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

Protein crystallography data

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

Resolution Low / High (Å) 44.20 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.177, 100.593, 79.579, 90, 97.6, 90
R / Rfree (%) 18.1 / 24.3

Other elements in 8baz:

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

Sodium binding site 1 out of 6 in 8baz

Go back to Sodium Binding Sites List in 8baz
Sodium binding site 1 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


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 Cyanocobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:33.3
occ:1.00
H A:VAL46 2.5 21.4 1.0
H A:ASN17 2.6 23.7 1.0
HA A:ASP45 2.6 25.5 1.0
OD1 A:ASP45 2.7 30.5 1.0
O A:GLU10 2.9 25.2 1.0
HA3 A:GLY11 2.9 24.3 1.0
H A:ALA18 3.0 22.6 1.0
O A:ASN12 3.1 26.6 1.0
H A:SER16 3.2 25.7 1.0
N A:ASN17 3.2 23.4 1.0
N A:ALA18 3.3 21.8 1.0
HB2 A:ALA18 3.3 23.6 1.0
N A:VAL46 3.3 20.4 1.0
HA A:SER16 3.3 25.1 1.0
OD1 A:ASN17 3.4 28.9 1.0
H A:ASN12 3.5 25.2 1.0
CA A:ASP45 3.5 26.3 1.0
N A:ASN12 3.6 25.6 1.0
CG A:ASP45 3.6 27.4 1.0
N A:SER16 3.6 25.9 1.0
CA A:GLY11 3.6 24.6 1.0
C A:GLY11 3.7 23.9 1.0
C A:ASN12 3.8 26.0 1.0
CA A:SER16 3.8 24.9 1.0
C A:ASN17 3.8 24.1 1.0
C A:ASP45 3.9 23.9 1.0
C A:GLU10 3.9 22.4 1.0
O A:GLY44 3.9 22.7 1.0
HG23 A:VAL46 3.9 23.3 1.0
C A:SER16 4.0 22.6 1.0
CA A:ALA18 4.0 22.6 1.0
CB A:ALA18 4.0 23.5 1.0
H A:TYR15 4.0 24.9 1.0
HA A:ALA18 4.0 22.7 1.0
HA A:VAL46 4.1 22.2 1.0
CA A:ASN17 4.1 25.8 1.0
CB A:ASP45 4.1 25.4 1.0
HA A:PHE13 4.2 22.4 1.0
N A:GLY11 4.2 23.7 1.0
CA A:VAL46 4.3 22.5 1.0
O A:GLY11 4.3 23.3 1.0
HG22 A:VAL46 4.3 23.2 1.0
HB3 A:ALA18 4.3 23.4 1.0
CA A:ASN12 4.4 24.6 1.0
HA2 A:GLY11 4.4 24.2 1.0
CG A:ASN17 4.4 28.5 1.0
OD2 A:ASP45 4.5 30.4 1.0
HB2 A:TYR15 4.5 29.4 1.0
HB2 A:ASP45 4.5 25.9 1.0
N A:ASP45 4.5 25.4 1.0
N A:PHE13 4.5 23.4 1.0
CG2 A:VAL46 4.5 23.4 1.0
C A:TYR15 4.5 25.2 1.0
C A:GLY44 4.6 23.1 1.0
O A:ASN17 4.7 28.6 1.0
N A:TYR15 4.8 24.7 1.0
H A:GLN14 4.8 24.4 1.0
HB1 A:ALA18 4.8 23.1 1.0
CA A:PHE13 4.8 22.0 1.0
CB A:ASN17 4.9 27.0 1.0
H A:ALA47 4.9 24.4 1.0
HA A:ASN17 4.9 25.3 1.0
HB3 A:ASP45 4.9 25.9 1.0

Sodium binding site 2 out of 6 in 8baz

Go back to Sodium Binding Sites List in 8baz
Sodium binding site 2 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


