Sodium in PDB 6i9o: Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis

Protein crystallography data

The structure of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis, PDB code: 6i9o was solved by T.N.Trinh, C.Cambillau, A.Roussel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.35 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.030, 52.220, 66.560, 90.00, 108.38, 90.00
R / Rfree (%) 18.4 / 21.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis (pdb code 6i9o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis, PDB code: 6i9o:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6i9o

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Sodium binding site 1 out of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:34.6
occ:1.00
O A:HOH350 2.3 54.1 1.0
O A:ALA117 2.3 35.4 1.0
O A:LEU123 2.3 38.1 1.0
O A:HIS120 2.4 34.7 1.0
O A:HOH459 2.5 41.7 1.0
O A:HOH425 2.7 40.4 1.0
C A:ALA117 3.3 35.8 1.0
C A:HIS120 3.5 36.4 1.0
C A:LEU123 3.6 37.4 1.0
O A:ASP121 3.7 46.0 1.0
CA A:ALA117 3.8 31.9 1.0
CA A:ASP121 3.8 38.4 1.0
C A:ASP121 3.8 42.8 1.0
N A:ASP121 4.0 35.5 1.0
CB A:ALA117 4.0 32.7 1.0
N A:LEU123 4.1 33.7 1.0
CA A:LEU123 4.4 32.8 1.0
O A:HOH468 4.4 42.3 1.0
N A:GLU118 4.4 31.5 1.0
CD A:LYS124 4.5 63.7 1.0
NZ A:LYS124 4.5 83.7 1.0
N A:LYS124 4.5 34.0 1.0
N A:PHE122 4.6 36.1 1.0
CA A:HIS120 4.6 32.2 1.0
N A:HIS120 4.6 31.9 1.0
CA A:LYS124 4.7 33.3 1.0
CA A:GLU118 4.9 31.2 1.0
CE A:LYS124 4.9 75.8 1.0
CB A:LEU123 4.9 31.6 1.0
O A:HOH397 4.9 39.4 1.0

Sodium binding site 2 out of 4 in 6i9o

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Sodium binding site 2 out of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:29.2
occ:1.00
O B:LEU123 2.2 32.1 1.0
O B:ALA117 2.3 27.5 1.0
O B:HOH329 2.4 41.1 1.0
O B:HOH438 2.4 42.2 1.0
O B:HIS120 2.4 30.2 1.0
O B:HOH453 2.5 33.5 1.0
C B:ALA117 3.3 28.7 1.0
C B:LEU123 3.4 32.3 1.0
C B:HIS120 3.5 30.7 1.0
CA B:ALA117 3.8 25.9 1.0
CA B:ASP121 3.9 32.9 1.0
C B:ASP121 4.0 38.8 1.0
CB B:ALA117 4.0 27.2 1.0
N B:LEU123 4.0 28.5 1.0
O B:HOH489 4.0 51.6 1.0
O B:ASP121 4.1 43.9 1.0
N B:ASP121 4.1 30.8 1.0
CA B:LEU123 4.3 27.9 1.0
O B:HOH469 4.4 37.0 1.0
N B:LYS124 4.4 29.9 1.0
N B:GLU118 4.5 26.8 1.0
N B:HIS120 4.6 26.2 1.0
CA B:HIS120 4.6 27.6 1.0
CA B:LYS124 4.6 29.9 1.0
N B:PHE122 4.7 31.4 1.0
CB B:LEU123 4.8 26.8 1.0
CA B:GLU118 4.9 28.6 1.0
O B:HOH389 5.0 33.2 1.0

Sodium binding site 3 out of 4 in 6i9o

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Sodium binding site 3 out of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:46.0
occ:1.00
O C:ALA117 2.2 36.3 1.0
O C:LEU123 2.2 45.2 1.0
O C:HIS120 2.2 41.3 1.0
O C:HOH357 2.8 69.2 1.0
O C:HOH433 2.9 56.2 1.0
C C:ALA117 3.2 36.9 1.0
C C:HIS120 3.3 42.5 1.0
C C:LEU123 3.4 44.8 1.0
CA C:ALA117 3.6 33.7 1.0
O C:ASP121 3.8 55.1 1.0
CA C:ASP121 3.8 46.2 1.0
C C:ASP121 3.8 52.1 1.0
N C:ASP121 3.9 42.7 1.0
N C:LEU123 3.9 41.6 1.0
CB C:ALA117 3.9 35.4 1.0
CA C:LEU123 4.2 40.8 1.0
N C:GLU118 4.4 32.5 1.0
CA C:HIS120 4.4 36.6 1.0
N C:HIS120 4.5 35.1 1.0
N C:LYS124 4.5 40.9 1.0
N C:PHE122 4.5 46.4 1.0
NZ C:LYS124 4.5 0.2 1.0
O C:HOH442 4.6 49.2 1.0
CD C:LYS124 4.6 74.6 1.0
CB C:LEU123 4.7 38.6 1.0
CA C:LYS124 4.7 40.4 1.0
CA C:GLU118 4.9 32.5 1.0
CE C:LYS124 4.9 91.6 1.0
C C:PHE122 5.0 47.2 1.0
N C:ALA117 5.0 32.5 1.0

Sodium binding site 4 out of 4 in 6i9o

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Sodium binding site 4 out of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:37.4
occ:1.00
O D:ALA117 2.2 35.8 1.0
O D:HIS120 2.2 39.4 1.0
O D:LEU123 2.4 37.0 1.0
O D:HOH431 2.7 47.2 1.0
C D:ALA117 3.3 35.1 1.0
C D:HIS120 3.3 38.7 1.0
C D:LEU123 3.6 38.9 1.0
CA D:ASP121 3.8 38.9 1.0
CA D:ALA117 3.8 29.6 1.0
O D:ASP121 3.8 46.6 1.0
C D:ASP121 3.9 44.7 1.0
N D:ASP121 3.9 37.9 1.0
N D:LEU123 4.0 37.0 1.0
CB D:ALA117 4.1 31.1 1.0
CA D:LEU123 4.3 34.1 1.0
CA D:HIS120 4.4 34.5 1.0
N D:HIS120 4.4 34.2 1.0
N D:GLU118 4.4 32.5 1.0
NZ D:LYS124 4.5 64.2 1.0
N D:PHE122 4.6 39.7 1.0
CD D:LYS124 4.6 52.5 1.0
N D:LYS124 4.6 35.7 1.0
O D:HOH370 4.7 51.7 1.0
CA D:GLU118 4.8 34.1 1.0
CB D:LEU123 4.8 31.2 1.0
CA D:LYS124 4.8 35.4 1.0
C D:GLU118 4.9 38.1 1.0
CE D:LYS124 4.9 59.5 1.0

Reference:

T.N.Trinh, C.Cambillau, A.Roussel. Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis To Be Published.
Page generated: Tue Dec 15 12:23:53 2020

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