Iodine in PDB 8kg4: Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form

The structure of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form, PDB code: 8kg4 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)	39.71 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.825, 50.853, 125.488, 90, 90, 90
R / Rfree (%)	16.9 / 18.8

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

Sodium

(Na)

2 atoms

Pages:

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

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 - Orthorhombic Form (pdb code 8kg4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form, PDB code: 8kg4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:24.4 occ:1.00 O A:HOH683 3.4 20.1 1.0 CG2 A:THR262 3.8 8.2 1.0 CB A:THR262 4.1 8.0 1.0 CA A:THR262 4.3 7.3 1.0 CE A:LYS305 4.8 16.9 1.0 OD2 A:ASP261 4.9 24.3 1.0 O A:ASP261 5.0 10.8 1.0

Iodine binding site 2 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:14.8 occ:1.00 N A:GLY373 3.4 9.7 1.0 N A:ASN372 3.8 9.2 1.0 N A:LYS371 3.9 6.0 1.0 CG2 A:VAL370 3.9 7.0 1.0 C A:LYS371 3.9 7.4 1.0 CA A:GLY373 4.0 11.3 1.0 CA A:LYS371 4.0 6.6 1.0 CB A:VAL370 4.1 6.1 1.0 C A:VAL370 4.2 5.7 1.0 O A:HOH647 4.3 10.7 1.0 C A:ASN372 4.4 11.2 1.0 O A:VAL370 4.5 6.3 1.0 CA A:ASN372 4.6 10.9 1.0 O A:LYS371 4.6 8.3 1.0 C A:GLY373 4.7 9.7 1.0 N A:GLN374 4.8 9.1 1.0 CA A:VAL370 4.8 5.8 1.0

Iodine binding site 3 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:51.9 occ:1.00 N A:ALA420 3.5 11.0 1.0 CA A:GLU419 3.8 30.0 1.0 CG A:GLU419 3.8 30.0 1.0 CB A:GLU419 4.0 30.0 1.0 OE1 A:GLU419 4.2 30.0 1.0 C A:GLU419 4.2 30.0 1.0 CB A:ALA420 4.3 14.3 1.0 O A:HOH748 4.4 28.4 1.0 CD A:GLU419 4.4 30.0 1.0 CA A:ALA420 4.6 12.3 1.0

Iodine binding site 4 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:30.9 occ:1.00 O A:HOH712 3.6 17.9 1.0 N A:HIS220 3.7 5.6 1.0 O A:HOH649 3.8 21.6 1.0 CD2 A:HIS220 3.9 7.4 1.0 CE1 A:PHE342 3.9 7.5 1.0 O A:HOH787 4.0 20.7 1.0 CA A:HIS219 4.1 7.2 1.0 CD1 A:PHE342 4.2 6.4 1.0 O A:SER218 4.2 12.6 1.0 CB A:HIS220 4.2 5.7 1.0 CG A:HIS220 4.3 6.1 1.0 C A:HIS219 4.4 6.5 1.0 CA A:HIS220 4.6 5.5 1.0 CZ A:PHE342 4.8 8.0 1.0 C A:SER218 4.9 8.9 1.0 N A:HIS219 5.0 7.8 1.0 O A:GLU340 5.0 6.1 1.0 NE2 A:HIS220 5.0 7.6 1.0

Iodine binding site 5 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:31.3 occ:1.00 I A:IOD508 2.3 46.5 1.0 O A:HOH780 3.4 18.4 1.0 O A:HOH653 3.6 9.9 1.0 CG2 A:THR274 4.0 10.4 1.0 CB A:LYS276 4.2 7.2 1.0 CG A:LYS276 4.7 8.6 1.0 OG1 A:THR286 4.8 9.6 1.0 CB A:THR274 4.9 9.4 1.0 CD A:LYS276 4.9 10.0 1.0

Iodine binding site 6 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:42.9 occ:1.00 CG2 A:THR325 3.8 7.4 1.0 O A:HOH699 3.8 12.6 1.0 CD A:LYS327 3.9 9.3 1.0 CB A:ALA332 4.1 7.4 1.0 O A:HOH718 4.2 22.4 1.0 CE A:LYS327 4.5 10.7 1.0 CB A:THR325 4.5 6.5 1.0 CB A:LYS327 4.5 6.8 1.0 NZ A:LYS327 4.5 11.2 1.0 CG A:LYS327 4.7 7.5 1.0 O A:HOH667 4.8 14.3 1.0

Iodine binding site 7 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:44.7 occ:1.00 O A:HOH621 3.2 24.8 1.0 N A:LYS227 3.5 7.0 1.0 CA A:GLU226 4.0 6.6 1.0 CB A:GLU226 4.1 7.4 1.0 C A:GLU226 4.2 6.4 1.0 CG A:GLU226 4.2 7.9 1.0 CB A:LYS227 4.4 10.4 1.0 CA A:LYS227 4.4 7.6 1.0 CG A:LYS227 4.6 13.8 1.0 O A:LYS227 4.6 7.5 1.0 CD A:GLU226 4.9 8.7 1.0

Iodine binding site 8 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:46.5 occ:1.00 I A:IOD505 2.3 31.3 1.0 OG1 A:THR286 4.2 9.6 1.0 O A:HOH653 4.2 9.9 1.0 CB A:THR286 4.3 7.8 1.0 CG2 A:THR274 4.3 10.4 1.0 CG2 A:THR286 4.4 9.8 1.0 O A:HOH780 4.5 18.4 1.0 CB A:THR274 4.5 9.4 1.0 OG1 A:THR274 4.9 12.2 1.0

Iodine binding site 9 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:54.4 occ:1.00 O A:HOH709 3.4 19.1 1.0 C A:ASN214 3.7 6.3 1.0 N A:ASP215 3.8 6.5 1.0 O A:ASN214 3.9 7.2 1.0 N A:ASN216 4.0 8.4 1.0 O A:HOH687 4.1 18.1 1.0 CB A:ASN216 4.1 14.3 1.0 CB A:ASN214 4.2 7.0 1.0 CA A:ASN214 4.2 6.0 1.0 CA A:ASP215 4.2 6.6 1.0 C A:ASP215 4.4 7.7 1.0 O A:HOH755 4.5 18.9 1.0 CA A:ASN216 4.6 10.6 1.0

Iodine binding site 10 out of 11 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:48.5 occ:1.00 O A:HOH769 3.0 22.2 1.0 N A:ASP280 3.5 7.3 1.0 CG A:ASP280 3.8 7.2 1.0 O A:HOH751 3.8 20.5 1.0 CB A:ASP280 3.8 7.7 1.0 OD1 A:ASP280 3.8 7.0 1.0 N A:ALA279 3.9 7.7 1.0 CB A:ASN278 4.0 6.6 1.0 CB A:ALA279 4.2 10.6 1.0 OD2 A:ASP280 4.3 9.0 1.0 C A:ALA279 4.3 8.2 1.0 CA A:ASP280 4.3 6.8 1.0 CA A:ALA279 4.3 9.0 1.0 O A:HOH641 4.5 7.0 1.0 C A:ASN278 4.6 6.5 1.0 CG A:ASN278 4.8 6.6 1.0 CA A:ASN278 4.9 6.1 1.0

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