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 Cyanocobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na415

b:38.9
occ:1.00
OG A:SER86 2.7 23.5 1.0
OD1 A:ASN63 2.8 25.0 1.0
HB2 A:SER86 3.1 22.2 1.0
O34 A:CBY401 3.3 30.7 1.0
HA A:ASN63 3.4 22.4 1.0
HD1 A:TRP104 3.4 23.7 1.0
CB A:SER86 3.5 22.0 1.0
CG A:ASN63 3.7 24.1 1.0
HB2 A:ASN63 3.9 23.4 1.0
HN3A A:CBY401 4.0 24.8 1.0
HE1 A:HIS65 4.0 30.8 1.0
HA A:SER86 4.1 21.6 1.0
HE1 A:PHE13 4.1 26.2 1.0
HD22 A:ASN62 4.1 18.6 1.0
CB A:ASN63 4.2 23.6 1.0
HB3 A:SER86 4.2 22.2 1.0
O A:ASN62 4.2 23.4 1.0
CA A:ASN63 4.2 22.2 1.0
CD1 A:TRP104 4.2 23.8 1.0
O A:THR85 4.2 24.7 1.0
HE1 A:TRP104 4.3 24.0 1.0
C32 A:CBY401 4.3 25.8 1.0
CA A:SER86 4.4 21.5 1.0
CE1 A:HIS65 4.5 31.4 1.0
N33 A:CBY401 4.5 24.4 1.0
ND2 A:ASN62 4.6 18.4 1.0
HG21 A:ILE103 4.6 22.7 1.0
NE1 A:TRP104 4.6 23.8 1.0
HZ A:PHE13 4.7 27.8 1.0
ND2 A:ASN63 4.9 24.4 1.0
CE1 A:PHE13 4.9 26.5 1.0
C A:ASN62 4.9 20.6 1.0
NE2 A:HIS65 4.9 29.2 1.0
HD21 A:ASN62 4.9 18.5 1.0
OD1 A:ASN62 5.0 23.8 1.0
N A:ASN63 5.0 20.7 1.0

Sodium binding site 3 out of 6 in 8baz

Go back to Sodium Binding Sites List in 8baz
Sodium binding site 3 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


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 Cyanocobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na416

b:31.6
occ:1.00
OE1 A:GLU135 2.5 28.6 1.0
OG A:SER133 2.6 23.6 1.0
O A:THR134 2.8 21.9 1.0
HG3 A:ARG88 2.8 19.8 1.0
HB A:ILE103 2.8 22.7 1.0
HE3 A:TRP149 3.2 23.3 1.0
H A:THR134 3.3 24.7 1.0
HA A:SER133 3.3 26.1 1.0
HE A:ARG88 3.4 21.7 1.0
HB2 A:GLU135 3.4 23.0 1.0
O A:GLN102 3.4 24.6 1.0
HA A:ILE103 3.5 22.6 1.0
C A:THR134 3.5 22.7 1.0
N A:THR134 3.6 24.6 1.0
CB A:SER133 3.6 25.2 1.0
HD3 A:ARG88 3.6 20.2 1.0
CB A:ILE103 3.6 22.4 1.0
HD12 A:ILE103 3.6 24.8 1.0
CG A:ARG88 3.6 19.7 1.0
HG13 A:ILE103 3.6 23.8 1.0
NE A:ARG88 3.7 21.8 1.0
HB2 A:SER133 3.7 25.0 1.0
HB3 A:TRP149 3.7 21.6 1.0
CD A:GLU135 3.7 27.7 1.0
CA A:SER133 3.8 26.0 1.0
CD A:ARG88 3.8 20.2 1.0
HA A:GLU135 3.8 21.4 1.0
CA A:ILE103 3.9 22.6 1.0
C A:GLN102 3.9 21.6 1.0
C A:SER133 4.0 26.9 1.0
N A:ILE103 4.0 20.9 1.0
CG1 A:ILE103 4.0 24.0 1.0
H A:SER150 4.0 23.2 1.0
HG2 A:ARG88 4.1 19.9 1.0
CB A:GLU135 4.1 23.2 1.0
CE3 A:TRP149 4.2 23.1 1.0
CA A:THR134 4.2 23.8 1.0
H A:TRP149 4.2 22.5 1.0
N A:GLU135 4.3 20.4 1.0
CD1 A:ILE103 4.3 25.0 1.0
CA A:GLU135 4.3 21.3 1.0
HB3 A:SER133 4.4 25.0 1.0
CZ A:ARG88 4.5 23.6 1.0
CG A:GLU135 4.5 25.6 1.0
HB3 A:SER150 4.5 23.0 1.0
HB3 A:ARG88 4.5 20.1 1.0
H A:ILE103 4.6 21.1 1.0
OE2 A:GLU135 4.6 28.3 1.0
CB A:ARG88 4.6 20.0 1.0
HA A:THR134 4.6 23.9 1.0
HZ3 A:TRP149 4.7 24.1 1.0
CB A:TRP149 4.7 21.6 1.0
H A:GLN102 4.7 22.2 1.0
HD2 A:ARG88 4.8 20.4 1.0
HB2 A:ARG88 4.8 20.3 1.0
CG2 A:ILE103 4.8 22.7 1.0
HD13 A:ILE103 4.8 24.7 1.0
NH2 A:ARG88 4.9 23.4 1.0
CZ3 A:TRP149 4.9 24.4 1.0
HG22 A:ILE103 4.9 22.5 1.0
HG12 A:ILE103 4.9 23.9 1.0
HB2 A:SER150 4.9 23.1 1.0
HH22 A:ARG88 4.9 23.5 1.0
N A:SER150 4.9 23.2 1.0
HB3 A:GLU135 5.0 23.2 1.0
O A:SER133 5.0 23.4 1.0
HD11 A:ILE103 5.0 24.8 1.0

