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Sodium in PDB 8bb0: The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.

Protein crystallography data

The structure of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin., PDB code: 8bb0 was solved by J.Whittaker, J.M.Felices Martinez, A.Guskov, D.J.Slotboom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.40 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.11, 101.099, 79.893, 90, 97.81, 90
R / Rfree (%) 14.3 / 17.5

Other elements in 8bb0:

The structure of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. (pdb code 8bb0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin., PDB code: 8bb0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 8bb0

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Sodium binding site 1 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:12.3
occ:1.00
 O A:HOH523 2.5 38.6 1.0
O A:HOH557 2.8 30.6 1.0
O A:HOH533 2.8 14.3 1.0
O A:GLY316 2.8 12.9 1.0
O A:HOH602 2.9 20.8 1.0
C A:GLY316 3.6 11.9 1.0
OE2 A:GLU230 3.6 21.4 0.7
OH A:TYR89 3.8 12.7 1.0
NE2 A:GLN48 3.8 14.7 1.0
O2 A:GOL422 3.9 40.7 1.0
OE2 A:GLU230 4.0 13.2 0.3
OE2 A:GLU10 4.0 12.2 1.0
CD A:GLU230 4.1 12.7 0.3
CA A:GLY316 4.1 12.0 1.0
CD A:GLU230 4.2 17.5 0.7
O A:HOH501 4.3 23.2 1.0
OE1 A:GLU230 4.3 17.9 0.7
O A:HOH555 4.3 14.0 1.0
O A:GLN48 4.3 12.9 1.0
OE1 A:GLU230 4.5 13.0 0.3
CB A:ALA317 4.5 12.3 1.0
N A:ALA317 4.6 11.8 1.0
CG A:GLU230 4.7 11.9 0.3
C2 A:GOL422 4.8 40.3 1.0
O A:TYR271 4.8 13.4 1.0
CD A:GLN48 4.8 13.1 1.0
CA A:ALA317 4.8 11.9 1.0

Sodium binding site 2 out of 10 in 8bb0

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Sodium binding site 2 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:20.3
occ:1.00
 OG A:SER150 2.7 12.8 1.0
O A:SER150 2.9 13.1 1.0
O A:SER131 3.0 14.8 1.0
O A:GLY132 3.2 13.0 1.0
CB A:SER150 3.2 12.4 1.0
CZ3 A:TRP104 3.3 13.6 1.0
C A:SER131 3.3 14.2 1.0
C A:SER150 3.5 12.3 1.0
CD2 A:TYR151 3.5 14.9 1.0
CE3 A:TRP104 3.7 13.0 1.0
CA A:SER131 3.7 15.3 1.0
CH2 A:TRP104 3.8 13.9 1.0
C A:GLY132 3.9 12.5 1.0
CA A:SER150 3.9 11.8 1.0
CG1 A:ILE103 4.0 14.4 1.0
N A:GLY132 4.0 13.4 1.0
CB A:TYR151 4.1 14.3 1.0
CG A:TYR151 4.2 14.7 1.0
CB A:SER133 4.2 11.3 1.0
CD1 A:ILE103 4.3 14.7 1.0
N A:TYR151 4.4 12.4 1.0
CE2 A:TYR151 4.4 15.4 1.0
CB A:SER131 4.4 15.9 1.0
CD2 A:TRP104 4.5 13.2 1.0
CA A:GLY132 4.5 13.6 1.0
N A:SER133 4.6 11.8 1.0
CZ2 A:TRP104 4.6 13.7 1.0
CA A:TYR151 4.8 13.4 1.0
N A:SER150 4.8 12.0 1.0
N A:TRP104 4.8 12.8 1.0
CE2 A:TRP104 4.9 12.9 1.0
N A:SER131 4.9 15.8 1.0
CA A:SER133 4.9 11.6 1.0
O A:GLU130 5.0 16.4 1.0

