17.7 1.0

Sodium binding site 6 out of 6 in 1jtt

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Sodium binding site 6 out of 6 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 6 of Degenerate Interfaces in Antigen-Antibody Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na305

b:27.2
occ:1.00
 O2 L:FMT404 2.4 28.7 1.0
O L:HOH440 2.4 24.1 1.0
OE1 L:GLU35 2.5 9.7 1.0
O L:HOH441 2.7 13.4 1.0
O L:HOH472 2.8 34.5 1.0
C L:FMT404 3.4 28.0 1.0
O L:HOH484 3.4 31.7 1.0
CD L:GLU35 3.7 11.2 1.0
O A:HOH471 3.7 24.9 1.0
O1 L:FMT404 4.1 24.4 1.0
OG A:SER105 4.1 24.1 1.0
OE2 L:GLU35 4.2 13.0 1.0
CB A:SER105 4.3 16.4 1.0
CG L:GLN57 4.3 13.3 1.0
CB L:GLN57 4.4 12.5 1.0
O L:GLU35 4.6 10.8 1.0
CA L:GLU35 4.6 11.7 1.0
OE1 L:GLN57 4.7 10.2 1.0
OD2 L:ASP52 4.8 12.7 1.0
CG L:GLU35 4.9 8.6 1.0
CB L:GLU35 4.9 9.2 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 Aug 17 05:22:28 2025

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