Atomistry » Iridium » PDB 1c1k-5de8 » 3irw
Atomistry »
  Iridium »
    PDB 1c1k-5de8 »
      3irw »

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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Go back to Iridium Binding Sites List in 3irw
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy