Sodium in PDB 7acg: In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol

Protein crystallography data

The structure of In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol, PDB code: 7acg was solved by L.Smithers, L.Van Dalsen, C.Boland, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.37 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 56.751, 74.187, 114.992, 90.00, 102.73, 90.00
R / Rfree (%) 18.4 / 22

Sodium Binding Sites:

The binding sites of Sodium atom in the In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol (pdb code 7acg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol, PDB code: 7acg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7acg

Go back to Sodium Binding Sites List in 7acg
Sodium binding site 1 out of 2 in the In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na515

b:30.3
occ:1.00
O A:ALA105 2.1 27.4 1.0
O A:GLU113 2.4 21.8 1.0
OE1 A:GLU113 2.4 27.2 1.0
O A:HOH689 2.4 33.6 1.0
O A:TYR110 2.5 27.0 1.0
O A:THR108 2.6 22.7 1.0
HG1 A:THR108 2.9 34.6 1.0
HB3 A:GLU113 2.9 29.1 1.0
HB1 A:ALA105 3.2 34.5 1.0
C A:ALA105 3.2 20.9 1.0
H A:THR108 3.2 28.1 1.0
C A:GLU113 3.4 27.1 1.0
CD A:GLU113 3.5 36.7 1.0
C A:TYR110 3.6 23.6 1.0
C A:THR108 3.6 23.2 1.0
H A:GLU113 3.6 23.9 1.0
HA A:ALA105 3.6 28.7 1.0
OG1 A:THR108 3.7 28.9 1.0
CB A:GLU113 3.7 24.3 1.0
CA A:ALA105 3.8 23.9 1.0
HA A:PRO111 3.9 28.6 1.0
CB A:ALA105 3.9 28.8 1.0
CA A:GLU113 4.0 22.0 1.0
N A:THR108 4.0 23.4 1.0
H A:TYR110 4.1 35.6 1.0
N A:TYR110 4.1 29.7 1.0
N A:GLU113 4.2 19.9 1.0
O A:HOH655 4.2 27.1 1.0
HA A:HIS114 4.2 28.0 1.0
CG A:GLU113 4.2 24.6 1.0
CA A:THR108 4.3 21.9 1.0
N A:GLY106 4.3 21.6 1.0
HA2 A:GLY106 4.3 35.5 1.0
HB2 A:TYR110 4.3 31.9 1.0
OE2 A:GLU113 4.3 27.8 1.0
HB3 A:ALA105 4.4 34.5 1.0
CA A:TYR110 4.4 22.4 1.0
N A:PRO111 4.4 23.7 1.0
H A:LEU107 4.5 34.3 1.0
C A:ALA109 4.5 38.9 1.0
N A:HIS114 4.5 18.3 1.0
CA A:PRO111 4.5 23.8 1.0
N A:ALA109 4.5 26.4 1.0
HB2 A:GLU113 4.5 29.1 1.0
CB A:THR108 4.6 27.9 1.0
HB2 A:ALA105 4.6 34.5 1.0
HA A:ALA109 4.6 34.0 1.0
HB3 A:HIS114 4.6 27.2 1.0
CA A:GLY106 4.7 29.6 1.0
N A:LEU107 4.7 28.6 1.0
HG3 A:GLU113 4.8 29.5 1.0
CA A:ALA109 4.8 28.3 1.0
CA A:HIS114 4.8 23.3 1.0
C A:PRO111 4.8 23.1 1.0
C A:GLY106 4.8 30.6 1.0
HA A:GLU113 4.9 26.4 1.0
HG23 A:THR108 4.9 35.3 1.0
CB A:TYR110 4.9 26.6 1.0
HG2 A:GLU113 4.9 29.5 1.0

Sodium binding site 2 out of 2 in 7acg

Go back to Sodium Binding Sites List in 7acg
Sodium binding site 2 out of 2 in the In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of In Meso Structure of the Alginate Exporter, Alge, From Pseudomonas Aeruginosa in 9.8 Monoacylglycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na516

b:54.6
occ:1.00
HE A:ARG286 2.1 28.9 1.0
HZ3 A:LYS294 2.2 63.2 1.0
HH21 A:ARG286 2.6 33.0 1.0
HE2 A:LYS294 2.7 39.9 1.0
HD3 A:LYS294 2.7 35.7 1.0
OD1 A:ASN288 2.8 34.0 1.0
OD1 A:ASN242 2.8 27.5 1.0
NE A:ARG286 2.8 24.1 1.0
NZ A:LYS294 2.9 52.7 1.0
HD21 A:ASN288 3.1 36.5 1.0
CE A:LYS294 3.1 33.2 1.0
HB3 A:SER237 3.3 36.1 1.0
NH2 A:ARG286 3.3 27.5 1.0
HA3 A:GLY327 3.3 32.5 1.0
CD A:LYS294 3.4 29.7 1.0
HZ2 A:LYS294 3.4 63.2 1.0
O A:ASN234 3.4 33.8 1.0
CZ A:ARG286 3.5 26.4 1.0
CG A:ASN288 3.5 26.3 1.0
HZ1 A:LYS294 3.5 63.2 1.0
ND2 A:ASN288 3.6 30.4 1.0
HA2 A:GLY327 3.6 32.5 1.0
HD2 A:ARG286 3.7 31.9 1.0
HA A:TYR235 3.7 43.6 1.0
CD A:ARG286 3.9 26.6 1.0
CA A:GLY327 3.9 27.1 1.0
HD2 A:LYS294 3.9 35.7 1.0
H A:SER237 4.0 38.6 1.0
HH22 A:ARG286 4.0 33.0 1.0
CG A:ASN242 4.0 26.4 1.0
HE3 A:LYS294 4.0 39.9 1.0
HB2 A:SER237 4.0 36.1 1.0
CB A:SER237 4.1 30.1 1.0
O A:GLY327 4.1 24.6 1.0
HG2 A:ARG286 4.2 32.2 1.0
HG2 A:LYS294 4.4 34.8 1.0
HD22 A:ASN288 4.4 36.5 1.0
C A:ASN234 4.4 31.6 1.0
C A:GLY327 4.5 29.6 1.0
CG A:LYS294 4.5 29.0 1.0
CA A:TYR235 4.5 36.3 1.0
HB2 A:ASN242 4.5 25.5 1.0
HD3 A:ARG286 4.6 31.9 1.0
O A:TYR235 4.6 34.7 1.0
CG A:ARG286 4.6 26.8 1.0
C A:TYR235 4.7 35.5 1.0
NH1 A:ARG286 4.7 29.0 1.0
N A:SER237 4.7 32.2 1.0
CB A:ASN242 4.9 21.2 1.0
HB3 A:ARG286 4.9 29.2 1.0
HD21 A:ASN242 4.9 27.8 1.0
HB3 A:LYS294 4.9 32.7 1.0
N A:TYR235 4.9 31.9 1.0
CB A:ASN288 4.9 24.4 1.0
ND2 A:ASN242 5.0 23.2 1.0
OG A:SER237 5.0 26.9 1.0
CA A:SER237 5.0 37.5 1.0

Reference:

L.Van Dalsen, L.Smithers, C.Boland, D.Weichert, M.Caffrey. 9.8 Mag. A New Host Lipid For in Meso (Lipid Cubic Phase) Crystallization of Integral Membrane Proteins Cryst.Growth Des. 2020.
ISSN: ESSN 1528-7505
DOI: 10.1021/ACS.CGD.0C01301
Page generated: Thu Dec 17 13:14:28 2020

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