Iodine in PDB 7w6b: Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis

The structure of Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis, PDB code: 7w6b was solved by R.K.Yadav, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.93 / 2.98
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.271, 422.928, 48.391, 90, 90, 90
R / Rfree (%)	25.3 / 30.5

The structure of Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis (pdb code 7w6b). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis, PDB code: 7w6b:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I902 b:64.1 occ:0.76 N A:ILE586 3.7 20.7 1.0 CA A:GLU585 4.2 21.3 1.0 CD1 A:ILE586 4.4 20.0 1.0 O A:ILE586 4.4 21.5 1.0 CB A:ILE586 4.5 20.1 1.0 O A:LYS584 4.5 20.7 1.0 CG1 A:ILE586 4.5 20.2 1.0 C A:GLU585 4.5 21.7 1.0 CA A:ILE586 4.6 20.5 1.0 CE A:LYS584 4.8 17.3 1.0 N A:GLU585 4.8 20.6 1.0 C A:LYS584 4.8 19.6 1.0

Iodine binding site 2 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I903 b:66.8 occ:0.65 CG A:ARG737 3.7 65.3 1.0 CD A:ARG737 3.9 69.9 1.0 O A:ILE736 3.9 41.7 1.0 CB A:ASN735 4.1 45.0 1.0 NE A:ARG737 4.1 80.3 1.0 C A:ILE736 4.1 43.4 1.0 N A:ILE736 4.4 39.0 1.0 N A:ARG737 4.4 48.1 1.0 O A:GLY764 4.4 39.4 1.0 CB A:ARG737 4.5 60.6 1.0 O A:ASN763 4.6 38.1 1.0 C A:ASN735 4.6 40.3 1.0 CZ A:ARG737 4.6 82.1 1.0 CA A:GLY764 4.6 39.3 1.0 CA A:ARG737 4.7 54.7 1.0 OD1 A:ASN735 4.7 51.2 1.0 CA A:ASN735 4.7 41.7 1.0 CA A:PRO743 4.7 56.5 1.0 C A:GLY764 4.8 40.4 1.0 CA A:ILE736 4.8 39.8 1.0 CB A:PRO743 4.8 57.2 1.0 CG A:ASN735 4.9 49.1 1.0 NH1 A:ARG737 4.9 82.6 1.0

Iodine binding site 3 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I904 b:57.7 occ:0.61 N A:ASP700 4.0 21.5 1.0 CG2 A:THR513 4.0 25.9 1.0 CB A:ASP700 4.2 23.1 1.0 OG1 A:THR513 4.2 25.7 1.0 CB A:VAL512 4.3 22.1 1.0 CG1 A:VAL512 4.3 21.6 1.0 OD2 A:ASP700 4.4 25.2 1.0 CB A:LYS699 4.4 18.2 1.0 CG A:ASP700 4.4 24.5 1.0 CB A:THR513 4.7 25.8 1.0 CA A:ASP700 4.7 21.8 1.0 CA A:LYS699 4.8 19.6 1.0 N A:THR513 4.9 24.9 1.0 C A:LYS699 4.9 20.4 1.0

Iodine binding site 4 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:66.6 occ:0.60 O A:HOH1016 3.4 13.2 1.0 N A:GLU564 3.5 41.8 1.0 CA A:PHE563 3.7 34.4 1.0 O A:LYS547 3.8 28.4 1.0 O A:ASN562 4.0 33.6 1.0 C A:PHE563 4.2 38.2 1.0 CD A:ARG546 4.3 28.6 1.0 CB A:ARG546 4.3 28.1 1.0 O A:GLU564 4.4 45.6 1.0 CB A:PHE563 4.5 34.1 1.0 CA A:GLU564 4.6 45.1 1.0 CD1 A:PHE563 4.6 33.4 1.0 CB A:GLU564 4.6 52.0 1.0 N A:LYS547 4.7 28.2 1.0 N A:PHE563 4.7 32.4 1.0 C A:LYS547 4.8 28.2 1.0 CG A:ARG546 4.8 28.3 1.0 C A:ASN562 4.8 33.1 1.0 CG A:GLU564 4.9 62.3 1.0 C A:GLU564 4.9 44.5 1.0

