Iodine in PDB 5wvc: Structure of the Card-Card Disk

The structure of Structure of the Card-Card Disk, PDB code: 5wvc was solved by S.C.Lin, Y.C.Lo, T.W.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.85 / 2.99
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	190.110, 190.110, 68.828, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 22.8

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Structure of the Card-Card Disk (pdb code 5wvc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Structure of the Card-Card Disk, PDB code: 5wvc:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:93.2 occ:0.45 OG1 C:THR22 3.3 47.8 1.0 CD C:ARG52 3.8 50.8 1.0 N C:SER23 3.9 44.8 1.0 CG C:ARG44 4.1 65.4 1.0 CA C:SER23 4.1 51.5 1.0 CB C:SER23 4.2 54.6 1.0 CA C:ARG44 4.3 55.9 1.0 CB C:THR22 4.3 41.2 1.0 CB C:ARG44 4.3 57.8 1.0 NE C:ARG52 4.3 61.4 1.0 C C:THR22 4.5 50.8 1.0 CD C:ARG44 4.6 77.6 1.0 I C:IOD102 4.6 0.2 0.9 SD C:MET26 4.9 51.6 1.0 CA C:THR22 5.0 48.6 1.0 N C:ARG44 5.0 53.9 1.0

Iodine binding site 2 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ C:I102 b:0.2 occ:0.86 CB C:LYS21 4.1 46.4 1.0 NH1 C:ARG52 4.1 66.0 1.0 OG1 C:THR22 4.2 47.8 1.0 CB C:SER23 4.2 54.6 1.0 N C:SER23 4.2 44.8 1.0 N C:THR22 4.2 50.7 1.0 CA C:LYS21 4.4 46.8 1.0 C C:LYS21 4.5 42.6 1.0 I C:IOD101 4.6 93.2 0.5 CG C:LYS21 4.7 77.6 1.0 CD C:ARG52 4.7 50.8 1.0 CD C:LYS21 4.8 84.7 1.0 CA C:SER23 4.9 51.5 1.0 CZ C:ARG52 4.9 79.2 1.0

Iodine binding site 3 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ D:I401 b:63.8 occ:0.73 NH1 D:ARG290 3.3 91.1 1.0 NH1 D:ARG293 3.6 83.1 1.0 CD D:ARG293 3.9 62.3 1.0 CG D:ARG290 4.0 60.4 1.0 CD D:ARG290 4.1 68.6 1.0 CA D:ARG290 4.2 72.7 1.0 CG D:GLN294 4.2 77.4 1.0 CB D:ARG290 4.3 62.7 1.0 NE2 D:GLN294 4.3 93.2 1.0 CB D:ARG293 4.3 61.6 1.0 CG D:ARG293 4.4 63.5 1.0 CZ D:ARG290 4.4 94.7 1.0 O D:ARG290 4.4 70.3 1.0 CD1 D:ILE274 4.6 67.6 1.0 CZ D:ARG293 4.6 67.8 1.0 NE D:ARG293 4.7 62.5 1.0 NE D:ARG290 4.8 85.5 1.0 CD D:GLN294 4.8 88.3 1.0 C D:ARG290 4.8 64.3 1.0

Iodine binding site 4 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ D:I402 b:0.1 occ:0.64 CD D:ARG215 3.9 60.9 1.0 NH1 D:ARG215 3.9 63.7 1.0 CA D:LEU285 3.9 56.5 1.0 N D:LEU285 4.0 59.6 1.0 CD1 D:LEU285 4.1 52.2 1.0 CG D:GLU219 4.1 72.3 1.0 CB D:LEU285 4.2 54.2 1.0 C D:MET284 4.3 69.4 1.0 CB D:MET284 4.5 80.9 1.0 CB D:GLU219 4.5 62.5 1.0 CD D:GLU219 4.5 92.6 1.0 O D:MET284 4.5 66.5 1.0 NE D:ARG215 4.6 82.6 1.0 CZ D:ARG215 4.6 75.8 1.0 CG D:ARG215 4.7 56.2 1.0 CE D:MET284 4.7 82.6 1.0 CG D:LEU285 4.8 51.5 1.0 CB D:PHE288 4.9 66.3 1.0 OE2 D:GLU219 4.9 95.4 1.0 OE1 D:GLU219 5.0 99.6 1.0

Iodine binding site 5 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ D:I403 b:0.5 occ:0.68 NH1 D:ARG211 3.3 0.6 1.0 CD1 D:LEU208 4.1 77.1 1.0 CA D:LEU208 4.1 66.6 1.0 CB D:ALA296 4.2 94.8 1.0 N D:LEU208 4.3 71.0 1.0 CB D:LEU208 4.3 67.0 1.0 NH2 D:ARG207 4.5 0.0 1.0 CZ D:ARG211 4.6 0.1 1.0 O D:ALA204 4.6 68.1 1.0 C D:ARG207 4.6 59.3 1.0 O D:ARG207 4.8 56.1 1.0 CG D:LEU208 4.8 69.4 1.0 CB D:ARG207 4.8 65.1 1.0 CD D:ARG211 4.9 0.4 1.0

