Iodine in PDB 7yww: Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)

The structure of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2), PDB code: 7yww was solved by N.Huwa, T.Classen, O.H.Weiergraeber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.87 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.32, 99.63, 93.74, 90, 90, 90
R / Rfree (%)	16.9 / 19.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iodine atom in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) (pdb code 7yww). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 20 binding sites of Iodine where determined in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2), PDB code: 7yww:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:23.1 occ:1.00 NZ A:LYS261 3.5 27.9 1.0 N A:SER233 3.7 23.5 1.0 CE A:LYS261 3.9 30.2 1.0 C A:SER233 4.0 23.8 1.0 N A:GLU234 4.0 21.8 1.0 CA A:GLY231 4.0 21.2 1.0 N A:SER232 4.1 21.7 1.0 C A:GLY231 4.1 21.6 1.0 CA A:SER233 4.1 24.1 1.0 CB A:SER233 4.2 25.0 1.0 CB A:GLU234 4.4 21.0 1.0 O A:SER233 4.4 24.9 1.0 CA A:GLU234 4.6 21.2 1.0 C A:SER232 4.8 23.8 1.0 O A:GLY231 4.8 21.8 1.0 CD A:LYS261 4.8 31.5 1.0 CG A:LYS261 4.9 30.2 1.0 CA A:SER232 5.0 22.8 1.0

Iodine binding site 2 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:24.8 occ:1.00 OG A:SER189 3.4 23.1 1.0 OG1 A:THR191 3.5 24.1 1.0 OG1 A:THR204 3.5 23.8 1.0 CA A:PHE203 3.9 19.8 1.0 N A:THR191 3.9 20.9 1.0 N A:THR204 4.0 20.8 1.0 CE A:LYS214 4.0 38.0 1.0 C A:PHE203 4.0 20.5 1.0 N A:PHE203 4.1 20.0 1.0 C A:ILE190 4.2 20.6 1.0 O A:SER202 4.2 20.6 1.0 CB A:THR191 4.2 23.0 1.0 O A:SER189 4.2 20.7 1.0 C A:SER202 4.2 20.6 1.0 CB A:SER189 4.3 21.8 1.0 C A:SER189 4.3 20.2 1.0 CA A:ILE190 4.3 20.1 1.0 N A:ILE190 4.3 19.8 1.0 CB A:THR204 4.4 23.6 1.0 CB A:SER202 4.5 23.1 1.0 NZ A:LYS214 4.5 40.4 1.0 CD A:LYS214 4.6 34.7 1.0 O A:HOH553 4.7 39.1 1.0 O A:PHE203 4.7 21.3 1.0 CA A:THR191 4.7 21.5 1.0 CG A:LYS214 4.8 30.9 1.0 CA A:THR204 4.8 21.9 1.0 O A:ILE190 4.8 20.7 1.0 O A:HOH534 4.9 38.7 1.0 CA A:SER189 4.9 20.5 1.0 O A:HOH513 5.0 49.3 1.0

Iodine binding site 3 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:28.9 occ:0.85 O A:HOH645 3.3 50.4 1.0 OG A:SER202 3.4 24.7 1.0 OG A:SER200 3.4 25.4 0.6 OG A:SER200 3.4 25.2 0.4 CD1 A:TYR193 3.8 23.9 1.0 C A:ILE201 3.9 21.5 1.0 N A:SER202 3.9 20.9 1.0 O A:THR191 3.9 22.7 1.0 CB A:PRO217 4.0 31.0 1.0 CE1 A:TYR193 4.0 25.4 1.0 CB A:SER200 4.0 24.8 0.6 CB A:SER200 4.0 24.9 0.4 N A:ILE201 4.0 22.2 1.0 CG2 A:THR191 4.0 23.5 1.0 CA A:ILE201 4.1 21.5 1.0 C A:SER200 4.1 23.0 0.4 CB A:SER202 4.2 23.1 1.0 C A:SER200 4.2 22.7 0.6 O A:SER200 4.3 22.9 0.4 C A:THR191 4.3 22.0 1.0 O A:ILE201 4.4 22.2 1.0 O A:SER200 4.4 22.5 0.6 O A:HOH642 4.4 56.8 1.0 CB A:THR191 4.5 23.0 1.0 CA A:LEU192 4.5 22.3 1.0 CA A:PRO217 4.6 30.5 1.0 CA A:SER202 4.6 21.4 1.0 N A:LEU192 4.7 21.9 1.0 CA A:SER200 4.7 23.9 0.4 CA A:SER200 4.7 23.6 0.6 C A:LEU192 4.9 22.3 1.0