Sodium binding site 3 out of 10 in 8bb0

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Sodium binding site 3 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:17.9
occ:1.00
 OG A:SER133 2.6 11.0 1.0
O A:THR134 2.7 11.8 1.0
OE1 A:GLU135 2.8 12.0 1.0
O A:GLN102 3.3 11.9 1.0
CB A:SER133 3.5 11.3 1.0
C A:THR134 3.5 11.1 1.0
N A:THR134 3.5 11.7 1.0
CB A:ILE103 3.5 14.1 1.0
CA A:SER133 3.6 11.6 1.0
CG A:ARG88 3.7 12.9 1.0
CA A:ILE103 3.7 13.3 1.0
C A:GLN102 3.8 12.6 1.0
NE A:ARG88 3.8 14.7 1.0
N A:ILE103 3.8 13.4 1.0
CD A:ARG88 3.9 13.7 1.0
C A:SER133 3.9 12.2 1.0
CD A:GLU135 3.9 11.3 1.0
CG1 A:ILE103 4.0 14.4 1.0
CA A:THR134 4.1 11.1 1.0
CB A:GLU135 4.2 11.3 1.0
N A:GLU135 4.3 11.2 1.0
CA A:GLU135 4.3 10.7 1.0
CE3 A:TRP149 4.4 11.4 1.0
CD1 A:ILE103 4.4 14.7 1.0
CZ A:ARG88 4.6 16.1 1.0
CG A:GLU135 4.7 11.4 1.0
CB A:ARG88 4.7 12.2 1.0
CG2 A:ILE103 4.7 13.9 1.0
CB A:TRP149 4.8 12.1 1.0
O A:SER133 4.9 11.8 1.0
OE2 A:GLU135 4.9 11.8 1.0
CA A:GLN102 4.9 12.2 1.0

Sodium binding site 4 out of 10 in 8bb0

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Sodium binding site 4 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:19.5
occ:1.00
 OD1 A:ASP45 2.7 15.4 1.0
O A:GLU10 2.8 12.7 1.0
N A:ASN17 3.2 12.7 1.0
N A:VAL46 3.2 13.2 1.0
N A:ALA18 3.2 11.9 1.0
OD1 A:ASN17 3.3 14.6 1.0
CA A:ASP45 3.4 13.4 1.0
O A:ASN12 3.4 13.3 1.0
CG A:ASP45 3.6 13.4 1.0
CA A:GLY11 3.7 12.7 1.0
N A:SER16 3.7 13.3 1.0
C A:GLY11 3.7 12.6 1.0
N A:ASN12 3.7 12.7 1.0
O A:GLY44 3.8 13.4 1.0
C A:ASP45 3.8 13.9 1.0
C A:ASN17 3.8 12.1 1.0
C A:GLU10 3.8 12.4 1.0
CA A:SER16 3.8 13.0 1.0
CB A:ALA18 3.9 12.1 1.0
CA A:ALA18 3.9 12.0 1.0
C A:ASN12 3.9 13.1 1.0
C A:SER16 3.9 12.7 1.0
CB A:ASP45 4.0 13.2 1.0
CA A:ASN17 4.0 12.2 1.0
CA A:VAL46 4.2 12.2 1.0
N A:GLY11 4.2 13.0 1.0
O A:GLY11 4.4 13.0 1.0
N A:ASP45 4.4 13.3 1.0
CG A:ASN17 4.4 13.2 1.0
CA A:ASN12 4.5 13.1 1.0
C A:GLY44 4.5 12.6 1.0
CG2 A:VAL46 4.5 12.4 1.0
OD2 A:ASP45 4.5 14.5 1.0
N A:PHE13 4.6 13.0 1.0
C A:TYR15 4.7 13.5 1.0
O A:ASN17 4.7 12.6 1.0
CB A:ASN17 4.8 12.6 1.0
N A:TYR15 4.9 13.3 1.0
CA A:PHE13 4.9 13.2 1.0
O A:ASP45 5.0 15.0 1.0

Sodium binding site 5 out of 10 in 8bb0

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Sodium binding site 5 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:20.0
occ:1.00
 O A:ILE173 2.7 14.9 1.0
OG1 A:THR190 2.7 12.9 1.0
OE2 A:GLU202 2.7 14.9 1.0
CB A:THR190 3.2 13.1 1.0
N A:ILE173 3.3 13.4 1.0
CA A:GLY192 3.4 14.9 1.0
N A:GLY192 3.5 14.1 1.0
CD A:GLU202 3.6 16.2 1.0
CG1 A:ILE173 3.6 13.5 1.0
CG A:GLU202 3.6 15.8 1.0
C A:ILE173 3.6 13.9 1.0
O A:HOH570 3.8 19.9 1.0
CA A:PRO204 3.8 14.0 1.0
C A:GLY172 3.8 13.2 1.0
CG2 A:THR190 3.9 14.3 1.0
CA A:ILE173 3.9 13.1 1.0
O A:ALA203 4.1 14.6 1.0
CA A:GLY172 4.1 13.4 1.0
CB A:PRO204 4.3 13.8 1.0
CB A:ILE173 4.3 13.3 1.0
C A:GLY192 4.4 14.6 1.0
CA A:THR190 4.5 12.5 1.0
O A:GLY172 4.5 13.8 1.0
N A:PRO204 4.6 14.0 1.0
C A:THR190 4.6 12.9 1.0
N A:ASP191 4.6 13.2 1.0
C A:ALA203 4.6 14.5 1.0
N A:SER205 4.6 14.0 1.0
C A:PRO204 4.7 13.7 1.0
C A:ASP191 4.7 14.1 1.0
CD1 A:ILE173 4.8 14.1 1.0
OE1 A:GLU202 4.8 20.0 1.0
N A:GLN174 4.9 12.6 1.0
O A:GLU202 4.9 15.0 1.0

