Atomistry » Iodine » PDB 7ben-7fgj » 7f7y
Atomistry »
  Iodine »
    PDB 7ben-7fgj »
      7f7y »

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

Go back to Iodine Binding Sites List in 7f7y
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

Go back to Iodine Binding Sites List in 7f7y
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

Go back to Iodine Binding Sites List in 7f7y
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

Go back to Iodine Binding Sites List in 7f7y
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

Go back to Iodine Binding Sites List in 7f7y
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

Go back to Iodine Binding Sites List in 7f7y
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

Go back to Iodine Binding Sites List in 7f7y
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

Go back to Iodine Binding Sites List in 7f7y
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy