Iridium in PDB 4y1n: Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine

The structure of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine, PDB code: 4y1n was solved by C.Zhao, K.R.Rajashankar, M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.44 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.738, 131.200, 84.640, 90.00, 91.71, 90.00
R / Rfree (%)	18.3 / 24.6

The structure of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Potassium	(K)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iridium atom in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine (pdb code 4y1n). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 28 binding sites of Iridium where determined in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine, PDB code: 4y1n:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir401 b:0.1 occ:0.49 IR A:IRI401 0.0 0.1 0.5 N4 A:IRI401 2.2 41.0 0.5 N1 A:IRI401 2.2 0.8 0.5 N3 A:IRI401 2.2 0.2 0.5 N6 A:IRI401 2.3 0.6 0.5 N2 A:IRI401 2.3 58.4 0.5 N5 A:IRI401 2.3 56.1 0.5 O6 A:G10 4.3 0.1 1.0 N7 A:G9 4.3 62.4 1.0 N7 A:G10 4.9 93.5 1.0

Iridium binding site 2 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir402 b:0.4 occ:1.00 IR A:IRI402 0.0 0.4 1.0 N4 A:IRI402 2.2 0.4 1.0 N2 A:IRI402 2.2 0.0 1.0 N3 A:IRI402 2.3 0.4 1.0 N1 A:IRI402 2.3 0.7 1.0 N5 A:IRI402 2.3 74.2 1.0 N6 A:IRI402 2.3 76.0 1.0 OP2 A:C70 3.8 79.2 1.0 OP2 A:G113 4.4 0.6 1.0 OP2 A:G114 4.4 0.1 1.0 N7 A:G114 4.5 0.3 1.0 P A:C70 4.8 94.5 1.0 OP1 A:C70 4.9 0.8 1.0

Iridium binding site 3 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir403 b:0.4 occ:1.00 IR A:IRI403 0.0 0.4 1.0 N5 A:IRI403 2.2 0.1 1.0 N1 A:IRI403 2.2 0.2 1.0 N4 A:IRI403 2.2 0.1 1.0 N2 A:IRI403 2.2 0.2 1.0 N6 A:IRI403 2.3 0.0 1.0 N3 A:IRI403 2.3 0.7 1.0 O6 A:G28 3.7 0.4 1.0 N7 A:G28 4.0 96.1 1.0 OP2 A:A27 4.1 87.6 1.0 C6 A:G28 4.4 92.1 1.0 N1 A:IRI405 4.4 0.5 0.9 C5 A:G28 4.5 87.5 1.0 OP1 A:A25 4.7 68.2 1.0 O5' A:A25 4.7 83.0 1.0 P A:A25 5.0 89.4 1.0 OP2 A:A25 5.0 0.7 1.0

Iridium binding site 4 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir404 b:0.4 occ:1.00 IR A:IRI404 0.0 0.4 1.0 N1 A:IRI404 2.2 37.2 1.0 N3 A:IRI404 2.2 60.0 1.0 N5 A:IRI404 2.2 0.5 1.0 N2 A:IRI404 2.3 0.7 1.0 N6 A:IRI404 2.3 0.2 1.0 N4 A:IRI404 2.3 0.7 1.0 O4 A:U255 3.9 0.9 1.0 O4 A:U256 4.0 0.8 1.0 O6 A:G14 4.2 95.1 1.0 O6 A:G16 4.2 0.4 1.0 O6 A:G15 4.3 83.4 1.0 N7 A:G14 4.6 97.5 1.0 O2' A:A12 4.7 0.4 1.0 N7 A:G15 4.7 82.7 1.0 C6 A:G14 4.8 92.2 1.0 C5 A:G14 5.0 85.0 1.0

Iridium binding site 5 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir405 b:1.0 occ:0.91 IR A:IRI405 0.0 1.0 0.9 N4 A:IRI405 2.2 96.9 0.9 N6 A:IRI405 2.2 0.1 0.9 N5 A:IRI405 2.2 0.7 0.9 N2 A:IRI405 2.2 0.8 0.9 N1 A:IRI405 2.3 0.5 0.9 N3 A:IRI405 2.3 86.0 0.9 N7 A:G30 4.8 0.4 1.0 O6 A:G30 4.8 91.8 1.0 O2' A:A35 4.9 0.3 1.0

