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Sodium in PDB 3fct: Mature Metal Chelatase Catalytic Antibody with Hapten

Protein crystallography data

The structure of Mature Metal Chelatase Catalytic Antibody with Hapten, PDB code: 3fct was solved by F.E.Romesberg, B.D.Santarsiero, D.Barnes, J.Yin, B.Spiller, P.G.Schultz, R.C.Stevens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 134.290, 100.689, 73.537, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 29.3

Other elements in 3fct:

The structure of Mature Metal Chelatase Catalytic Antibody with Hapten also contains other interesting chemical elements:

Cadmium (Cd) 1 atom
Magnesium (Mg) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Mature Metal Chelatase Catalytic Antibody with Hapten (pdb code 3fct). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Mature Metal Chelatase Catalytic Antibody with Hapten, PDB code: 3fct:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3fct

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Sodium binding site 1 out of 7 in the Mature Metal Chelatase Catalytic Antibody with Hapten


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mature Metal Chelatase Catalytic Antibody with Hapten within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:14.2
occ:1.00
 NZ A:LYS45 2.9 39.1 1.0
O A:HOH1030 2.9 50.1 1.0
CE A:LYS39 3.2 25.8 1.0
OE1 A:GLN42 3.7 30.2 1.0
CD A:LYS39 3.8 26.5 1.0
CE A:LYS45 4.1 37.3 1.0
NE2 A:GLN42 4.2 31.5 1.0
CD A:GLN42 4.4 30.0 1.0
NZ A:LYS39 4.4 26.0 1.0
O A:HOH973 4.7 28.1 1.0
CD A:LYS45 5.0 34.3 1.0

Sodium binding site 2 out of 7 in 3fct

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Sodium binding site 2 out of 7 in the Mature Metal Chelatase Catalytic Antibody with Hapten


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mature Metal Chelatase Catalytic Antibody with Hapten within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na905

b:16.3
occ:1.00
 O B:HOH1055 2.9 52.0 1.0
OD2 B:ASP209 2.9 36.3 1.0
OD1 B:ASP209 2.9 35.5 1.0
CG B:ASP209 3.3 34.1 1.0
O B:HOH948 3.8 22.8 1.0
CG B:LYS207 3.8 28.0 1.0
CD B:LYS207 4.0 28.2 1.0
ND2 B:ASN198 4.0 22.4 1.0
CB B:ASN198 4.2 20.4 1.0
O B:VAL208 4.6 29.9 1.0
CG B:ASN198 4.6 21.9 1.0
CB B:ASP209 4.8 33.1 1.0
OD1 B:ASN200 4.8 20.9 1.0

Sodium binding site 3 out of 7 in 3fct

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Sodium binding site 3 out of 7 in the Mature Metal Chelatase Catalytic Antibody with Hapten


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mature Metal Chelatase Catalytic Antibody with Hapten within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na909

b:16.8
occ:1.00
 O B:TYR32 2.8 40.6 1.0
OH B:TYR27 3.0 42.6 1.0
O B:PHE29 3.1 41.8 1.0
CE B:MET34 3.5 20.7 1.0
CD1 B:PHE29 3.5 45.3 1.0
C B:TYR32 3.6 41.1 1.0
CE2 B:TYR27 3.6 43.3 1.0
CZ B:TYR27 3.7 44.0 1.0
CB B:TYR32 3.7 43.2 1.0
CE1 B:PHE29 3.7 44.5 1.0
CG B:PRO53 3.9 38.0 1.0
CA B:TYR32 4.0 41.8 1.0
N B:TYR32 4.0 41.5 1.0
C B:PHE29 4.1 41.8 1.0
O B:TRP33 4.3 35.5 1.0
CA B:PHE29 4.3 41.3 1.0
CD B:ARG98 4.5 32.7 1.0
C B:TRP33 4.5 36.8 1.0
CG B:PHE29 4.5 44.8 1.0
CB B:PRO53 4.5 37.3 1.0
CB B:MET34 4.6 28.8 1.0
N B:TRP33 4.6 40.4 1.0
CD B:PRO53 4.7 37.1 1.0
SD B:MET34 4.7 22.6 1.0
N B:MET34 4.8 33.9 1.0
CZ B:PHE29 4.8 44.6 1.0
CD2 B:TYR27 4.9 41.8 1.0
CG B:ARG98 4.9 32.0 1.0
CG B:TYR32 4.9 45.5 1.0
O B:THR28 5.0 39.9 1.0
CA B:MET34 5.0 30.8 1.0

Sodium binding site 4 out of 7 in 3fct

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Sodium binding site 4 out of 7 in the Mature Metal Chelatase Catalytic Antibody with Hapten


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mature Metal Chelatase Catalytic Antibody with Hapten within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na904

b:50.4
occ:1.00
 OD2 C:ASP170 2.6 23.9 1.0
OD1 C:ASN138 2.7 23.5 1.0
O C:HOH997 2.8 37.2 1.0
OD2 C:ASP167 3.3 31.3 1.0
CG C:ASN138 3.3 21.6 1.0
O C:HOH972 3.4 27.3 1.0
ND2 C:ASN138 3.7 20.6 1.0
NE2 D:HIS165 3.8 28.0 1.0
CE1 D:HIS165 3.8 26.8 1.0
CG C:ASP170 3.9 23.7 1.0
O D:HOH283 4.2 33.3 1.0
O C:HOH969 4.2 26.8 1.0
CG C:ASP167 4.2 28.9 1.0
CB C:ASN138 4.4 20.5 1.0
OG1 C:THR172 4.6 13.4 1.0
CB C:ASP170 4.7 23.7 1.0
OD1 C:ASP170 4.7 27.2 1.0
OD1 C:ASP167 4.8 31.8 1.0

Sodium binding site 5 out of 7 in 3fct

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Sodium binding site 5 out of 7 in the Mature Metal Chelatase Catalytic Antibody with Hapten


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Mature Metal Chelatase Catalytic Antibody with Hapten within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na906

b:20.0
occ:1.00
 OD1 C:ASP60 2.7 24.9 1.0
O C:HOH987 2.8 31.8 1.0
N C:ARG61 3.0 21.5 1.0
CB C:ARG61 3.2 18.9 1.0
CG C:ARG61 3.3 14.4 1.0
CB C:PRO59 3.4 14.8 1.0
N C:ASP60 3.4 20.6 1.0
NH1 C:ARG61 3.5 15.7 1.0
CA C:ARG61 3.7 20.4 1.0
O C:HOH940 3.7 21.0 1.0
C C:ASP60 3.9 23.0 1.0
CD C:ARG61 3.9 13.4 1.0
CG C:ASP60 3.9 25.0 1.0
C C:PRO59 3.9 19.1 1.0
CA C:PRO59 4.0 16.9 1.0
CA C:ASP60 4.1 22.4 1.0
O C:HOH950 4.1 22.6 1.0
CZ C:ARG61 4.5 15.3 1.0
O C:HOH992 4.6 33.6 1.0
CB C:ASP60 4.6 23.5 1.0
NE C:ARG61 4.6 13.9 1.0
CG C:PRO59 4.7 14.2 1.0
O C:PRO59 4.7 20.4 1.0
OD2 C:ASP60 4.8 25.9 1.0
O C:ASP60 4.9 23.8 1.0
C C:ARG61 5.0 20.5 1.0

Sodium binding site 6 out of 7 in 3fct

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Sodium binding site 6 out of 7 in the Mature Metal Chelatase Catalytic Antibody with Hapten


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Mature Metal Chelatase Catalytic Antibody with Hapten within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na907

b:15.0
occ:1.00
 O C:HOH933 2.6 18.7 1.0
O C:HOH962 2.8 25.1 1.0
O C:HOH1036 2.8 71.7 1.0
CE C:LYS45 3.2 26.6 1.0
O C:HOH1014 3.7 42.8 1.0
CE C:LYS39 3.7 20.4 1.0
OE1 C:GLN42 3.9 32.8 1.0
CD C:LYS45 4.1 26.6 1.0
NZ C:LYS45 4.1 23.5 1.0
CD C:LYS39 4.4 20.0 1.0
NE2 C:GLN42 4.6 31.3 1.0
O C:HOH937 4.6 20.3 1.0
CD C:GLN42 4.7 30.6 1.0
NE2 C:GLN37 4.8 14.0 1.0
NZ C:LYS39 4.9 20.0 1.0

Sodium binding site 7 out of 7 in 3fct

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Sodium binding site 7 out of 7 in the Mature Metal Chelatase Catalytic Antibody with Hapten


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Mature Metal Chelatase Catalytic Antibody with Hapten within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na910

b:20.1
occ:1.00
 N C:GLY100 2.9 27.1 1.0
O C:MET4 2.9 31.7 1.0
N C:GLN6 3.2 31.4 1.0
CA C:THR5 3.4 30.9 1.0
CA C:GLY100 3.5 27.9 1.0
O C:HOH983 3.5 29.6 1.0
C C:THR5 3.7 30.9 1.0
C C:MET4 3.8 31.6 1.0
C C:GLY99 3.9 26.6 1.0
N C:THR5 4.1 31.7 1.0
CA C:GLY99 4.1 27.2 1.0
CA C:GLN6 4.3 32.2 1.0
CB C:GLN6 4.3 31.6 1.0
CB C:THR5 4.4 29.9 1.0
OG1 C:THR5 4.6 27.8 1.0
CG2 C:THR5 4.6 28.9 1.0
O C:GLN6 4.6 33.4 1.0
C C:GLY100 4.8 28.4 1.0
O C:GLY99 4.9 26.4 1.0
NZ C:LYS9 4.9 47.2 1.0
O C:THR5 4.9 31.8 1.0
C C:GLN6 5.0 33.6 1.0

Reference:

F.E.Romesberg, B.D.Santarsiero, B.Spiller, J.Yin, D.Barnes, P.G.Schultz, R.C.Stevens. Structural and Kinetic Evidence For Strain in Biological Catalysis. Biochemistry V. 37 14404 1998.
ISSN: ISSN 0006-2960
PubMed: 9772166
DOI: 10.1021/BI981578C
Page generated: Mon Oct 7 09:45:27 2024

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