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Iodine in PDB 7f7y: Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae

Protein crystallography data

The structure of Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae, PDB code: 7f7y 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) 54.98 / 2.13
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 73.49, 82.659, 362.193, 90, 90, 90
R / Rfree (%) 19.8 / 23.5

Other elements in 7f7y:

The structure of Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae also contains other interesting chemical elements:

Potassium (K) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae (pdb code 7f7y). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae, PDB code: 7f7y:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 7f7y

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Iodine binding site 1 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2201

b:21.9
occ:0.92
 O A:HOH2393 3.3 16.9 1.0
ND2 A:ASN59 3.3 19.5 1.0
N A:TYR135 3.6 8.5 1.0
OD1 A:ASN59 3.8 23.0 1.0
CG A:ASN59 4.0 21.8 1.0
CA A:ALA134 4.1 10.3 1.0
O A:VAL186 4.2 11.7 1.0
CD1 A:TYR135 4.2 8.0 1.0
CG1 A:ILE188 4.3 13.1 1.0
CA A:TYR187 4.3 13.3 1.0
CB A:TYR135 4.3 8.1 1.0
C A:ALA134 4.4 9.9 1.0
O A:VAL133 4.4 11.3 1.0
CA A:TYR135 4.5 8.2 1.0
O A:TYR135 4.5 8.8 1.0
N A:ILE188 4.6 12.2 1.0
CG2 A:VAL186 4.6 11.6 1.0
CD1 A:ILE188 4.6 14.1 1.0
C A:VAL186 4.6 12.2 1.0
C A:TYR187 4.7 11.9 1.0
N A:TYR187 4.7 12.6 1.0
CG A:TYR135 4.8 7.8 1.0
C A:TYR135 5.0 8.8 1.0
CB A:ALA134 5.0 11.1 1.0

Iodine binding site 2 out of 9 in 7f7y

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Iodine binding site 2 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2204

b:32.3
occ:1.00
 NZ A:LYS308 3.8 13.4 1.0
CB B:GLN234 3.9 23.3 1.0
O A:HOH2434 4.0 20.0 1.0
ND2 B:ASN228 4.1 24.9 1.0
CB B:ASN228 4.1 22.7 1.0
N A:ASP258 4.1 11.2 1.0
O A:THR256 4.2 9.7 1.0
CG B:GLN234 4.2 23.2 1.0
OD2 A:ASP258 4.2 20.0 1.0
CA A:ARG257 4.3 10.5 1.0
CG A:ASP258 4.3 16.3 1.0
CG B:ASN228 4.6 22.6 1.0
C A:ARG257 4.6 10.6 1.0
CD B:GLN234 4.7 25.0 1.0
CB A:ASP258 4.7 13.8 1.0
OD1 A:ASP258 4.7 15.9 1.0
CG B:PRO227 5.0 21.7 1.0
CA B:ASN228 5.0 22.7 1.0
N B:ASN228 5.0 21.3 1.0

Iodine binding site 3 out of 9 in 7f7y

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Iodine binding site 3 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2205

b:64.2
occ:1.00
 NZ A:LYS255 3.9 16.1 1.0
O A:GLY250 4.4 15.1 1.0
CA A:ALA251 4.5 15.0 1.0
N A:ALA251 4.6 15.8 1.0
C A:GLY250 4.6 15.9 1.0
CE A:LYS255 4.7 15.1 1.0

Iodine binding site 4 out of 9 in 7f7y

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Iodine binding site 4 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2206

b:83.0
occ:1.00
 NZ A:LYS368 3.8 20.0 1.0
CA A:ASN228 3.9 22.7 1.0
CB A:ASN228 3.9 22.9 1.0
O A:PRO227 4.1 19.0 1.0
I A:IOD2207 4.1 85.2 1.0
C A:PRO227 4.2 19.0 1.0
N A:ASN228 4.2 19.9 1.0
CG A:ASN228 4.3 23.1 1.0
CB A:PRO227 4.5 16.9 1.0
ND2 A:ASN228 4.6 23.6 1.0
OD1 A:ASN228 4.8 22.6 1.0
CE A:LYS368 4.9 18.0 1.0
CG A:PRO227 4.9 17.3 1.0

Iodine binding site 5 out of 9 in 7f7y

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Iodine binding site 5 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2207

b:85.2
occ:1.00
 O A:HOH2506 3.7 16.9 1.0
ND2 A:ASN228 3.8 23.6 1.0
CB A:GLN234 3.8 23.2 1.0
I A:IOD2206 4.1 83.0 1.0
CG A:GLN234 4.2 24.5 1.0
CB A:ASN228 4.2 22.9 1.0
CG A:ASN228 4.5 23.1 1.0
CD A:GLN234 4.7 24.9 1.0
O A:GLN234 4.9 24.9 1.0