Sodium binding site 6 out of 10 in 8bb0

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Sodium binding site 6 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:20.7
occ:1.00
 OG1 A:THR134 2.7 11.6 1.0
O A:ASP105 2.9 13.1 1.0
O A:ARG107 3.1 12.3 1.0
O A:GLN102 3.4 11.9 1.0
CG2 A:THR134 3.5 11.7 1.0
N A:ARG107 3.6 12.7 1.0
CB A:THR134 3.6 11.2 1.0
C A:ARG107 3.6 12.3 1.0
C A:ASP105 3.7 12.7 1.0
C A:TYR106 3.8 13.3 1.0
N A:THR134 3.8 11.7 1.0
CB A:GLN102 3.9 12.4 1.0
N A:GLN102 4.1 11.8 1.0
CA A:TYR106 4.1 13.6 1.0
CA A:ARG107 4.1 12.7 1.0
C A:GLN102 4.2 12.6 1.0
N A:TYR106 4.2 13.3 1.0
N A:ILE108 4.3 12.3 1.0
O A:TYR106 4.3 13.8 1.0
CA A:GLN102 4.3 12.2 1.0
CA A:THR134 4.3 11.1 1.0
C A:SER133 4.3 12.2 1.0
CG1 A:ILE108 4.4 12.8 1.0
CG A:GLN102 4.5 12.4 1.0
CB A:ASP105 4.5 13.3 1.0
SD A:MET127 4.6 14.8 1.0
CA A:ASP105 4.6 12.9 1.0
CA A:ILE108 4.6 12.1 1.0
SG A:CYS124 4.7 17.5 1.0
CA A:SER133 4.7 11.6 1.0
N A:SER133 4.8 11.8 1.0

Sodium binding site 7 out of 10 in 8bb0

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Sodium binding site 7 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:24.0
occ:1.00
 O A:HOH534 2.6 61.7 1.0
O05 A:I2A426 3.2 21.2 1.0
O13 A:I2A426 3.5 16.7 1.0
N12 A:I2A426 3.5 13.7 1.0
C49 A:I2A426 3.6 14.5 1.0
C54 A:I2A426 3.8 13.0 1.0
C59 A:I2A426 3.9 13.0 1.0
C33 A:I2A426 3.9 15.5 1.0
C32 A:I2A426 3.9 14.8 1.0
C35 A:I2A426 4.0 17.2 1.0
C36 A:I2A426 4.0 18.3 1.0
N A:I2A426 4.3 13.1 1.0
C11 A:I2A426 4.4 14.4 1.0
C60 A:I2A426 4.4 13.2 1.0
C10 A:I2A426 4.5 14.1 1.0
C58 A:I2A426 4.5 13.6 1.0
C12 A:I2A426 4.6 16.1 1.0
C37 A:I2A426 4.6 20.8 1.0
C52 A:I2A426 4.8 16.2 1.0
C13 A:I2A426 4.8 16.1 1.0
N03 A:I2A426 4.9 14.3 1.0
O A:I2A426 4.9 24.1 1.0

Sodium binding site 8 out of 10 in 8bb0

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Sodium binding site 8 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:23.8
occ:1.00
 O A:HOH735 2.5 37.8 1.0
O A:VAL231 2.8 12.4 1.0
OE1 A:GLN136 2.8 11.6 1.0
O A:HOH744 3.0 36.3 1.0
CG1 A:VAL179 3.4 14.5 1.0
NE2 A:GLN232 3.6 16.1 1.0
CD A:GLN136 3.7 11.8 1.0
O A:LEU178 3.7 14.9 1.0
O A:HOH513 3.7 70.3 1.0
NE2 A:GLN136 4.0 12.5 1.0
C A:VAL231 4.0 11.6 1.0
CD A:GLN232 4.0 15.2 1.0
O A:HOH628 4.1 31.7 1.0
C A:LEU178 4.4 13.3 1.0
N A:LEU178 4.4 12.7 1.0
OE1 A:GLN232 4.5 16.6 1.0
CB A:SER177 4.5 11.7 1.0
OE1 A:GLU230 4.5 17.9 0.7
CG2 A:VAL231 4.6 13.0 1.0
O A:HOH667 4.7 18.7 1.0
CA A:GLN232 4.8 12.7 1.0
N A:GLN232 4.8 12.5 1.0
CG A:GLN232 4.8 13.9 1.0
CB A:VAL179 4.9 13.5 1.0
OE1 A:GLU230 5.0 13.0 0.3
CA A:VAL231 5.0 12.0 1.0

Sodium binding site 9 out of 10 in 8bb0

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Sodium binding site 9 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:16.3
occ:1.00
 S A:SCN414 2.6 48.8 1.0
O A:ASP191 2.6 14.7 1.0
O A:GLY193 2.7 15.3 1.0
O A:ASP226 2.7 15.3 1.0
O A:HOH592 2.7 20.6 1.0
CD1 A:TRP227 3.6 15.8 1.0
C A:GLY192 3.6 14.6 1.0
C A:SCN414 3.6 50.4 1.0
C A:GLY193 3.7 15.2 1.0
C A:ASP226 3.7 14.7 1.0
O A:GLY192 3.7 15.7 1.0
C A:ASP191 3.8 14.1 1.0
CE1 A:TYR201 3.9 17.5 1.0
CA A:GLY192 3.9 14.9 1.0
CA A:TRP227 3.9 14.1 1.0
CB A:TRP227 4.0 15.1 1.0
N A:GLY193 4.0 14.0 1.0
CG A:TRP227 4.2 16.3 1.0
CD1 A:TYR201 4.2 16.4 1.0
N A:TRP227 4.2 14.7 1.0
N A:GLY192 4.3 14.1 1.0
O A:GLY225 4.4 16.6 1.0
CA A:GLY193 4.5 14.7 1.0
C A:GLY225 4.5 15.6 1.0
N A:TYR194 4.5 16.6 1.0
N A:SCN414 4.6 52.2 1.0
O A:GLU202 4.6 15.0 1.0
CA A:TYR194 4.7 17.0 1.0
NE1 A:TRP227 4.7 15.6 1.0
N A:ASP226 4.8 15.4 1.0
CA A:GLY225 4.9 17.0 1.0
CA A:ASP226 4.9 15.1 1.0
CA A:ASP191 5.0 13.2 1.0
N A:GLY225 5.0 16.7 1.0

Sodium binding site 10 out of 10 in 8bb0

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Sodium binding site 10 out of 10 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:17.7
occ:1.00
 O B:GLY193 2.5 15.9 1.0
O B:ASP191 2.6 15.6 1.0
O B:ASP226 2.7 14.7 1.0
O B:HOH602 2.8 18.2 1.0
O B:HOH720 3.1 45.6 1.0
C B:GLY193 3.5 15.9 1.0
CD1 B:TRP227 3.5 16.0 1.0
O B:GLY192 3.6 15.9 1.0
C B:GLY192 3.6 14.6 1.0
C B:ASP191 3.7 14.4 1.0
C B:ASP226 3.7 14.7 1.0
CA B:GLY192 3.8 14.3 1.0
N B:GLY193 3.9 15.1 1.0
CA B:TRP227 4.0 14.7 1.0
CB B:TRP227 4.0 15.2 1.0
CE1 B:TYR201 4.1 19.0 1.0
CG B:TRP227 4.1 15.8 1.0
CD1 B:TYR201 4.2 18.5 1.0
N B:GLY192 4.3 13.7 1.0
N B:TRP227 4.3 14.5 1.0
N B:TYR194 4.3 17.0 1.0
CA B:GLY193 4.4 16.1 1.0
CA B:TYR194 4.4 18.2 1.0
O B:GLU202 4.5 17.2 1.0
O B:GLY225 4.5 16.8 1.0
C B:GLY225 4.6 16.4 1.0
NE1 B:TRP227 4.6 17.0 1.0
N B:ASP226 4.8 15.6 1.0
CA B:ASP226 4.9 15.1 1.0
CA B:ASP191 5.0 14.4 1.0
CA B:GLY225 5.0 17.5 1.0

Reference:

J.Whittaker, A.Guskov. The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Hydroxycobinamide. To Be Published.
Page generated: Wed Oct 9 10:39:36 2024

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