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Sodium in PDB 1nj9: Cocaine Hydrolytic Antibody 15A10

Protein crystallography data

The structure of Cocaine Hydrolytic Antibody 15A10, PDB code: 1nj9 was solved by N.A.Larsen, P.De Prada, S.X.Deng, X.Zhu, D.W.Landry, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.500, 108.400, 111.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 28.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Cocaine Hydrolytic Antibody 15A10 (pdb code 1nj9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Cocaine Hydrolytic Antibody 15A10, PDB code: 1nj9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1nj9

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Sodium binding site 1 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na1001

b:12.5
occ:1.00
 NH1 L:ARG61 3.6 21.7 1.0
CB L:ARG61 3.9 30.3 1.0
N L:ARG61 3.9 30.5 1.0
CG L:ARG61 4.1 29.1 1.0
CD L:ARG61 4.2 27.8 1.0
N L:ALA60 4.2 30.2 1.0
CB L:PRO59 4.3 31.2 1.0
CA L:ARG61 4.5 29.9 1.0
CB L:ALA60 4.6 29.6 1.0
CZ L:ARG61 4.7 24.1 1.0
CA L:ALA60 4.8 29.7 1.0
C L:ALA60 4.8 29.5 1.0
CA L:PRO59 4.8 32.3 1.0
C L:PRO59 4.8 31.0 1.0
NE L:ARG61 4.9 27.1 1.0

Sodium binding site 2 out of 8 in 1nj9

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Sodium binding site 2 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na1003

b:12.7
occ:1.00
 OD1 L:ASP41 2.7 46.2 1.0
CG L:ASP41 3.5 44.2 1.0
CB L:LYS39 3.6 33.4 1.0
OD2 L:ASP41 3.7 43.9 1.0
CD L:PRO40 4.2 40.2 1.0
CG L:LYS39 4.3 31.1 1.0
N L:PRO40 4.4 38.5 1.0
CE L:LYS39 4.4 28.5 1.0
CD L:LYS39 4.4 29.6 1.0
C L:LYS39 4.4 36.4 1.0
CA L:LYS39 4.5 34.8 1.0
NZ L:LYS39 4.7 25.5 1.0
C L:PRO40 4.7 40.8 1.0
O L:HOH1014 4.7 14.4 1.0
O L:PRO40 4.8 41.0 1.0
CB L:ASP41 4.9 42.7 1.0
O L:LYS39 4.9 36.5 1.0
CA L:PRO40 5.0 40.1 1.0
N L:ASP41 5.0 41.7 1.0

Sodium binding site 3 out of 8 in 1nj9

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Sodium binding site 3 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1002

b:10.8
occ:1.00
 O H:THR203 2.8 24.4 1.0
CG H:LYS204 3.8 33.3 1.0
CE H:LYS204 3.8 38.6 1.0
CA H:PRO199 3.9 22.8 1.0
C H:THR203 3.9 23.9 1.0
N H:PRO199 4.0 21.7 1.0
O H:HIS198 4.0 20.8 1.0
C H:HIS198 4.1 20.6 1.0
CB H:ALA197 4.1 16.3 1.0
C H:SER202 4.2 24.6 1.0
N H:THR203 4.2 23.7 1.0
N H:HIS198 4.3 20.4 1.0
CD H:LYS204 4.4 35.0 1.0
CA H:SER202 4.4 26.3 1.0
O H:SER202 4.5 24.1 1.0
CA H:ALA197 4.6 18.9 1.0
C H:ALA197 4.6 20.0 1.0
CA H:THR203 4.6 22.3 1.0
CB H:PRO199 4.8 22.2 1.0
CD H:PRO199 4.8 22.6 1.0
O H:PRO199 4.8 23.6 1.0
C H:PRO199 4.9 22.9 1.0
N H:LYS204 4.9 24.9 1.0
N H:SER202 4.9 27.7 1.0
CA H:HIS198 4.9 20.3 1.0

Sodium binding site 4 out of 8 in 1nj9

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Sodium binding site 4 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1004

b:31.3
occ:1.00
 O H:HOH1017 2.6 4.8 1.0
OXT H:ARG212 2.8 32.1 1.0
O H:PRO211 3.8 27.9 1.0
C H:ARG212 4.0 31.6 1.0
O H:HOH1023 4.5 17.1 1.0
O H:ARG212 4.6 33.5 1.0
C H:PRO211 4.9 26.6 1.0

Sodium binding site 5 out of 8 in 1nj9

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Sodium binding site 5 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1005

b:13.6
occ:1.00
 N H:TRP153 2.8 19.7 1.0
CA H:GLY156 2.9 21.6 1.0
O H:LEU158 3.0 29.5 1.0
O H:HOH1026 3.1 24.4 1.0
N H:GLY156 3.3 22.3 1.0
O H:TRP153 3.4 20.6 1.0
CA H:THR152 3.4 20.5 1.0
CB H:THR152 3.4 20.7 1.0
C H:THR152 3.6 20.5 1.0
C H:GLY156 3.7 21.4 1.0
CA H:TRP153 3.8 19.1 1.0
C H:LEU158 3.9 26.0 1.0
C H:TRP153 4.0 20.4 1.0
CB H:TRP153 4.1 17.0 1.0
CG2 H:THR152 4.2 20.9 1.0
O H:GLY156 4.3 20.3 1.0
N H:SER157 4.4 22.5 1.0
CA H:SER159 4.4 24.1 1.0
N H:SER159 4.4 25.8 1.0
OG1 H:THR152 4.5 24.1 1.0
CG2 H:VAL162 4.6 20.2 1.0
N H:LEU158 4.6 23.9 1.0
C H:SER155 4.6 22.7 1.0
O H:THR152 4.8 20.6 1.0
N H:THR152 4.8 21.6 1.0
CD1 H:TRP153 4.9 15.0 1.0
CG H:TRP153 4.9 15.4 1.0
CA H:LEU158 4.9 25.3 1.0
O H:VAL151 5.0 19.2 1.0

