Iodine in PDB 4ikm: X-Ray Structure of CARD8 Card Domain

The structure of X-Ray Structure of CARD8 Card Domain, PDB code: 4ikm was solved by T.Jin, M.Huang, P.Smith, J.Jiang, T.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.44 / 2.46
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.877, 94.877, 219.390, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 25.3

Pages:

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

Binding sites:

The binding sites of Iodine atom in the X-Ray Structure of CARD8 Card Domain (pdb code 4ikm). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the X-Ray Structure of CARD8 Card Domain, PDB code: 4ikm:
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 X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I100 b:0.9 occ:0.66 IE A:IYR100 0.0 0.9 0.7 CE A:IYR100 2.1 69.5 1.0 CF A:IYR100 3.0 66.3 1.0 CD A:IYR100 3.1 63.0 1.0 OF A:IYR100 3.1 72.0 1.0 ND2 A:ASN101 3.4 92.7 1.0 CA A:GLN73 3.6 53.4 1.0 N A:GLN73 3.8 54.2 1.0 CB A:GLN73 4.1 52.4 1.0 C A:ALA72 4.1 60.7 1.0 O A:ALA72 4.2 66.9 1.0 CG A:IYR100 4.3 62.3 1.0 CC A:IYR100 4.4 51.9 1.0 CG A:ASN101 4.5 89.1 1.0 CG A:GLN73 4.6 61.9 1.0 C A:GLN73 4.8 64.7 1.0 CB A:ALA72 4.8 50.0 1.0 CH A:IYR100 4.9 56.6 1.0 O A:GLY69 4.9 55.5 1.0 O A:GLN73 4.9 70.2 1.0 CB A:ASN101 5.0 78.4 1.0

Iodine binding site 2 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I172 b:88.4 occ:0.71 I1 A:TYI172 0.0 88.4 0.7 CE1 A:TYI172 2.1 87.5 1.0 CD1 A:TYI172 3.0 81.7 1.0 CZ A:TYI172 3.1 88.2 0.1 OH A:TYI172 3.2 93.2 1.0 O A:GLY175 3.3 1.0 1.0 C A:GLY175 3.7 0.4 1.0 CE2 A:TYR177 3.9 60.5 1.0 N A:LYS176 4.2 0.1 1.0 CZ A:TYR177 4.3 64.0 1.0 CG A:TYI172 4.4 77.7 0.0 CA A:LYS176 4.4 96.5 1.0 CE2 A:TYI172 4.4 85.2 0.0 OH A:TYR177 4.4 66.2 1.0 CA A:GLY175 4.4 0.0 1.0 CD2 A:TYR177 4.5 59.0 1.0 C A:LYS176 4.7 90.4 1.0 O1 A:EDO505 4.7 77.5 1.0 O A:LYS176 4.8 89.8 1.0 N A:GLY175 4.8 0.9 1.0 C2 A:EDO505 4.8 74.4 1.0 CD2 A:TYI172 4.9 79.3 1.0

Iodine binding site 3 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I172 b:0.1 occ:0.77 I2 A:TYI172 0.0 0.1 0.8 CE2 A:TYI172 2.1 85.2 0.0 CD2 A:TYI172 3.0 79.3 1.0 CZ A:TYI172 3.1 88.2 0.1 OH A:TYI172 3.3 93.2 1.0 CA A:ALA174 3.5 0.1 1.0 N A:ALA174 3.9 0.1 1.0 N A:GLY175 4.0 0.9 1.0 C A:ALA174 4.2 0.2 1.0 CG A:TYI172 4.3 77.7 0.0 CE1 A:TYI172 4.4 87.5 1.0 CB A:ALA174 4.4 0.9 1.0 CD1 A:TYI172 4.9 81.7 1.0

