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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

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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

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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

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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

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