Iodine in PDB 8kb2: Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative

The structure of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative, PDB code: 8kb2 was solved by A.Prajapati, A.Palva, I.Von Ossowski, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.58 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.903, 50.898, 125.623, 90, 90, 90
R / Rfree (%)	17.9 / 21.1

The structure of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative (pdb code 8kb2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative, PDB code: 8kb2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:26.4 occ:0.88 N A:GLY373 3.3 24.9 1.0 N A:ASN372 3.8 23.6 1.0 CG2 A:VAL370 3.9 14.8 1.0 CA A:GLY373 3.9 25.2 1.0 N A:LYS371 4.0 17.2 1.0 C A:LYS371 4.0 21.0 1.0 CA A:LYS371 4.0 19.5 1.0 CB A:VAL370 4.2 15.1 1.0 O A:HOH623 4.3 21.9 1.0 C A:VAL370 4.3 15.5 1.0 C A:ASN372 4.4 25.8 1.0 O A:VAL370 4.5 14.8 1.0 CA A:ASN372 4.5 26.2 1.0 O A:LYS371 4.7 19.5 1.0 C A:GLY373 4.8 24.5 1.0 N A:GLN374 4.9 22.7 1.0 CA A:VAL370 4.9 14.9 1.0

Iodine binding site 2 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:29.9 occ:0.69 CG2 A:THR262 3.9 19.0 1.0 CB A:THR262 4.2 18.1 1.0 CA A:THR262 4.3 18.5 1.0 CD A:LYS305 4.8 27.3 1.0 O A:ASP261 4.9 23.6 1.0

Iodine binding site 3 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:31.6 occ:0.28 NE2 A:GLN455 3.6 23.1 1.0 O A:HOH745 3.7 36.9 1.0 CG A:GLN455 4.6 21.3 1.0 CD A:GLN455 4.6 22.4 1.0

Iodine binding site 4 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:34.8 occ:0.22 CG A:HIS380 4.0 18.3 1.0 CB A:HIS380 4.1 16.6 1.0 ND1 A:HIS380 4.2 20.2 1.0 CD2 A:HIS380 4.4 20.6 1.0 CE1 A:HIS380 4.6 21.0 1.0 ND2 A:ASN392 4.7 43.9 1.0 OG1 A:THR388 4.8 25.9 1.0 NE2 A:HIS380 4.8 21.0 1.0 CB A:ASN395 5.0 18.2 1.0

Iodine binding site 5 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:36.9 occ:0.27 CG2 A:THR325 3.9 17.4 1.0 CD A:LYS327 4.0 26.3 1.0 CB A:ALA332 4.1 19.7 1.0 O A:HOH687 4.2 32.0 1.0 O A:HOH693 4.2 27.1 1.0 CE A:LYS327 4.5 27.8 1.0 NZ A:LYS327 4.6 29.1 1.0 CB A:THR325 4.7 16.3 1.0 CB A:LYS327 4.7 18.6 1.0 CG A:LYS327 4.8 22.5 1.0

Iodine binding site 6 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:29.8 occ:0.19 N A:ASN330 3.6 21.5 1.0 CB A:ASN330 3.8 25.4 1.0 CB A:ASP329 4.0 22.3 1.0 CG A:GLU331 4.0 35.0 1.0 CA A:ASN330 4.1 22.9 1.0 N A:GLU331 4.3 21.8 1.0 ND2 A:ASN330 4.4 26.9 1.0 C A:ASN330 4.4 23.1 1.0 CG A:ASN330 4.6 26.6 1.0 C A:ASP329 4.6 20.6 1.0 O A:VAL328 4.7 16.3 1.0 CD A:GLU331 4.7 38.9 1.0 OE2 A:GLU331 4.7 43.1 1.0 CB A:GLU331 4.9 26.3 1.0 CA A:ASP329 4.9 20.4 1.0 OD2 A:ASP329 5.0 28.0 1.0

Iodine binding site 7 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:40.9 occ:0.22 C A:ASN214 3.7 22.4 1.0 N A:ASP215 3.8 22.1 1.0 N A:ASN216 3.9 26.8 1.0 O A:ASN214 3.9 20.8 1.0 CB A:ASN216 4.0 38.6 1.0 O A:HOH610 4.1 27.6 1.0 CB A:ASN214 4.2 23.6 1.0 CA A:ASN214 4.2 21.1 1.0 CA A:ASP215 4.2 23.2 1.0 O A:HOH716 4.2 34.5 1.0 C A:ASP215 4.4 25.4 1.0 CA A:ASN216 4.6 32.6 1.0

Iodine binding site 8 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:30.1 occ:0.18 O A:HOH617 4.3 31.1 1.0

Iodine binding site 9 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:36.6 occ:0.22 I A:IOD513 2.2 34.1 0.3 CG A:LYS358 3.9 29.3 1.0 ND2 A:ASN355 4.1 36.6 1.0 NZ A:LYS466 4.2 43.4 1.0 I A:IOD512 4.2 37.2 0.3 CE A:LYS358 4.4 40.6 1.0 CB A:LYS358 4.4 26.4 1.0 CD A:LYS358 4.4 34.9 1.0 OD2 A:ASP352 4.5 31.1 1.0 CE A:LYS466 4.6 42.6 1.0 OH A:TYR435 4.8 21.9 1.0 CB A:ASN355 4.8 33.3 1.0 CG A:ASN355 4.9 35.0 1.0 CG A:ASP352 5.0 27.0 1.0

Iodine binding site 10 out of 13 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:48.5 occ:0.18 NZ A:LYS358 3.0 44.7 1.0 CE A:LYS358 3.7 40.6 1.0 I A:IOD512 4.2 37.2 0.3

A.Prajapati, A.Palva, I.Von Ossowski, V.Krishnan. The Crystal Structure of the N-Terminal Domain of the Backbone Pilin Lrpa Reveals A New Closure-and-Twist Motion For Assembling Dynamic Pili in Ligilactobacillus Ruminis. Acta Crystallogr D Struct 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38935340
DOI: 10.1107/S2059798324005114