Sodium binding site 4 out of 6 in 8baz

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Sodium binding site 4 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


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 Cyanocobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na417

b:27.5
occ:1.00
O A:GLY193 2.6 30.3 1.0
O A:ASP191 2.7 24.6 1.0
O A:HOH570 2.7 48.2 1.0
O A:ASP226 2.8 32.6 1.0
O A:HOH515 2.8 30.9 1.0
HD1 A:TRP227 2.8 40.5 1.0
HE1 A:TYR201 3.0 32.7 1.0
HA A:TRP227 3.4 33.1 1.0
HA3 A:GLY192 3.5 26.4 1.0
CD1 A:TRP227 3.6 41.0 1.0
C A:GLY192 3.7 26.5 1.0
C A:GLY193 3.7 27.7 1.0
C A:ASP226 3.8 33.1 1.0
HB2 A:TRP227 3.8 35.7 1.0
O A:GLY192 3.8 26.6 1.0
C A:ASP191 3.8 24.6 1.0
HD1 A:TYR201 3.8 31.2 1.0
CE1 A:TYR201 3.9 32.7 1.0
CA A:GLY192 4.0 26.9 1.0
HA A:TYR194 4.0 28.8 1.0
N A:GLY193 4.1 27.1 1.0
CA A:TRP227 4.1 32.7 1.0
CB A:TRP227 4.2 35.7 1.0
CG A:TRP227 4.2 41.2 1.0
CD1 A:TYR201 4.3 31.1 1.0
N A:TRP227 4.3 33.4 1.0
H A:GLY225 4.3 32.6 1.0
N A:GLY192 4.4 24.9 1.0
H A:GLY193 4.4 27.3 1.0
CA A:GLY193 4.5 29.3 1.0
C A:GLY225 4.5 31.8 1.0
O A:GLY225 4.5 36.6 1.0
HA2 A:GLY225 4.6 32.9 1.0
O A:GLU202 4.6 30.1 1.0
HD3 A:PRO204 4.7 26.9 1.0
N A:TYR194 4.7 27.5 1.0
HG3 A:PRO204 4.7 28.0 1.0
NE1 A:TRP227 4.7 41.8 1.0
HB2 A:ASP191 4.7 26.1 1.0
N A:ASP226 4.8 30.8 1.0
CA A:TYR194 4.8 29.1 1.0
HD3 A:PRO228 4.8 28.4 1.0
CA A:GLY225 4.9 33.5 1.0
HE1 A:TRP227 4.9 40.8 1.0
HA2 A:GLY192 4.9 26.4 1.0
CA A:ASP226 4.9 31.8 1.0
N A:GLY225 4.9 32.5 1.0

Sodium binding site 5 out of 6 in 8baz

Go back to Sodium Binding Sites List in 8baz
Sodium binding site 5 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


