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Iridium in PDB 3irw: Structure of A C-Di-Gmp Riboswitch From V. Cholerae

Protein crystallography data

The structure of Structure of A C-Di-Gmp Riboswitch From V. Cholerae, PDB code: 3irw was solved by K.D.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.69 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.461, 45.123, 76.573, 90.00, 96.79, 90.00
R / Rfree (%) 19.6 / 25.1

Other elements in 3irw:

The structure of Structure of A C-Di-Gmp Riboswitch From V. Cholerae also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae (pdb code 3irw). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 9 binding sites of Iridium where determined in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae, PDB code: 3irw:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iridium binding site 1 out of 9 in 3irw

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Iridium binding site 1 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir670

b:43.6
occ:1.00
 IR R:IRI670 0.0 43.6 1.0
N1 R:IRI670 2.0 40.6 1.0
N5 R:IRI670 2.0 38.3 1.0
N6 R:IRI670 2.0 39.3 1.0
N3 R:IRI670 2.0 38.4 1.0
N4 R:IRI670 2.0 38.3 1.0
N2 R:IRI670 2.0 38.5 1.0
OP1 R:A47 3.5 26.4 1.0
O R:HOH182 3.6 48.1 1.0
OP1 R:A49 3.9 25.9 1.0
O3' R:C46 4.3 32.1 1.0
P R:A47 4.4 26.5 1.0
OP2 R:A49 4.4 26.4 1.0
O5' R:A47 4.5 27.9 1.0
P R:A49 4.7 25.5 1.0

Iridium binding site 2 out of 9 in 3irw

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Iridium binding site 2 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir2

b:75.6
occ:1.00
 IR R:IRI2 0.0 75.6 1.0
N1 R:IRI2 2.0 75.4 1.0
N5 R:IRI2 2.0 75.5 1.0
N3 R:IRI2 2.0 75.6 1.0
N2 R:IRI2 2.0 75.3 1.0
N4 R:IRI2 2.0 74.6 1.0
N6 R:IRI2 2.0 75.9 1.0
O R:HOH104 3.7 25.2 1.0
O6 R:G57 3.8 45.9 1.0
N6 R:IRI672 3.9 75.8 0.5
O R:HOH102 4.1 65.3 1.0
N7 R:G56 4.2 52.4 1.0
N7 R:G57 4.2 49.6 1.0
O6 R:G56 4.2 53.8 1.0
O4 R:U81 4.3 34.8 1.0
O2 R:U53 4.6 51.0 1.0
O6 R:G80 4.6 35.6 1.0
C6 R:G57 4.7 46.1 1.0
N4 R:C58 4.8 44.2 1.0
C5 R:G57 4.9 47.7 1.0
C6 R:G56 4.9 52.7 1.0
C5 R:G56 4.9 52.3 1.0
O2' R:U53 4.9 45.5 1.0

Iridium binding site 3 out of 9 in 3irw

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Iridium binding site 3 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir3

b:64.9
occ:1.00
 IR R:IRI3 0.0 64.9 1.0
N4 R:IRI3 2.0 64.7 1.0
N1 R:IRI3 2.0 65.1 1.0
N3 R:IRI3 2.0 65.9 1.0
N6 R:IRI3 2.0 63.4 1.0
N5 R:IRI3 2.0 62.8 1.0
N2 R:IRI3 2.0 63.1 1.0
O1P R:C2E1 3.1 32.6 1.0
O2P R:C2E1 4.3 29.2 1.0
P1 R:C2E1 4.4 30.1 1.0
N7 R:G20 4.4 68.9 1.0
O6 R:G20 4.4 67.2 1.0
N7 R:G19 4.7 62.3 1.0
O6 R:G19 4.9 57.7 1.0

Iridium binding site 4 out of 9 in 3irw

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Iridium binding site 4 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir4

b:48.5
occ:0.50
 IR R:IRI4 0.0 48.5 0.5
N1 R:IRI4 2.0 47.8 0.5
N2 R:IRI4 2.0 46.6 0.5
N6 R:IRI4 2.0 48.3 0.5
N3 R:IRI4 2.0 47.7 0.5
N5 R:IRI4 2.0 48.8 0.5
N4 R:IRI4 2.0 47.6 0.5
N2 R:IRI7 3.3 77.5 0.5
N3 R:IRI7 3.4 77.4 0.5
N7 R:G86 3.6 40.4 1.0
O R:HOH172 3.7 43.6 1.0
O6 R:G87 3.8 36.2 1.0
OP2 R:G86 3.9 41.4 1.0
N6 R:IRI7 4.1 77.8 0.5
C8 R:G86 4.2 40.0 1.0
IR R:IRI7 4.4 78.0 0.5
N7 R:G87 4.6 35.4 1.0
C6 R:G87 4.7 34.7 1.0
C5 R:G86 4.8 41.4 1.0
OP2 R:G85 4.8 42.0 1.0
N4 R:C52 4.8 34.9 1.0

