Iodine in PDB 6qe4: Re-Refinement of 5OLI Human IBA57-I3C

The structure of Re-Refinement of 5OLI Human IBA57-I3C, PDB code: 6qe4 was solved by V.Calderone, S.Ciofi-Baffoni, S.Gourdoupis, L.Banci, V.Nasta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.84 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.111, 43.048, 59.281, 77.92, 75.63, 71.67
R / Rfree (%)	20.6 / 22.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Re-Refinement of 5OLI Human IBA57-I3C (pdb code 6qe4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Re-Refinement of 5OLI Human IBA57-I3C, PDB code: 6qe4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:21.5 occ:0.60 I3 A:I3C401 0.0 21.5 0.6 C6 A:I3C401 2.0 27.3 0.6 C1 A:I3C401 3.0 29.4 0.6 C5 A:I3C401 3.0 27.7 0.6 C7 A:I3C401 3.2 28.4 0.6 N13 A:I3C401 3.2 26.1 0.6 O A:LEU292 3.3 32.5 1.0 O8 A:I3C401 3.6 27.4 0.6 O9 A:I3C401 3.7 28.9 0.6 CA A:GLY279 3.7 30.9 1.0 CD A:LYS248 3.8 56.4 1.0 CD2 A:LEU292 4.0 34.1 1.0 C A:GLY279 4.0 32.8 1.0 CG A:LEU292 4.1 31.3 1.0 C A:LEU292 4.1 31.5 1.0 N A:LYS280 4.1 29.1 1.0 C2 A:I3C401 4.3 31.3 0.6 CD1 A:TRP294 4.3 54.2 1.0 C4 A:I3C401 4.4 31.5 0.6 N A:GLY279 4.4 34.9 1.0 CB A:LEU292 4.5 26.2 1.0 CG A:LYS248 4.5 43.4 1.0 O A:VAL278 4.6 36.3 1.0 NE1 A:TRP294 4.7 55.1 1.0 CB A:LYS280 4.7 31.7 1.0 O A:GLY279 4.7 35.1 1.0 CD A:LYS280 4.8 50.8 1.0 C A:VAL278 4.8 37.7 1.0 N A:LEU293 4.8 29.0 1.0 CA A:LEU293 4.8 32.0 1.0 NZ A:LYS248 4.9 78.2 1.0 C3 A:I3C401 4.9 32.1 0.6 CE A:LYS280 4.9 50.2 1.0 CE A:LYS248 4.9 68.0 1.0 CG A:LYS280 5.0 45.2 1.0 CA A:LEU292 5.0 25.8 1.0 CB A:LYS248 5.0 31.9 1.0

Iodine binding site 2 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:33.0 occ:0.60 I2 A:I3C401 0.0 33.0 0.6 C4 A:I3C401 2.0 31.5 0.6 C3 A:I3C401 3.0 32.1 0.6 C5 A:I3C401 3.0 27.7 0.6 N13 A:I3C401 3.2 26.1 0.6 C10 A:I3C401 3.3 33.4 0.6 O11 A:I3C401 3.6 33.0 0.6 O A:THR277 3.8 48.7 1.0 O12 A:I3C401 3.9 33.5 0.6 C2 A:I3C401 4.3 31.3 0.6 CG2 A:THR277 4.3 50.1 1.0 C6 A:I3C401 4.4 27.3 0.6 NE1 A:TRP294 4.5 55.1 1.0 CB A:THR277 4.5 55.2 1.0 C A:THR277 4.7 48.4 1.0 C1 A:I3C401 4.9 29.4 0.6

Iodine binding site 3 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:32.8 occ:0.60 I1 A:I3C401 0.0 32.8 0.6 C2 A:I3C401 2.0 31.3 0.6 C1 A:I3C401 3.0 29.4 0.6 C3 A:I3C401 3.0 32.1 0.6 C7 A:I3C401 3.2 28.4 0.6 C10 A:I3C401 3.2 33.4 0.6 O12 A:I3C401 3.4 33.5 0.6 O9 A:I3C401 3.5 28.9 0.6 O8 A:I3C401 3.7 27.4 0.6 O11 A:I3C401 3.8 33.0 0.6 NZ A:LYS248 4.0 78.2 1.0 NZ A:LYS280 4.0 53.1 1.0 C6 A:I3C401 4.3 27.3 0.6 C4 A:I3C401 4.3 31.5 0.6 C5 A:I3C401 4.9 27.7 0.6