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 Cyanocobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na418

b:46.9
occ:1.00
HE22 A:GLN152 2.5 29.3 1.0
H A:ASP128 2.6 29.7 1.0
OG A:SER131 2.6 29.2 1.0
HA A:MET127 2.8 28.0 1.0
NE2 A:GLN152 3.0 29.6 1.0
HE21 A:GLN152 3.2 29.2 1.0
OD1 A:ASP128 3.2 29.2 1.0
HG3 A:MET127 3.2 30.2 1.0
N A:ASP128 3.4 30.0 1.0
O A:HOH522 3.5 36.9 1.0
HA2 A:GLY132 3.7 23.3 1.0
CA A:MET127 3.7 27.4 1.0
CG A:ASP128 3.7 32.2 1.0
C A:SER131 3.8 25.2 1.0
O A:SER131 3.8 27.1 1.0
HG2 A:MET127 3.9 30.2 1.0
H A:SER131 3.9 27.4 1.0
CB A:SER131 3.9 27.3 1.0
CG A:MET127 3.9 30.1 1.0
N A:GLY132 4.0 24.0 1.0
C A:MET127 4.0 27.4 1.0
CD A:GLN152 4.1 27.2 1.0
CA A:SER131 4.2 27.5 1.0
OD2 A:ASP128 4.2 37.0 1.0
O A:ASP128 4.2 26.4 1.0
HB2 A:SER131 4.3 27.6 1.0
CB A:MET127 4.3 29.3 1.0
CA A:ASP128 4.3 31.5 1.0
CA A:GLY132 4.4 23.2 1.0
OE1 A:GLN152 4.4 28.5 1.0
O A:ASP126 4.4 26.9 1.0
N A:SER131 4.4 26.6 1.0
H A:GLY132 4.5 24.0 1.0
CB A:ASP128 4.5 30.8 1.0
HB3 A:SER131 4.6 27.9 1.0
HB3 A:ASP128 4.6 31.2 1.0
C A:ASP128 4.7 30.6 1.0
HB2 A:MET127 4.7 29.1 1.0
N A:MET127 4.8 28.5 1.0
HA3 A:GLY132 4.8 23.5 1.0

Sodium binding site 6 out of 6 in 8baz

Go back to Sodium Binding Sites List in 8baz
Sodium binding site 6 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


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 Cyanocobalamin. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na416

b:27.0
occ:1.00
O B:GLY193 2.6 33.2 1.0
O B:ASP191 2.7 25.9 1.0
O B:HOH590 2.7 46.1 1.0
O B:ASP226 2.7 30.0 1.0
HD1 B:TRP227 2.8 38.9 1.0
O B:HOH542 2.8 35.6 1.0
HE1 B:TYR201 3.2 32.5 1.0
HA B:TRP227 3.3 32.4 1.0
CD1 B:TRP227 3.5 38.8 1.0
HA3 B:GLY192 3.6 28.4 1.0
HB2 B:TRP227 3.7 34.8 1.0
C B:GLY193 3.7 30.2 1.0
C B:ASP226 3.7 32.4 1.0
C B:GLY192 3.7 29.0 1.0
O B:GLY192 3.8 30.4 1.0
C B:ASP191 3.8 25.6 1.0
HD1 B:TYR201 3.9 31.3 1.0
HA B:TYR194 4.0 30.7 1.0
CA B:TRP227 4.0 32.4 1.0
CA B:GLY192 4.0 29.2 1.0
CE1 B:TYR201 4.0 32.8 1.0
N B:GLY193 4.1 28.9 1.0
CB B:TRP227 4.1 34.5 1.0
CG B:TRP227 4.1 39.3 1.0
N B:TRP227 4.2 31.2 1.0
N B:GLY192 4.4 25.9 1.0
CD1 B:TYR201 4.4 30.5 1.0
H B:GLY225 4.4 34.7 1.0
O B:GLY225 4.4 32.1 1.0
H B:GLY193 4.4 29.1 1.0
C B:GLY225 4.5 31.5 1.0
CA B:GLY193 4.5 31.2 1.0
HA2 B:GLY225 4.5 33.9 1.0
NE1 B:TRP227 4.6 41.9 1.0
N B:TYR194 4.6 31.1 1.0
HB2 B:ASP191 4.7 27.6 1.0
O B:GLU202 4.7 24.1 1.0
HD3 B:PRO204 4.7 26.4 1.0
CA B:TYR194 4.7 30.5 1.0
HG3 B:PRO204 4.7 27.3 1.0
N B:ASP226 4.8 31.3 1.0
HD3 B:PRO228 4.8 30.6 1.0
HE1 B:TRP227 4.8 41.4 1.0
CA B:GLY225 4.9 34.2 1.0
CA B:ASP226 4.9 32.6 1.0
HA2 B:GLY192 4.9 28.5 1.0
CA B:ASP191 5.0 25.6 1.0
N B:GLY225 5.0 35.1 1.0

Reference:

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

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