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Sodium in PDB 5azp: Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa

Protein crystallography data

The structure of Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa, PDB code: 5azp was solved by R.Yonehara, E.Yamashita, A.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.69
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 257.515, 257.515, 81.825, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa (pdb code 5azp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa, PDB code: 5azp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5azp

Go back to Sodium Binding Sites List in 5azp
Sodium binding site 1 out of 3 in the Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa


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 Membrane Protein From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na516

b:32.1
occ:1.00
OD1 A:ASP73 2.2 26.9 1.0
O A:HOH893 2.3 35.7 1.0
O A:HOH811 2.4 36.6 1.0
O A:ASP73 2.6 24.6 1.0
OG B:SER332 2.7 24.7 1.0
O B:HOH880 2.8 47.9 1.0
CG A:ASP73 3.4 27.6 1.0
CB B:SER332 3.4 22.8 1.0
C A:ASP73 3.5 22.7 1.0
OD1 A:ASP77 3.8 39.8 1.0
NH2 B:ARG336 3.8 34.7 0.5
CA A:ASP73 3.9 23.2 1.0
CB A:ASN76 3.9 25.9 1.0
O B:HOH1051 4.1 50.5 1.0
OD2 A:ASP73 4.2 27.9 1.0
CB A:ASP73 4.2 23.6 1.0
CG A:ASP77 4.4 32.9 1.0
CA B:SER332 4.5 21.1 1.0
N A:VAL74 4.5 22.5 1.0
OD1 B:ASP329 4.5 30.6 1.0
NH1 B:ARG336 4.5 17.6 0.5
N A:ASP77 4.6 24.6 1.0
OD2 A:ASP77 4.6 35.4 1.0
CA A:ASN76 4.7 24.0 1.0
ND2 A:ASN76 4.7 29.2 1.0
O1 A:FMT512 4.7 48.5 1.0
C A:ASN76 4.7 24.4 1.0
N A:ASN76 4.8 22.6 1.0
CG A:ASN76 4.9 27.8 1.0
O B:HOH1165 4.9 55.0 1.0
CZ B:ARG336 4.9 33.6 0.5
O A:HOH639 4.9 46.2 1.0
CA A:VAL74 5.0 22.6 1.0
OD2 B:ASP329 5.0 27.5 1.0

Sodium binding site 2 out of 3 in 5azp

Go back to Sodium Binding Sites List in 5azp
Sodium binding site 2 out of 3 in the Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa


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 Membrane Protein From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na513

b:27.9
occ:1.00
OD1 B:ASP73 2.3 21.9 1.0
O B:HOH781 2.3 35.1 1.0
O B:HOH877 2.5 36.3 1.0
O B:ASP73 2.5 22.0 1.0
OG C:SER332 2.6 22.2 1.0
O C:HOH707 2.8 42.0 1.0
C B:ASP73 3.4 20.3 1.0
CB C:SER332 3.4 20.8 1.0
CG B:ASP73 3.4 21.9 1.0
OD1 B:ASP77 3.7 38.1 1.0
CB B:ASN76 3.8 24.4 1.0
CA B:ASP73 3.8 19.0 1.0
O B:HOH1172 4.2 43.4 1.0
CB B:ASP73 4.2 19.2 1.0
CG B:ASP77 4.2 31.5 1.0
OD2 B:ASP73 4.3 22.1 1.0
OD2 B:ASP77 4.4 32.8 1.0
OD1 C:ASP329 4.4 30.5 1.0
CA C:SER332 4.4 19.3 1.0
N B:VAL74 4.5 19.2 1.0
N B:ASP77 4.5 23.9 1.0
OD1 B:ASN76 4.6 29.4 1.0
NH2 C:ARG336 4.6 25.9 1.0
CG B:ASN76 4.7 27.9 1.0
CA B:ASN76 4.7 23.4 1.0
C B:ASN76 4.7 23.9 1.0
N B:ASN76 4.8 21.4 1.0
OD2 C:ASP329 4.9 27.5 1.0

Sodium binding site 3 out of 3 in 5azp

Go back to Sodium Binding Sites List in 5azp
Sodium binding site 3 out of 3 in the Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Membrane Protein From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na516

b:30.5
occ:1.00
O A:HOH690 2.3 33.9 1.0
OD1 C:ASP73 2.3 26.2 1.0
O C:HOH785 2.4 38.8 1.0
O C:ASP73 2.5 22.6 1.0
OG A:SER332 2.7 23.8 1.0
O2 A:FMT514 2.8 54.5 1.0
C A:FMT514 3.1 49.7 1.0
O1 A:FMT514 3.1 49.9 1.0
C C:ASP73 3.4 22.9 1.0
CB A:SER332 3.4 22.4 1.0
CG C:ASP73 3.4 24.7 1.0
OD1 C:ASP77 3.7 38.4 1.0
CB C:ASN76 3.9 25.5 1.0
CA C:ASP73 3.9 22.5 1.0
O A:HOH610 4.2 45.5 1.0
CG C:ASP77 4.2 32.9 1.0
CB C:ASP73 4.2 23.7 1.0
OD2 C:ASP73 4.3 24.6 1.0
OD2 C:ASP77 4.3 35.8 1.0
N C:VAL74 4.4 22.1 1.0
CA A:SER332 4.4 20.9 1.0
OD1 A:ASP329 4.5 28.0 1.0
NH2 A:ARG336 4.5 28.3 1.0
N C:ASP77 4.6 22.7 1.0
ND2 C:ASN76 4.6 29.2 1.0
O A:HOH720 4.7 62.4 1.0
CA C:ASN76 4.7 24.0 1.0
C C:ASN76 4.7 23.6 1.0
N C:ASN76 4.8 22.5 1.0
CG C:ASN76 4.8 29.0 1.0
CA C:VAL74 4.8 22.9 1.0
O C:HOH1063 4.8 36.2 1.0
O C:HOH857 4.8 40.3 1.0

Reference:

R.Yonehara, E.Yamashita, A.Nakagawa. Crystal Structures of Oprn and Oprj, Outer Membrane Factors of Multidrug Tripartite Efflux Pumps of Pseudomonas Aeruginosa. Proteins V. 84 759 2016.
ISSN: ESSN 1097-0134
PubMed: 26914226
DOI: 10.1002/PROT.25022
Page generated: Tue Dec 15 10:24:22 2020

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