Iodine binding site 4 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I211 b:1.0 occ:1.00 I1 A:TYI211 0.0 1.0 1.0 CE1 A:TYI211 2.1 1.0 1.0 CD1 A:TYI211 3.0 0.4 1.0 CZ A:TYI211 3.1 0.9 1.0 OH A:TYI211 3.2 0.9 1.0 OG A:SER212 4.0 90.1 1.0 OE1 A:GLU215 4.2 93.2 1.0 O A:HOH638 4.3 78.6 1.0 CG A:TYI211 4.4 0.1 1.0 CE2 A:TYI211 4.4 0.4 1.0 CB A:SER212 4.6 82.1 1.0 CA A:SER212 4.6 74.2 1.0 O A:HOH655 4.9 74.1 1.0 CD2 A:TYI211 4.9 0.1 1.0 O A:HOH642 4.9 87.9 1.0 N A:SER212 4.9 68.8 1.0

Iodine binding site 5 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I211 b:0.2 occ:1.00 I2 A:TYI211 0.0 0.2 1.0 CE2 A:TYI211 2.1 0.4 1.0 CZ A:TYI211 3.1 0.9 1.0 CD2 A:TYI211 3.1 0.1 1.0 OH A:TYI211 3.2 0.9 1.0 OE2 A:GLU215 3.6 86.0 1.0 CB A:ALA232 3.8 64.0 1.0 ND2 A:ASN228 3.9 55.7 1.0 O A:HOH627 4.2 67.2 1.0 CD A:GLU215 4.2 88.0 1.0 CD1 A:TRP231 4.2 62.3 1.0 CE1 A:TYI211 4.4 1.0 1.0 CA A:ALA232 4.4 70.0 1.0 CG A:TYI211 4.4 0.1 1.0 NE1 A:TRP231 4.4 59.2 1.0 OD1 A:ASN228 4.5 54.9 1.0 OE1 A:GLU215 4.5 93.2 1.0 CG A:ASN228 4.6 61.7 1.0 O A:HOH638 4.8 78.6 1.0 CD1 A:TYI211 4.9 0.4 1.0 ND2 A:ASN235 5.0 88.3 1.0 N A:ALA232 5.0 69.2 1.0

Iodine binding site 6 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I243 b:0.2 occ:0.25 IE A:IYR243 0.0 0.2 0.3 CE A:IYR243 2.1 85.9 1.0 CF A:IYR243 3.0 91.6 1.0 CD A:IYR243 3.0 89.2 1.0 OF A:IYR243 3.1 81.3 1.0 CD1 A:TRP233 3.3 72.5 1.0 CG A:TRP233 3.3 73.0 1.0 CG2 A:VAL245 3.4 73.3 1.0 CD A:ARG317 3.6 81.7 1.0 NE1 A:TRP233 3.7 69.3 1.0 CB A:TRP233 3.8 72.5 1.0 CD2 A:TRP233 3.9 70.0 1.0 NH1 A:ARG317 3.9 88.7 1.0 CE2 A:TRP233 4.1 67.6 1.0 CA A:TRP233 4.3 74.4 1.0 CG A:IYR243 4.3 94.9 1.0 CC A:IYR243 4.3 92.7 1.0 CG A:ARG317 4.5 82.7 1.0 NE A:ARG317 4.6 91.3 1.0 CZ A:ARG317 4.7 91.4 1.0 CE3 A:TRP233 4.7 73.1 1.0 CD1 A:ILE236 4.8 76.9 1.0 CH A:IYR243 4.8 97.1 1.0 CG2 A:ILE117 4.8 72.6 1.0 CB A:VAL245 4.9 78.6 1.0 O A:TRP233 4.9 85.9 1.0

Iodine binding site 7 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:90.7 occ:1.00 I1 A:TYI308 0.0 90.7 1.0 CE1 A:TYI308 2.1 71.0 1.0 CZ A:TYI308 3.0 82.3 1.0 CD1 A:TYI308 3.1 79.9 1.0 OH A:TYI308 3.1 82.2 1.0 OD1 A:ASN295 3.4 64.5 1.0 CG A:ASN295 3.4 77.0 1.0 CB A:ASN295 3.6 67.5 1.0 O A:LEU291 3.8 65.3 1.0 CD1 A:LEU312 3.8 79.5 1.0 ND2 A:ASN295 4.1 72.0 1.0 O A:HOH626 4.1 54.1 1.0 CG1 A:VAL303 4.1 59.6 1.0 C A:LEU291 4.2 70.1 1.0 CD2 A:LEU312 4.3 87.7 1.0 CE2 A:TYI308 4.3 84.8 1.0 CD1 A:LEU300 4.4 58.4 1.0 CG A:TYI308 4.4 81.9 1.0 CB A:LEU291 4.4 75.7 1.0 CG A:LEU312 4.5 86.5 1.0 N A:GLU292 4.5 70.8 1.0 CA A:GLU292 4.6 80.9 1.0 CB A:LEU300 4.7 58.4 1.0 O A:GLY301 4.7 78.2 1.0 CD2 A:TYI308 4.9 83.1 1.0 CA A:ASN295 4.9 65.8 1.0 CA A:LEU291 4.9 67.0 1.0 CG A:LEU300 4.9 58.0 1.0

Iodine binding site 8 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:0.4 occ:1.00 I2 A:TYI308 0.0 0.4 1.0 CE2 A:TYI308 2.1 84.8 1.0 CZ A:TYI308 3.1 82.3 1.0 CD2 A:TYI308 3.1 83.1 1.0 OH A:TYI308 3.2 82.2 1.0 OE1 A:GLU311 3.5 0.5 1.0 O A:ASP288 4.2 92.5 1.0 CB A:GLU292 4.2 83.7 1.0 CD A:GLU311 4.3 0.6 1.0 CG A:GLU292 4.3 88.7 1.0 CE1 A:TYI308 4.4 71.0 1.0 CG A:TYI308 4.4 81.9 1.0 OE1 A:GLU292 4.4 0.7 1.0 CD A:GLU292 4.5 98.2 1.0 OE2 A:GLU311 4.7 0.9 1.0 CB A:ASP288 4.8 83.5 1.0 C A:ASP288 4.9 91.6 1.0 CD1 A:TYI308 4.9 79.9 1.0 CB A:GLU311 4.9 0.9 1.0

Iodine binding site 9 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I342 b:0.3 occ:1.00 I1 A:TYI342 0.0 0.3 1.0 CE1 A:TYI342 2.1 83.3 1.0 CD1 A:TYI342 3.1 70.4 1.0 CZ A:TYI342 3.1 87.4 1.0 OH A:TYI342 3.2 98.4 1.0 CG A:TYI342 4.4 69.5 1.0 CE2 A:TYI342 4.4 82.7 1.0 CD A:ARG440 4.7 71.8 1.0 CD2 A:TYI342 4.9 64.0 1.0 OG1 A:THR346 4.9 79.8 1.0 CD A:ARG345 5.0 79.6 1.0

Iodine binding site 10 out of 15 in the X-Ray Structure of CARD8 Card Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of X-Ray Structure of CARD8 Card Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I342 b:85.8 occ:1.00 I2 A:TYI342 0.0 85.8 1.0 CE2 A:TYI342 2.1 82.7 1.0 CD2 A:TYI342 3.1 64.0 1.0 CZ A:TYI342 3.1 87.4 1.0 OH A:TYI342 3.2 98.4 1.0 ND2 A:ASN368 3.9 64.6 1.0 CG A:ASN368 4.1 76.6 1.0 CG A:ARG440 4.3 68.3 1.0 CB A:SER443 4.3 68.3 1.0 CG A:TYI342 4.4 69.5 1.0 CE1 A:TYI342 4.4 83.3 1.0 OD1 A:ASN368 4.4 77.0 1.0 OG A:SER443 4.4 75.7 1.0 CE1 A:PHE439 4.5 77.9 1.0 OG1 A:THR346 4.6 79.8 1.0 CB A:ASN368 4.6 64.8 1.0 CD1 A:PHE439 4.7 79.4 1.0 O A:HOH618 4.7 59.3 1.0 CA A:ARG440 4.8 57.0 1.0 CD A:ARG440 4.9 71.8 1.0 CD1 A:TYI342 4.9 70.4 1.0 CB A:ARG440 5.0 71.2 1.0

T.Jin, M.Huang, P.Smith, J.Jiang, T.S.Xiao. The Structure of the CARD8 Caspase-Recruitment Domain Suggests Its Association with the Fiind Domain and Procaspases Through Adjacent Surfaces. Acta Crystallogr.,Sect.F V. 69 482 2013.
ISSN: ESSN 1744-3091
PubMed: 23695559
DOI: 10.1107/S1744309113010075