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: Sun Dec 13 22:39:41 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy