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Sodium in PDB 3qg6: Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody

Protein crystallography data

The structure of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody, PDB code: 3qg6 was solved by R.N.Kirchdoerfer, J.D.Janda, G.F.Kaufmann, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.360, 98.498, 73.670, 90.00, 114.03, 90.00
R / Rfree (%) 18.4 / 23.9

Other elements in 3qg6:

The structure of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody also contains other interesting chemical elements:

Zinc (Zn) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody (pdb code 3qg6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody, PDB code: 3qg6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3qg6

Go back to Sodium Binding Sites List in 3qg6
Sodium binding site 1 out of 2 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na215

b:34.0
occ:1.00
SG D:CYS4 3.9 28.8 1.0
CB D:CYS4 4.1 29.8 1.0
NE2 A:HIS27D 4.3 46.8 1.0
O A:THR91 4.4 26.1 1.0
O D:CYS4 4.5 27.4 1.0
CE1 A:TYR32 4.6 31.1 1.0
CZ A:TYR32 4.7 35.9 1.0
CD2 A:HIS27D 4.7 47.0 1.0
OH A:TYR96 4.7 19.3 1.0
CE1 A:HIS27D 4.9 47.5 1.0
O D:ILE7 4.9 25.4 1.0
OH A:TYR32 4.9 39.2 1.0
CD1 A:TYR32 5.0 29.4 1.0

Sodium binding site 2 out of 2 in 3qg6

Go back to Sodium Binding Sites List in 3qg6
Sodium binding site 2 out of 2 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na214

b:28.2
occ:1.00
SG C:CYS4 4.0 27.1 1.0
NE2 L:HIS27D 4.1 45.6 1.0
CB C:CYS4 4.1 32.5 1.0
O L:THR91 4.3 20.0 1.0
CZ L:TYR32 4.3 29.9 1.0
CD2 L:HIS27D 4.5 45.6 1.0
CE1 L:TYR32 4.5 26.8 1.0
OH L:TYR32 4.5 32.9 1.0
O C:CYS4 4.6 29.0 1.0
CE1 L:HIS27D 4.6 46.7 1.0
CE2 L:TYR32 4.6 29.4 1.0
O C:ILE7 4.8 15.0 1.0
OH L:TYR96 4.8 14.1 1.0
CD1 L:TYR32 4.9 26.2 1.0

Reference:

R.N.Kirchdoerfer, A.L.Garner, C.E.Flack, J.M.Mee, A.R.Horswill, K.D.Janda, G.F.Kaufmann, I.A.Wilson. Structural Basis For Ligand Recognition and Discrimination of A Quorum-Quenching Antibody. J.Biol.Chem. V. 286 17351 2011.
ISSN: ISSN 0021-9258
PubMed: 21454495
DOI: 10.1074/JBC.M111.231258
Page generated: Tue Dec 15 06:22:47 2020

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