Iodine binding site 6 out of 9 in 7f7y

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Iodine binding site 6 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2208

b:50.7
occ:1.00
 OG1 A:THR325 3.2 10.8 1.0
OD1 A:ASP361 3.4 35.6 1.0
O A:HOH2452 3.5 24.3 1.0
O A:HOH2313 3.7 20.5 1.0
CD A:LYS264 3.8 19.4 1.0
O A:LYS264 3.9 9.0 1.0
CB A:GLN266 3.9 8.7 1.0
O A:LYS323 3.9 8.6 1.0
CB A:THR325 3.9 10.2 1.0
N A:THR325 4.0 8.3 1.0
C A:TYR324 4.1 8.2 1.0
CA A:TYR324 4.2 7.3 1.0
C A:LYS323 4.3 8.6 1.0
N A:GLN266 4.3 7.6 1.0
N A:TYR324 4.4 7.8 1.0
O A:TYR324 4.5 8.6 1.0
CG A:LYS264 4.6 16.4 1.0
CB A:LYS323 4.6 10.9 1.0
CA A:THR325 4.6 9.5 1.0
C A:LYS264 4.6 9.4 1.0
CG A:ASP361 4.6 28.9 1.0
CA A:ASP361 4.8 16.1 1.0
CA A:GLN266 4.8 8.1 1.0
N A:ASP361 4.8 16.3 1.0
CB A:LYS264 4.8 13.0 1.0
C A:ILE265 5.0 8.0 1.0

Iodine binding site 7 out of 9 in 7f7y

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Iodine binding site 7 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I901

b:19.5
occ:0.94
 O B:HOH1108 3.4 10.0 1.0
ND2 B:ASN59 3.4 21.4 1.0
N B:TYR135 3.5 8.1 1.0
O B:HOH1025 3.6 13.8 1.0
OD1 B:ASN59 3.9 17.1 1.0
CD2 B:TYR135 4.1 6.9 1.0
CG B:ASN59 4.1 19.4 1.0
CG1 B:ILE188 4.1 10.6 1.0
O B:VAL186 4.1 10.5 1.0
CB B:TYR135 4.2 7.3 1.0
CA B:ALA134 4.2 10.7 1.0
C B:ALA134 4.3 9.3 1.0
CA B:TYR187 4.4 12.1 1.0
CA B:TYR135 4.4 8.1 1.0
O B:VAL133 4.5 12.7 1.0
CG2 B:VAL186 4.5 10.5 1.0
C B:VAL186 4.6 10.9 1.0
N B:ILE188 4.6 10.7 1.0
O B:TYR135 4.6 8.8 1.0
CG B:TYR135 4.6 7.0 1.0
CD1 B:ILE188 4.6 11.2 1.0
N B:TYR187 4.7 11.0 1.0
C B:TYR187 4.8 11.0 1.0
C B:TYR135 5.0 8.4 1.0

Iodine binding site 8 out of 9 in 7f7y

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Iodine binding site 8 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I905

b:80.4
occ:1.00
 NZ B:LYS255 4.1 19.8 1.0
CE B:LYS255 4.6 19.0 1.0
O B:GLY250 4.6 14.9 1.0
CA B:ALA251 4.6 15.6 1.0
C B:GLY250 4.7 17.3 1.0
N B:ALA251 4.8 15.5 1.0

Iodine binding site 9 out of 9 in 7f7y

Go back to Iodine Binding Sites List in 7f7y
Iodine binding site 9 out of 9 in the Crystal Structure of Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae


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 Protein Pitb From Pilus Islet-2 of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I906

b:50.4
occ:1.00
 OG1 B:THR325 3.3 15.5 1.0
OD1 B:ASP361 3.3 46.6 1.0
N B:THR325 3.8 14.1 1.0
O B:LYS264 3.9 14.1 1.0
CB B:GLN266 4.0 15.1 1.0
CB B:THR325 4.0 16.7 1.0
O B:LYS323 4.1 10.5 1.0
C B:TYR324 4.1 12.7 1.0
CD B:LYS264 4.1 28.5 1.0
O B:HOH1189 4.3 38.2 1.0
C B:LYS323 4.3 11.6 1.0
N B:GLN266 4.3 13.8 1.0
CA B:TYR324 4.4 11.5 1.0
CB B:LYS323 4.5 13.7 1.0
CG B:LYS264 4.5 24.2 1.0
CG B:ASP361 4.5 41.6 1.0
C B:LYS264 4.5 15.9 1.0
O B:TYR324 4.5 11.6 1.0
N B:TYR324 4.6 11.3 1.0
CA B:THR325 4.6 15.2 1.0
CB B:LYS264 4.7 21.0 1.0
CA B:ASP361 4.8 28.2 1.0
N B:ASP361 4.8 27.7 1.0
CA B:GLN266 4.8 14.4 1.0
C B:ILE265 5.0 14.2 1.0

Reference:

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
Page generated: Mon Aug 12 01:06:09 2024

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