Iridium binding site 5 out of 9 in 3irw

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Iridium binding site 5 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir5

b:0.1
occ:0.75
 IR R:IRI5 0.0 0.1 0.8
N2 R:IRI5 2.0 0.9 0.8
N1 R:IRI5 2.0 0.9 0.8
N6 R:IRI5 2.0 0.7 0.8
N4 R:IRI5 2.0 0.1 0.8
N5 R:IRI5 2.0 0.5 0.8
N3 R:IRI5 2.0 0.6 0.8
O2B R:GTP8 3.4 97.4 1.0
O6 R:G97 3.5 66.2 1.0
O1B R:GTP8 3.7 96.9 1.0
O4 R:U10 3.9 55.8 1.0
PB R:GTP8 4.1 97.2 1.0
C6 R:G97 4.5 66.8 1.0
O6 R:G9 4.5 50.5 1.0
O3B R:GTP8 4.7 98.1 1.0
O4 R:U96 4.8 0.9 1.0
N7 R:G97 4.8 69.0 1.0

Iridium binding site 6 out of 9 in 3irw

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Iridium binding site 6 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir6

b:73.5
occ:0.50
 IR R:IRI6 0.0 73.5 0.5
N4 R:IRI6 2.0 72.8 0.5
N5 R:IRI6 2.0 72.5 0.5
N6 R:IRI6 2.0 72.7 0.5
N2 R:IRI6 2.0 72.3 0.5
N1 R:IRI6 2.0 72.3 0.5
N3 R:IRI6 2.0 72.4 0.5
O R:HOH180 3.8 62.7 1.0
O6 R:G32 4.2 59.1 1.0
N7 R:G32 4.6 52.1 1.0
C6 R:G32 4.9 54.8 1.0

Iridium binding site 7 out of 9 in 3irw

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Iridium binding site 7 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir7

b:78.0
occ:0.50
 IR R:IRI7 0.0 78.0 0.5
N3 R:IRI7 2.0 77.4 0.5
N5 R:IRI7 2.0 77.7 0.5
N1 R:IRI7 2.0 77.8 0.5
N6 R:IRI7 2.0 77.8 0.5
N2 R:IRI7 2.0 77.5 0.5
N4 R:IRI7 2.0 77.4 0.5
N6 R:IRI4 3.2 48.3 0.5
N3 R:IRI4 3.6 47.7 0.5
N7 R:G87 4.0 35.4 1.0
O6 R:G88 4.1 39.2 1.0
N4 R:IRI4 4.1 47.6 0.5
IR R:IRI4 4.4 48.5 0.5
O4 R:U89 4.4 35.8 1.0
N7 R:G88 4.5 37.8 1.0
O6 R:G87 4.6 36.2 1.0
OP2 R:G87 4.8 34.0 1.0
C5 R:G87 4.8 34.5 1.0
C8 R:G87 4.8 34.5 1.0
C6 R:G88 5.0 37.5 1.0
C6 R:G87 5.0 34.7 1.0

Iridium binding site 8 out of 9 in 3irw

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Iridium binding site 8 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir671

b:86.2
occ:0.50
 IR R:IRI671 0.0 86.2 0.5
N2 R:IRI671 2.0 85.9 0.5
N1 R:IRI671 2.0 86.1 0.5
N3 R:IRI671 2.0 86.0 0.5
N4 R:IRI671 2.0 85.9 0.5
N6 R:IRI671 2.0 85.5 0.5
N5 R:IRI671 2.0 85.6 0.5
OP2 R:C84 4.3 40.5 1.0
O2' R:G83 4.3 27.2 1.0
OP1 R:A25 4.6 37.0 1.0
O3' R:A24 4.9 40.3 1.0

Iridium binding site 9 out of 9 in 3irw

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Iridium binding site 9 out of 9 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ir672

b:76.5
occ:0.50
 IR R:IRI672 0.0 76.5 0.5
N6 R:IRI672 2.0 75.8 0.5
N1 R:IRI672 2.0 75.7 0.5
N2 R:IRI672 2.0 75.9 0.5
N3 R:IRI672 2.0 75.6 0.5
N4 R:IRI672 2.0 75.6 0.5
N5 R:IRI672 2.0 75.6 0.5
N7 R:G79 3.7 45.6 1.0
O6 R:G79 4.3 49.4 1.0
O R:HOH104 4.4 25.2 1.0
C5 R:G79 4.5 46.4 1.0
C8 R:G79 4.6 46.2 1.0
C6 R:G79 4.8 46.9 1.0
N2 R:IRI2 4.9 75.3 1.0

Reference:

K.D.Smith, S.V.Lipchock, T.D.Ames, J.Wang, R.R.Breaker, S.A.Strobel. Structural Basis of Ligand Binding By A C-Di-Gmp Riboswitch. Nat.Struct.Mol.Biol. V. 16 1218 2009.
ISSN: ISSN 1545-9993
PubMed: 19898477
DOI: 10.1038/NSMB.1702
Page generated: Mon Aug 12 03:21:06 2024

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