Sodium binding site 6 out of 8 in 1nj9

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Sodium binding site 6 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1000

b:16.9
occ:1.00
 N A:ALA33 3.0 28.7 1.0
N A:TYR32 3.4 28.8 1.0
O A:THR28 3.5 31.2 1.0
CA A:TYR32 3.6 29.1 1.0
CB A:ALA33 3.7 26.9 1.0
O A:VAL50 3.7 48.5 1.0
C A:TYR32 3.7 29.3 1.0
CA A:ALA33 3.9 27.0 1.0
CA A:SER29 3.9 30.4 1.0
O A:SER29 4.0 29.7 1.0
C A:VAL50 4.1 47.6 1.0
C A:THR28 4.1 30.5 1.0
CA A:VAL50 4.1 46.7 1.0
C A:ASN31 4.1 26.7 1.0
CD1 A:LEU66 4.1 33.0 1.0
CG1 A:VAL50 4.1 46.2 1.0
C A:SER29 4.2 29.2 1.0
O A:ALA33 4.2 25.7 1.0
N A:SER29 4.3 30.3 1.0
N A:ASN31 4.5 25.6 1.0
CB A:ASN31 4.6 25.3 1.0
C A:ALA33 4.6 26.5 1.0
CD1 A:ILE27C 4.6 33.8 1.0
CA A:ASN31 4.6 26.0 1.0
CB A:VAL50 4.8 46.3 1.0
O A:ASN31 4.8 26.6 1.0
O A:TYR32 4.8 30.8 1.0
CD2 A:LEU66 4.9 34.4 1.0
CG A:LEU66 5.0 34.4 1.0

Sodium binding site 7 out of 8 in 1nj9

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Sodium binding site 7 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:20.5
occ:1.00
 O B:GLN105 3.7 28.8 1.0
O B:GLY106 3.8 29.4 1.0
C B:GLY106 4.1 30.1 1.0
CG1 B:VAL89 4.1 21.9 1.0
CD2 A:HIS42 4.1 51.5 1.0
O B:HOH1015 4.2 7.9 1.0
N B:THR107 4.5 28.6 1.0
N B:LEU108 4.5 24.4 1.0
C B:GLN105 4.5 27.9 1.0
CA B:GLY106 4.5 30.0 1.0
CA B:THR107 4.7 26.8 1.0
O B:HOH1029 4.8 15.9 1.0
C B:THR107 4.9 25.7 1.0
N B:GLY106 4.9 28.7 1.0
CB B:LEU108 5.0 22.6 1.0

Sodium binding site 8 out of 8 in 1nj9

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Sodium binding site 8 out of 8 in the Cocaine Hydrolytic Antibody 15A10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Cocaine Hydrolytic Antibody 15A10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1007

b:15.8
occ:1.00
 O B:LEU158 3.1 34.6 1.0
CA B:SER159 3.8 33.6 1.0
N B:TRP153 4.0 15.4 1.0
C B:LEU158 4.0 33.0 1.0
CA B:THR152 4.1 18.7 1.0
CA B:GLY156 4.1 19.9 1.0
CB B:THR152 4.3 17.6 1.0
N B:SER159 4.3 33.9 1.0
CG2 B:VAL162 4.3 20.7 1.0
CB B:SER159 4.5 33.9 1.0
C B:THR152 4.6 16.2 1.0
CD1 B:TRP153 4.6 12.5 1.0
CG2 B:THR152 4.7 20.7 1.0
C B:GLY156 4.7 21.8 1.0
CG1 B:VAL162 4.7 20.2 1.0
C B:SER159 4.9 33.2 1.0
O B:GLY156 4.9 21.9 1.0
CB B:VAL162 4.9 21.4 1.0
O B:VAL151 4.9 23.5 1.0
O B:SER159 4.9 33.8 1.0
N B:GLY156 4.9 18.7 1.0
O B:TRP153 4.9 12.2 1.0
CB B:TRP153 5.0 12.8 1.0
CA B:TRP153 5.0 13.6 1.0

Reference:

N.A.Larsen, P.De Prada, S.X.Deng, A.Mittal, M.Braskett, X.Zhu, I.A.Wilson, D.W.Landry. Crystallographic and Biochemical Analysis of Cocaine-Degrading Antibody 15A10. Biochemistry V. 43 8067 2004.
ISSN: ISSN 0006-2960
PubMed: 15209502
DOI: 10.1021/BI049495L
Page generated: Sun Oct 6 20:37:14 2024

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