Iodine binding site 4 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:43.1 occ:0.56 N A:SER183 3.7 30.4 1.0 OE1 A:GLU182 3.7 35.5 0.4 N A:HIS208 3.8 32.7 1.0 CG A:ASP207 3.9 30.5 1.0 CB A:GLU182 3.9 32.9 0.4 CB A:ASP207 4.0 29.6 1.0 N A:ALA209 4.0 36.8 1.0 CB A:GLU182 4.0 37.0 0.6 CB A:SER183 4.1 31.2 1.0 O A:SER183 4.1 27.5 1.0 OD2 A:ASP207 4.1 30.8 1.0 CB A:HIS208 4.2 38.7 1.0 OD1 A:ASP207 4.2 30.6 1.0 CA A:HIS208 4.3 36.0 1.0 CA A:SER183 4.4 29.7 1.0 C A:HIS208 4.4 37.0 1.0 CB A:ALA209 4.4 37.4 1.0 CA A:GLU182 4.5 32.0 0.4 CA A:GLU182 4.5 34.0 0.6 C A:GLU182 4.5 30.6 0.4 C A:GLU182 4.6 31.8 0.6 CD A:GLU182 4.6 35.1 0.4 CG A:GLU182 4.7 40.5 0.6 CG A:GLU182 4.7 34.1 0.4 C A:ASP207 4.7 30.1 1.0 C A:SER183 4.7 28.0 1.0 CA A:ALA209 4.9 37.4 1.0 CA A:ASP207 4.9 28.4 1.0

Iodine binding site 5 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:47.4 occ:0.44 O A:HOH567 3.2 62.5 1.0 OH A:TYR205 3.5 34.8 1.0 OG1 A:THR181 3.9 45.7 1.0 OE1 A:GLU182 3.9 45.4 0.6 CE1 A:TYR205 4.0 30.1 1.0 CA A:ILE180 4.1 30.4 1.0 CB A:ILE180 4.2 30.5 1.0 N A:THR181 4.2 34.9 1.0 CG2 A:ILE180 4.2 31.5 1.0 CB A:ALA215 4.2 25.7 1.0 CB A:HIS213 4.2 30.9 1.0 CZ A:TYR205 4.2 32.3 1.0 CA A:ALA215 4.4 25.4 1.0 O A:LYS214 4.5 27.3 1.0 N A:ALA215 4.7 25.1 1.0 C A:ILE180 4.7 32.5 1.0 I A:IOD408 4.7 71.7 0.6 CG A:HIS213 4.7 34.3 1.0 C A:LYS214 4.8 26.1 1.0 OE2 A:GLU182 4.8 44.8 0.6 CD A:GLU182 4.8 43.9 0.6 CB A:THR181 4.9 43.1 1.0 O A:ASP179 4.9 27.4 1.0 CG2 A:THR181 5.0 44.5 1.0

Iodine binding site 6 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:56.0 occ:0.65 CD1 A:TYR264 3.8 24.7 1.0 O A:HOH511 4.1 42.6 1.0 CE1 A:TYR264 4.1 25.4 1.0 CZ A:PHE267 4.2 23.9 1.0 CD1 A:ILE226 4.2 27.6 1.0 O A:HOH603 4.2 33.4 1.0 CG2 A:ILE226 4.3 25.6 1.0 CE1 A:PHE267 4.5 24.0 1.0 O A:HOH614 4.7 29.0 1.0 CG A:TYR264 5.0 23.8 1.0

