Sodium in PDB 8ts5: Structure of the Apo FABS1C_C1

Protein crystallography data

The structure of Structure of the Apo FABS1C_C1, PDB code: 8ts5 was solved by A.U.Singer, H.A.Bruce, L.L.Blazer, J.J.Adams, F.Sicheri, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.56 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.688, 73.792, 174.202, 90, 96.37, 90
R / Rfree (%) 22 / 26.4

Other elements in 8ts5:

The structure of Structure of the Apo FABS1C_C1 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Apo FABS1C_C1 (pdb code 8ts5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of the Apo FABS1C_C1, PDB code: 8ts5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8ts5

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Sodium binding site 1 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na313

b:39.3
occ:1.00
 OG1 G:THR196 3.4 21.7 1.0
CG2 A:VAL193 3.5 24.8 1.0
O G:HOH495 3.6 34.0 1.0
O A:HOH475 3.6 28.6 1.0
CB A:SER201 3.8 19.4 1.0
NA A:NA315 3.8 37.1 1.0
O A:SER201 3.8 24.1 1.0
O G:HOH486 3.9 27.1 1.0
OG A:SER201 3.9 21.4 1.0
CB G:THR196 3.9 23.1 1.0
C A:SER201 4.0 25.9 1.0
N A:LEU202 4.3 19.7 1.0
CA A:LEU202 4.3 28.2 1.0
C A:LEU202 4.5 29.3 1.0
CA A:SER201 4.5 23.5 1.0
CG2 G:THR196 4.6 20.3 1.0
CG1 A:VAL193 4.6 20.5 1.0
CB A:VAL193 4.7 22.4 1.0
CD1 A:LEU165 4.7 26.2 1.0
N A:SER203 4.9 22.9 1.0
O A:LEU202 5.0 23.1 1.0

Sodium binding site 2 out of 8 in 8ts5

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Sodium binding site 2 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na314

b:38.0
occ:1.00
 OG1 A:THR175 3.2 29.7 1.0
O A:ASN221 3.2 26.4 1.0
O A:THR175 3.3 26.4 1.0
C A:THR175 3.5 29.3 1.0
N A:SER177 3.5 28.7 1.0
C A:VAL176 3.6 29.8 1.0
N A:VAL176 3.7 24.9 1.0
CA A:VAL176 3.7 23.8 1.0
OG A:SER177 3.8 30.1 1.0
CB A:SER177 4.0 24.8 1.0
C A:ASN221 4.0 24.8 1.0
N A:ASN223 4.0 24.2 1.0
CB A:THR175 4.0 26.2 1.0
CB A:ASN223 4.2 22.7 1.0
O A:VAL176 4.3 28.6 1.0
CA A:SER177 4.3 27.7 1.0
CA A:THR175 4.4 24.9 1.0
CB A:ASN221 4.4 23.2 1.0
N A:VAL222 4.6 19.1 1.0
CA A:VAL222 4.6 17.9 1.0
C A:VAL222 4.7 25.0 1.0
CA A:ASN223 4.7 24.9 1.0
CA A:ASN221 4.8 19.0 1.0

Sodium binding site 3 out of 8 in 8ts5

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Sodium binding site 3 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na315

b:37.1
occ:1.00
 O A:PRO191 2.6 23.2 1.0
CA A:LEU202 3.0 28.2 1.0
N A:SER203 3.5 22.9 1.0
O A:SER201 3.5 24.1 1.0
CB A:LEU202 3.5 25.9 1.0
C A:PRO191 3.6 27.7 1.0
OG G:SER180 3.7 27.7 1.0
C A:LEU202 3.7 29.3 1.0
CB G:SER180 3.8 19.7 1.0
CB A:PHE190 3.8 23.3 1.0
NA A:NA313 3.8 39.3 1.0
CA A:ALA192 3.8 24.7 1.0
N A:LEU202 4.0 19.7 1.0
N A:ALA192 4.1 21.7 1.0
C A:SER201 4.2 25.9 1.0
O A:PHE190 4.2 23.1 1.0
N A:VAL193 4.2 18.9 1.0
C A:PHE190 4.2 26.5 1.0
C A:ALA192 4.3 23.4 1.0
CG1 A:VAL193 4.3 20.5 1.0
OG G:SER194 4.4 30.7 1.0
O G:HOH495 4.5 34.0 1.0
CA A:PHE190 4.6 16.8 1.0
N A:PRO191 4.6 26.0 1.0
CA A:PRO191 4.7 24.1 1.0
CA A:SER203 4.7 20.3 1.0
CG2 A:VAL193 4.8 24.8 1.0
O A:LEU202 4.9 23.1 1.0
O A:SER203 4.9 23.0 1.0
CG A:PHE190 5.0 25.0 1.0
CG A:LEU202 5.0 22.4 1.0

Sodium binding site 4 out of 8 in 8ts5

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Sodium binding site 4 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na316

b:43.6
occ:1.00
 CG A:GLU97 3.0 42.8 1.0
CB A:GLU97 3.8 31.6 1.0
CD A:GLU97 3.8 53.4 1.0
OE1 A:GLU97 4.3 62.7 1.0
OE2 A:GLU97 4.4 64.2 1.0

Sodium binding site 5 out of 8 in 8ts5

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Sodium binding site 5 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na310

b:50.7
occ:1.00
 O G:HOH406 3.6 27.8 0.4
O G:VAL128 4.1 30.4 1.0
CG1 G:VAL128 4.4 33.5 1.0
CB G:VAL128 4.7 38.1 1.0
O G:HOH464 4.7 35.8 1.0
C G:VAL128 4.8 32.1 1.0
O G:HOH406 4.9 29.4 0.6

Sodium binding site 6 out of 8 in 8ts5

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Sodium binding site 6 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na311

b:48.7
occ:1.00
 OE1 G:GLU161 2.3 40.9 1.0
CD G:GLU161 3.0 41.2 1.0
CB G:GLU161 3.3 34.6 1.0
CG G:GLU161 3.3 36.5 1.0
C1 G:EDO309 3.9 36.6 1.0
CG G:PRO159 3.9 30.5 1.0
O1 G:EDO309 4.1 43.9 1.0
OE2 G:GLU161 4.1 43.9 1.0
O G:HOH514 4.2 44.0 1.0
CB G:PRO159 4.2 29.1 1.0
CA G:GLU161 4.4 32.2 1.0
N G:GLU161 4.4 32.4 1.0
C2 G:EDO309 4.5 39.0 1.0
O G:GLU161 4.8 29.6 1.0

Sodium binding site 7 out of 8 in 8ts5

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Sodium binding site 7 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:47.5
occ:1.00
 O B:SER57 3.4 42.0 1.0
O B:SER33 3.6 37.5 1.0
O B:ILE30 3.8 32.8 1.0
CB B:ALA80 3.9 44.2 1.0
CG1 B:ILE56 4.3 41.4 1.0
C B:SER57 4.3 45.4 1.0
CA B:SER58 4.5 42.6 1.0
CG2 B:ILE56 4.5 36.7 1.0
C B:ILE30 4.6 35.5 1.0
CD1 B:ILE56 4.6 38.8 1.0
O B:ILE56 4.7 38.7 1.0
O B:TYR31 4.7 37.5 1.0
C B:SER33 4.7 37.0 1.0
N B:SER58 4.8 40.9 1.0
CA B:TYR31 4.8 35.4 1.0
CG B:MET35 4.8 34.5 1.0
CG2 B:ILE30 4.8 37.5 1.0
C B:TYR31 5.0 37.5 1.0

Sodium binding site 8 out of 8 in 8ts5

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Sodium binding site 8 out of 8 in the Structure of the Apo FABS1C_C1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Apo FABS1C_C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:45.9
occ:1.00
 O B:HOH485 2.3 46.4 1.0
O B:VAL174 2.6 40.3 1.0
N B:VAL174 3.1 29.8 1.0
OE1 B:GLU172 3.4 35.6 1.0
C B:VAL174 3.6 36.3 1.0
CB B:PRO173 3.6 32.0 1.0
CG1 B:VAL174 3.8 30.2 1.0
CA B:PRO173 3.8 31.9 1.0
CA B:VAL174 3.9 32.5 1.0
C B:PRO173 4.0 30.3 1.0
CD B:GLU172 4.1 33.1 1.0
OE2 B:GLU172 4.4 35.3 1.0
CD2 B:LEU202 4.4 39.2 1.0
CB B:VAL174 4.4 32.2 1.0
OH B:TYR169 4.5 28.7 1.0
N B:THR175 4.8 40.0 1.0

Reference:

H.A.Bruce, A.U.Singer, E.V.Filippova, L.L.Blazer, J.J.Adams, L.Enderle, M.Ben-David, E.H.Radley, D.Y.L.Mao, V.Pau, S.Orlicky, F.Sicheri, I.Kourinov, S.Atwell, A.A.Kossiakoff, S.S.Sidhu. Engineered Antigen-Binding Fragments For Enhanced Crystallization of Antibody:Antigen Complexes. Protein Sci. E4824 2023.
ISSN: ESSN 1469-896X
PubMed: 37945533
DOI: 10.1002/PRO.4824
Page generated: Wed Oct 9 13:42:21 2024

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