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Sodium in PDB 6lgy: Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium

Protein crystallography data

The structure of Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium, PDB code: 6lgy was solved by X.Wang, Y.Lyu, Y.Ji, Z.Sun, X.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.80 / 2.25
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 45.469, 185.578, 75.081, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium (pdb code 6lgy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium, PDB code: 6lgy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6lgy

Go back to Sodium Binding Sites List in 6lgy
Sodium binding site 1 out of 2 in the Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:35.2
occ:1.00
O A:MET257 2.2 34.5 1.0
OE1 A:GLN258 2.3 36.2 1.0
O A:VAL255 2.3 35.8 1.0
O A:GLU254 2.3 29.6 1.0
ND1 A:HIS71 2.7 33.0 1.0
C A:VAL255 2.8 35.5 1.0
CE1 A:HIS71 3.1 33.2 1.0
CA A:VAL255 3.2 34.0 1.0
C A:MET257 3.2 37.5 1.0
C A:GLU254 3.4 28.4 1.0
CD A:GLN258 3.4 32.9 1.0
N A:MET257 3.6 30.8 1.0
N A:GLY256 3.7 35.8 1.0
N A:VAL255 3.8 31.8 1.0
C A:GLY256 3.8 28.2 1.0
CG A:HIS71 3.8 34.9 1.0
CA A:MET257 4.0 38.7 1.0
CG A:GLN258 4.1 28.2 1.0
O A:HOH514 4.1 41.2 1.0
N A:GLN258 4.2 37.4 1.0
O A:HOH524 4.2 34.2 1.0
CA A:GLY256 4.3 28.4 1.0
NE2 A:HIS71 4.3 33.0 1.0
CG A:MET75 4.4 31.7 1.0
O A:GLY256 4.4 34.0 1.0
NE2 A:GLN258 4.5 28.4 1.0
CA A:GLN258 4.5 29.5 1.0
CB A:HIS71 4.5 33.2 1.0
CB A:VAL255 4.6 32.1 1.0
CD2 A:HIS71 4.7 32.4 1.0
CA A:GLU254 4.7 34.2 1.0
CE A:MET75 4.8 29.8 1.0
CG1 A:VAL255 4.8 30.6 1.0
O A:ILE253 4.9 35.5 1.0
CB A:GLN258 4.9 30.5 1.0

Sodium binding site 2 out of 2 in 6lgy

Go back to Sodium Binding Sites List in 6lgy
Sodium binding site 2 out of 2 in the Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Cysteine-Pair Mutant (P10C-S291C) of A Bacterial Bile Acid Transporter in An Inward-Facing State Complexed with Glycine and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:35.8
occ:1.00
O A:GLY105 2.3 44.6 1.0
O A:HOH532 2.4 42.4 1.0
O A:HOH504 2.4 42.9 1.0
OG A:SER104 2.4 41.5 1.0
OG A:SER108 2.4 36.0 1.0
OG A:SER126 2.5 33.0 1.0
CB A:SER126 3.2 36.7 1.0
CB A:SER108 3.4 36.3 1.0
C A:GLY105 3.5 39.3 1.0
CB A:SER104 3.6 30.2 1.0
OE2 A:GLU254 4.0 37.9 1.0
OD1 A:ASN109 4.0 61.3 1.0
C A:SER104 4.1 38.3 1.0
OE1 A:GLU254 4.2 45.6 1.0
N A:GLY105 4.2 37.2 1.0
O A:SER104 4.2 33.5 1.0
O A:THR106 4.2 36.3 1.0
N A:SER108 4.2 30.5 1.0
CA A:SER126 4.2 38.0 1.0
CA A:SER108 4.3 33.7 1.0
C A:THR106 4.4 42.8 1.0
N A:THR106 4.4 42.2 1.0
CA A:THR106 4.4 44.0 1.0
CA A:GLY105 4.4 41.1 1.0
CG A:ASN109 4.4 44.9 1.0
O A:HOH514 4.5 41.2 1.0
CA A:SER104 4.5 33.1 1.0
ND2 A:ASN109 4.5 49.0 1.0
N A:ASN109 4.5 31.9 1.0
CD A:GLU254 4.5 38.4 1.0
C A:SER108 4.9 38.4 1.0

Reference:

X.Wang, Y.Lyu, Y.Ji, Z.Sun, X.Zhou. Crystal Structures and Docking of A Bacterial Bile Acid Transporter Reveal Its Potential Substrate-Binding Mechanism To Be Published.
Page generated: Tue Dec 15 12:32:59 2020

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