Iodine binding site 6 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ D:I404 b:0.3 occ:0.67 NH2 D:ARG215 3.7 78.1 1.0 CB D:ARG215 3.9 63.5 1.0 NE D:ARG215 3.9 82.6 1.0 CZ D:ARG215 4.1 75.8 1.0 N D:ARG215 4.6 55.7 1.0 CA D:ARG215 4.7 55.6 1.0 CG D:ARG215 4.8 56.2 1.0 SG D:CSO212 4.9 0.4 1.0 CD D:ARG215 4.9 60.9 1.0

Iodine binding site 7 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ B:I401 b:78.2 occ:0.82 NH1 B:ARG290 3.5 0.0 1.0 NE B:ARG293 3.7 75.7 1.0 CD B:ARG293 3.7 67.4 1.0 CG B:ARG290 3.7 79.0 1.0 CZ B:ARG290 4.1 0.8 1.0 CD1 B:ILE274 4.3 53.2 1.0 CD B:ARG290 4.3 0.5 1.0 CG B:GLN294 4.3 79.9 1.0 CB B:PRO271 4.3 48.5 1.0 NE2 B:GLN294 4.4 80.9 1.0 O B:ARG290 4.4 72.2 1.0 NE B:ARG290 4.4 0.6 1.0 NZ B:LYS297 4.4 0.5 1.0 CG B:ARG293 4.5 69.4 1.0 CA B:ARG290 4.6 67.8 1.0 CB B:ARG290 4.6 71.4 1.0 CZ B:ARG293 4.7 58.3 1.0 CB B:ARG293 4.7 61.7 1.0 NH2 B:ARG290 4.8 0.5 1.0 CD B:GLN294 4.9 84.3 1.0 C B:ARG290 4.9 61.8 1.0

Iodine binding site 8 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ B:I402 b:0.6 occ:0.88 CB B:ARG215 4.0 52.9 1.0 N B:ARG215 4.4 67.3 1.0 CD B:ARG215 4.5 84.1 1.0 CA B:ARG215 4.7 60.0 1.0 CG B:ARG215 4.8 60.7 1.0 CB B:LEU214 4.8 65.4 1.0 CA B:CSO212 4.8 70.0 1.0 O B:ARG211 4.9 59.9 1.0

Iodine binding site 9 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ E:I101 b:0.3 occ:0.80 OG1 E:THR22 3.6 57.0 1.0 NH1 E:ARG52 3.8 74.2 1.0 N E:SER23 3.9 59.5 1.0 N E:THR22 3.9 61.9 1.0 CD E:ARG52 4.1 66.9 1.0 CB E:SER23 4.1 57.0 1.0 CB E:LYS21 4.2 59.9 1.0 C E:LYS21 4.2 58.5 1.0 CA E:LYS21 4.2 61.3 1.0 CZ E:ARG52 4.5 89.0 1.0 CG E:GLN49 4.6 81.5 1.0 NE E:ARG52 4.6 81.7 1.0 CA E:SER23 4.6 64.0 1.0 CG E:LYS21 4.6 54.2 1.0 CA E:THR22 4.7 57.6 1.0 CB E:THR22 4.7 59.2 1.0 C E:THR22 4.8 61.2 1.0 CB E:GLN49 4.9 73.5 1.0 O E:LYS21 5.0 50.0 1.0

Iodine binding site 10 out of 11 in the Structure of the Card-Card Disk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of the Card-Card Disk within 5.0Å range: probe atom residue distance (Å) B Occ F:I1201 b:63.6 occ:1.00 NH1 F:ARG293 3.6 72.7 1.0 CD F:ARG293 4.0 59.6 1.0 OE1 F:GLN294 4.1 80.7 1.0 CD1 F:ILE274 4.2 50.4 1.0 CG F:ARG290 4.2 58.2 1.0 CZ F:ARG293 4.5 67.3 1.0 CG F:PRO271 4.6 54.0 1.0 CA F:ARG290 4.6 59.9 1.0 CA F:PRO271 4.6 56.1 1.0 NE F:ARG293 4.6 66.1 1.0 CB F:PRO271 4.7 57.2 1.0 CB F:ARG290 4.8 56.6 1.0 CG F:ARG293 4.8 59.3 1.0 CD F:GLN294 4.8 76.5 1.0 CB F:ARG293 5.0 61.7 1.0

T.W.Su, C.Y.Yang, W.P.Kao, B.J.Kuo, S.M.Lin, J.Y.Lin, Y.C.Lo, S.C.Lin. Structural Insights Into Dd-Fold Assembly and Caspase-9 Activation By the Apaf-1 Apoptosome. Structure V. 25 407 2017.
ISSN: ISSN 1878-4186
PubMed: 28111022
DOI: 10.1016/J.STR.2016.12.019