Iodine binding site 5 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I906 b:61.9 occ:0.82 CB A:ASN725 4.0 67.8 1.0 CG1 A:VAL722 4.0 75.9 1.0 CG2 A:VAL719 4.0 64.8 1.0 CE2 A:PHE730 4.1 56.0 1.0 CB A:LYS728 4.2 73.3 1.0 CG1 A:VAL719 4.2 61.8 1.0 CA A:LYS728 4.2 75.5 1.0 CZ A:PHE730 4.2 58.4 1.0 CG2 A:VAL722 4.3 73.6 1.0 OH A:TYR799 4.4 59.3 1.0 O A:LEU727 4.4 74.5 1.0 CB A:VAL719 4.5 63.1 1.0 ND2 A:ASN725 4.6 67.3 1.0 CB A:VAL722 4.6 72.5 1.0 CG A:ASN725 4.7 70.2 1.0 C A:LEU727 4.7 73.8 1.0 CB A:LYS772 4.8 63.4 1.0 CD A:LYS772 4.8 69.3 1.0 N A:LYS728 4.9 69.7 1.0

Iodine binding site 6 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I907 b:83.4 occ:0.96 N A:LYS496 3.7 65.3 1.0 CA A:PHE495 3.9 67.0 1.0 CG A:PRO51 4.1 62.5 1.0 CB A:PHE495 4.2 62.1 1.0 CB A:PRO51 4.2 61.8 1.0 CD A:PRO51 4.3 64.4 1.0 C A:PHE495 4.4 66.8 1.0 O A:LYS496 4.5 61.0 1.0 CB A:LYS496 4.5 66.0 1.0 CE1 A:TYR59 4.6 48.5 1.0 CA A:LYS496 4.7 63.1 1.0 O A:THR494 4.7 70.2 1.0 CD1 A:TYR59 4.7 50.2 1.0

Iodine binding site 7 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I908 b:54.0 occ:0.71 OG1 A:THR747 3.7 40.1 1.0 N A:THR749 3.8 36.9 1.0 OG1 A:THR749 3.8 37.8 1.0 C A:TYR748 3.8 36.4 1.0 CA A:THR749 4.2 37.4 1.0 O A:TYR748 4.2 35.3 1.0 CA A:TYR748 4.2 37.0 1.0 CA A:PRO758 4.2 38.1 1.0 CB A:PRO758 4.2 38.4 1.0 O A:THR747 4.3 37.3 1.0 C A:THR747 4.4 38.5 1.0 N A:TYR748 4.4 38.0 1.0 CB A:THR749 4.5 36.5 1.0 CB A:THR747 4.7 39.9 1.0 CG2 A:THR749 4.9 35.8 1.0 N A:PRO758 5.0 39.3 1.0

Iodine binding site 8 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I909 b:93.1 occ:0.54 NZ A:LYS587 3.0 26.6 1.0 CE A:LYS587 3.7 26.4 1.0 CD A:LYS598 3.7 15.2 1.0 NZ A:LYS598 3.8 16.2 1.0 CE A:LYS598 4.3 15.7 1.0 CG1 A:VAL589 4.5 25.9 1.0

Iodine binding site 9 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I910 b:68.0 occ:0.61 CA A:THR591 4.0 35.6 1.0 N A:GLU592 4.0 38.8 1.0 O A:HOH1014 4.0 17.8 1.0 CB A:THR591 4.3 34.7 1.0 C A:THR591 4.3 37.6 1.0 O A:GLY590 4.9 33.8 1.0 CB A:GLU592 4.9 40.8 1.0

Iodine binding site 10 out of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis


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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range: probe atom residue distance (Å) B Occ A:I911 b:60.4 occ:0.44 OD1 A:ASN551 2.2 29.5 1.0 O A:SER525 2.9 32.2 1.0 CG A:ASN551 3.2 26.3 1.0 O A:VAL552 3.3 26.9 1.0 ND2 A:ASN551 3.6 26.2 1.0 C A:VAL552 3.8 26.6 1.0 C A:SER525 3.8 30.8 1.0 N A:VAL552 3.8 24.7 1.0 CA A:SER525 4.1 30.4 1.0 CB A:SER525 4.1 31.8 1.0 N A:SER553 4.3 29.7 1.0 CA A:VAL552 4.4 25.3 1.0 CB A:ASN551 4.5 25.2 1.0 CA A:SER553 4.5 33.6 1.0 C A:ASN551 4.7 24.3 1.0 CA A:ASN551 4.7 24.3 1.0 OG A:SER525 5.0 34.9 1.0

R.K.Yadav, V.Krishnan. New Structural Insights Into the Pi-2 Pilus From Streptococcus Oralis, An Early Dental Plaque Colonizer. Febs J. V. 289 6342 2022.
ISSN: ISSN 1742-464X
PubMed: 35561142
DOI: 10.1111/FEBS.16527