Iodine binding site 7 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:54.9 occ:0.48 OG A:SER183 3.4 32.6 1.0 N A:VAL163 3.5 31.4 1.0 CB A:SER183 3.8 31.2 1.0 O A:HOH549 4.0 44.0 1.0 CB A:VAL163 4.0 30.0 1.0 CA A:SER183 4.1 29.7 1.0 CA A:PRO162 4.2 37.0 1.0 CG2 A:VAL163 4.3 30.0 1.0 CA A:VAL163 4.3 29.8 1.0 O A:VAL163 4.3 30.9 1.0 C A:PRO162 4.4 34.6 1.0 CB A:PRO162 4.5 38.4 1.0 CD A:PRO184 4.6 27.1 1.0 CE2 A:TYR302 4.7 25.7 1.0 C A:VAL163 4.8 29.1 1.0 O A:HOH516 4.9 54.7 1.0 N A:SER183 5.0 30.4 1.0 CD2 A:TYR302 5.0 24.6 1.0

Iodine binding site 8 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:71.7 occ:0.57 NE1 A:TRP218 3.4 26.1 1.0 N A:GLY216 3.5 26.4 1.0 O A:HOH566 3.7 32.3 1.0 CA A:ALA215 4.1 25.4 1.0 CE2 A:TRP218 4.2 25.2 1.0 C A:ALA215 4.3 25.3 1.0 CZ2 A:TRP218 4.3 24.7 1.0 O A:HOH659 4.4 68.1 1.0 CA A:GLY216 4.4 28.3 1.0 CB A:ALA215 4.4 25.7 1.0 CD1 A:TRP218 4.5 25.8 1.0 O A:ASP179 4.5 27.4 1.0 I A:IOD405 4.7 47.4 0.4 O A:GLY216 4.8 34.0 1.0 O A:HOH556 4.9 67.4 1.0 O A:HOH547 4.9 49.9 1.0 C A:GLY216 5.0 31.3 1.0

Iodine binding site 9 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:57.0 occ:0.49 O A:HOH619 3.0 40.2 1.0 OG A:SER249 3.1 34.5 1.0 O A:HOH522 3.4 31.7 1.0 ND2 A:ASN297 3.9 27.9 1.0 CB A:SER249 3.9 32.5 1.0 O A:HOH617 4.0 36.5 1.0 OE1 A:GLU174 4.1 44.0 1.0 CB A:GLU174 4.3 38.9 1.0 CD2 A:TYR295 4.5 30.5 1.0 CD A:GLU174 4.5 43.5 1.0 OD1 A:ASN297 4.6 28.0 1.0 CG A:ASN297 4.6 27.6 1.0 CG A:GLU174 4.7 41.1 1.0 O A:HOH515 4.7 49.8 1.0 N A:GLY175 4.8 35.2 1.0 CA A:SER249 4.9 30.2 1.0

Iodine binding site 10 out of 20 in the Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Monocot Chimeric Jacalin JAC1 From Oryza Sativa: Lectin Domain (Crystal Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:44.2 occ:0.38 O A:HOH653 2.4 29.7 0.6 OG1 A:THR250 3.0 29.8 1.0 N A:PRO245 3.6 26.0 1.0 C A:GLY244 3.7 25.3 1.0 CD A:PRO245 3.7 26.6 1.0 CG2 A:THR250 3.8 29.1 1.0 CB A:THR250 3.8 28.7 1.0 CA A:PRO245 3.9 26.3 1.0 CA A:GLY244 4.0 24.7 1.0 CB A:PRO245 4.0 26.8 1.0 CA A:THR250 4.2 26.9 1.0 O A:GLY244 4.2 24.7 1.0 O A:HOH562 4.4 29.7 1.0 CG A:PRO245 4.4 27.0 1.0 N A:GLY244 4.8 24.2 1.0 O A:HOH657 4.9 53.9 1.0 O A:SER249 4.9 30.4 1.0 O A:HOH578 5.0 47.0 1.0 N A:THR250 5.0 27.4 1.0

N.Huwa, O.H.Weiergraber, A.V.Fejzagic, C.Kirsch, U.Schaffrath, T.Classen. The Crystal Structure of the Defense Conferring Rice Protein Os JAC1 Reveals A Carbohydrate Binding Site on the Dirigent-Like Domain. Biomolecules V. 12 2022.
ISSN: ESSN 2218-273X
PubMed: 36009020
DOI: 10.3390/BIOM12081126