Iodine binding site 4 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:43.4 occ:0.40 I3 A:I3C402 0.0 43.4 0.4 C6 A:I3C402 2.0 41.3 0.4 C1 A:I3C402 3.0 38.5 0.4 C5 A:I3C402 3.0 42.4 0.4 N13 A:I3C402 3.2 43.1 0.4 C7 A:I3C402 3.2 36.7 0.4 O9 A:I3C402 3.5 36.2 0.4 O8 A:I3C402 3.8 36.1 0.4 CZ2 A:TRP188 4.1 29.1 1.0 OD1 A:ASN287 4.2 66.7 1.0 CA A:GLY286 4.2 31.9 1.0 N A:ASN287 4.2 34.6 1.0 C2 A:I3C402 4.3 36.7 0.4 C4 A:I3C402 4.3 42.6 0.4 C A:GLY286 4.6 37.3 1.0 CH2 A:TRP188 4.7 30.3 1.0 C3 A:I3C402 4.8 40.2 0.4 CB A:ASN287 4.8 39.5 1.0 CG A:ASN287 4.9 73.9 1.0

Iodine binding site 5 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:44.5 occ:0.40 I2 A:I3C402 0.0 44.5 0.4 C4 A:I3C402 2.0 42.6 0.4 C3 A:I3C402 3.0 40.2 0.4 C5 A:I3C402 3.0 42.4 0.4 N13 A:I3C402 3.2 43.1 0.4 C10 A:I3C402 3.2 40.8 0.4 O12 A:I3C402 3.6 42.1 0.4 O11 A:I3C402 3.8 39.9 0.4 C6 A:I3C402 4.3 41.3 0.4 C2 A:I3C402 4.3 36.7 0.4 CG A:ASN287 4.7 73.9 1.0 C1 A:I3C402 4.8 38.5 0.4 CB A:ASN287 4.8 39.5 1.0 ND2 A:ASN287 4.8 71.3 1.0

Iodine binding site 6 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:31.4 occ:0.40 I1 A:I3C402 0.0 31.4 0.4 C2 A:I3C402 2.0 36.7 0.4 C1 A:I3C402 3.0 38.5 0.4 C3 A:I3C402 3.0 40.2 0.4 C7 A:I3C402 3.2 36.7 0.4 C10 A:I3C402 3.2 40.8 0.4 O11 A:I3C402 3.5 39.9 0.4 O8 A:I3C402 3.5 36.1 0.4 O9 A:I3C402 3.7 36.2 0.4 O12 A:I3C402 3.8 42.1 0.4 CG1 A:VAL288 3.9 33.0 1.0 O A:HOH518 3.9 44.3 1.0 NE2 A:GLN192 4.0 40.6 1.0 CG A:GLN192 4.1 33.4 1.0 CD A:GLN192 4.2 52.1 1.0 C6 A:I3C402 4.3 41.3 0.4 C4 A:I3C402 4.3 42.6 0.4 CG2 A:VAL288 4.3 30.9 1.0 CD1 A:LEU196 4.4 31.3 1.0 CD2 A:LEU196 4.7 34.4 1.0 CB A:VAL288 4.7 31.9 1.0 CG A:LEU196 4.8 30.6 1.0 OE1 A:GLN192 4.9 53.0 1.0 C5 A:I3C402 4.9 42.4 0.4

Iodine binding site 7 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:42.2 occ:0.40 I3 A:I3C403 0.0 42.2 0.4 C6 A:I3C403 2.0 42.2 0.4 C1 A:I3C403 3.0 42.7 0.4 C5 A:I3C403 3.0 41.3 0.4 C7 A:I3C403 3.2 42.3 0.4 N13 A:I3C403 3.2 40.6 0.4 O9 A:I3C403 3.5 41.8 0.4 NZ A:LYS119 3.7 1.0 1.0 O8 A:I3C403 3.7 42.4 0.4 C2 A:I3C403 4.3 44.0 0.4 C4 A:I3C403 4.3 40.5 0.4 C3 A:I3C403 4.8 43.0 0.4