Iridium binding site 6 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir406 b:0.8 occ:1.00 IR A:IRI406 0.0 0.8 1.0 N5 A:IRI406 2.2 86.1 1.0 N4 A:IRI406 2.2 0.4 1.0 N2 A:IRI406 2.2 0.8 1.0 N1 A:IRI406 2.3 70.1 1.0 N6 A:IRI406 2.3 0.2 1.0 N3 A:IRI406 2.3 66.8 1.0 O6 A:G36 3.9 81.7 1.0 O4 A:U37 4.5 95.4 1.0 C6 A:G36 4.9 80.5 1.0 N7 A:G36 4.9 71.8 1.0

Iridium binding site 7 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir407 b:0.4 occ:1.00 IR A:IRI407 0.0 0.4 1.0 N6 A:IRI407 2.2 0.7 1.0 N3 A:IRI407 2.2 35.3 1.0 N5 A:IRI407 2.3 0.3 1.0 N2 A:IRI407 2.3 0.9 1.0 N1 A:IRI407 2.3 71.5 1.0 N4 A:IRI407 2.3 0.1 1.0 O6 A:G244 4.1 0.7 1.0 OP1 A:C39 4.2 81.8 1.0 OP2 A:G243 4.3 95.3 1.0 N7 A:G244 4.6 95.6 1.0 O3' A:C38 4.9 94.0 1.0 N5 A:IRI408 4.9 0.5 0.6 OP1 A:C38 4.9 79.8 1.0 C6 A:G244 4.9 97.6 1.0

Iridium binding site 8 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir408 b:0.4 occ:0.58 IR A:IRI408 0.0 0.4 0.6 N2 A:IRI408 2.2 39.3 0.6 N1 A:IRI408 2.2 46.4 0.6 N6 A:IRI408 2.2 53.1 0.6 N5 A:IRI408 2.2 0.5 0.6 N3 A:IRI408 2.3 0.8 0.6 N4 A:IRI408 2.3 69.6 0.6 O6 A:G244 4.1 0.7 1.0 N2 A:IRI407 4.2 0.9 1.0 N7 A:G242 4.2 0.8 1.0 O6 A:G243 4.3 83.2 1.0 O6 A:G242 4.6 78.3 1.0 C6 A:G244 4.7 97.6 1.0 N7 A:G243 4.7 74.8 1.0

Iridium binding site 9 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir409 b:0.5 occ:0.70 IR A:IRI409 0.0 0.5 0.7 N1 A:IRI409 2.2 72.0 0.7 N5 A:IRI409 2.2 1.0 0.7 N4 A:IRI409 2.2 0.0 0.7 N3 A:IRI409 2.3 0.1 0.7 N2 A:IRI409 2.3 88.6 0.7 N6 A:IRI409 2.3 80.9 0.7 N7 A:G41 4.0 94.5 1.0 OP2 A:G41 4.4 80.5 1.0 O6 A:G41 4.7 91.9 1.0 C8 A:G41 4.8 87.1 1.0 OP2 A:C40 4.8 0.1 1.0 C5 A:G41 4.9 79.1 1.0

Iridium binding site 10 out of 28 in the Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of Oceanobacillus Iheyensis Group II Intron Domain 1 with Iridium Hexamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir410 b:0.9 occ:0.96 IR A:IRI410 0.0 0.9 1.0 N4 A:IRI410 2.2 67.0 1.0 N3 A:IRI410 2.2 0.1 1.0 N6 A:IRI410 2.2 0.6 1.0 N1 A:IRI410 2.3 0.5 1.0 N5 A:IRI410 2.3 0.2 1.0 N2 A:IRI410 2.3 86.0 1.0 OP1 A:G173 4.2 71.8 1.0 OP2 A:A120 4.3 65.6 1.0 OP1 A:A240 4.5 81.3 1.0 OP1 A:C119 4.5 74.8 1.0

C.Zhao, K.R.Rajashankar, M.Marcia, A.M.Pyle. Crystal Structure of Group II Intron Domain 1 Reveals A Template For Rna Assembly. Nat.Chem.Biol. V. 11 967 2015.
ISSN: ESSN 1552-4469
PubMed: 26502156
DOI: 10.1038/NCHEMBIO.1949