Iodine binding site 8 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:38.5 occ:0.40 I2 A:I3C403 0.0 38.5 0.4 C4 A:I3C403 2.0 40.5 0.4 C5 A:I3C403 3.0 41.3 0.4 C3 A:I3C403 3.0 43.0 0.4 N13 A:I3C403 3.2 40.6 0.4 C10 A:I3C403 3.3 44.7 0.4 O12 A:I3C403 3.6 45.2 0.4 CD A:PRO35 3.8 67.4 1.0 O11 A:I3C403 3.9 45.6 0.4 C6 A:I3C403 4.3 42.2 0.4 C2 A:I3C403 4.4 44.0 0.4 CG A:PRO35 4.4 73.5 1.0 CD A:LYS119 4.6 0.7 1.0 C1 A:I3C403 4.9 42.7 0.4 NZ A:LYS119 4.9 1.0 1.0 CB A:LYS119 4.9 77.8 1.0

Iodine binding site 9 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:45.5 occ:0.40 I1 A:I3C403 0.0 45.5 0.4 C2 A:I3C403 2.0 44.0 0.4 C1 A:I3C403 3.0 42.7 0.4 C3 A:I3C403 3.0 43.0 0.4 C7 A:I3C403 3.1 42.3 0.4 C10 A:I3C403 3.3 44.7 0.4 O11 A:I3C403 3.4 45.6 0.4 O8 A:I3C403 3.5 42.4 0.4 O A:VAL120 3.5 63.8 1.0 O9 A:I3C403 3.8 41.8 0.4 CG2 A:THR121 3.8 67.1 1.0 O12 A:I3C403 3.9 45.2 0.4 N A:VAL120 3.9 65.2 1.0 C A:VAL120 4.1 61.1 1.0 C6 A:I3C403 4.3 42.2 0.4 C4 A:I3C403 4.4 40.5 0.4 CA A:LYS119 4.5 73.7 1.0 C A:LYS119 4.6 69.1 1.0 CA A:VAL120 4.6 59.6 1.0 O A:ARG118 4.7 75.6 1.0 N A:THR121 4.7 56.8 1.0 C5 A:I3C403 4.9 41.3 0.4

Iodine binding site 10 out of 12 in the Re-Refinement of 5OLI Human IBA57-I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Re-Refinement of 5OLI Human IBA57-I3C within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:23.7 occ:0.40 I3 A:I3C404 0.0 23.7 0.4 C6 A:I3C404 2.1 30.4 0.4 O9 A:I3C404 3.0 36.3 0.4 C5 A:I3C404 3.1 35.1 0.4 C1 A:I3C404 3.1 33.4 0.4 N13 A:I3C404 3.2 33.8 0.4 O A:ASP159 3.3 20.9 1.0 C7 A:I3C404 3.4 34.6 0.4 O A:PRO160 3.8 20.1 1.0 C A:PRO160 4.0 19.6 1.0 N A:ALA163 4.1 24.4 1.0 CA A:THR162 4.1 21.0 1.0 N A:THR162 4.1 19.6 1.0 C A:THR162 4.1 23.7 1.0 CA A:PRO160 4.2 17.7 1.0 O A:HOH507 4.3 33.0 1.0 C4 A:I3C404 4.4 42.0 0.4 O8 A:I3C404 4.4 34.0 0.4 C A:ASP159 4.5 20.6 1.0 C2 A:I3C404 4.5 35.0 0.4 OD1 A:ASN222 4.5 30.1 1.0 C A:ARG161 4.5 20.4 1.0 N A:ARG161 4.6 17.7 1.0 O A:THR162 4.8 22.5 1.0 CA A:ALA163 4.9 25.8 1.0 N A:PRO160 4.9 17.4 1.0 O A:HOH546 4.9 33.4 1.0 O A:ARG161 4.9 20.4 1.0 C3 A:I3C404 5.0 38.6 0.4

S.Gourdoupis, V.Nasta, S.Ciofi-Baffoni, L.Banci, V.Calderone. In-House High-Energy-Remote Sad Phasing Using the Magic Triangle: How to Tackle the P1 Low Symmetry Using Multiple Orientations of the Same Crystal of Human IBA57 to Increase the Multiplicity. Acta Crystallogr D Struct V. 75 317 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 30950402
DOI: 10.1107/S2059798319000214