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Iridium in PDB 5od5: Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst

Protein crystallography data

The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5 was solved by A.K.Duhme-Klair, D.J.Raines, J.E.Clarke, E.V.Blagova, E.J.Dodson, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.42 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.692, 62.759, 68.195, 87.38, 76.90, 79.27
R / Rfree (%) 17.7 / 22.3

Other elements in 5od5:

The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst also contains other interesting chemical elements:

Iron (Fe) 3 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst (pdb code 5od5). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 8 binding sites of Iridium where determined in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iridium binding site 1 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 1 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir402

b:46.0
occ:0.31
C6 A:9RT404 1.2 62.7 0.4
N2 A:9RT404 1.4 52.3 0.4
C5 A:9RT404 1.7 58.6 0.4
S1 A:9RT404 1.8 55.7 0.4
C4 A:9RT404 1.9 54.7 0.4
NE2 A:HIS227 2.5 32.8 0.5
CE1 A:HIS227 2.6 38.4 0.5
CE1 A:HIS227 2.7 67.5 0.0
O1 A:9RT404 2.7 51.8 0.4
C7 A:9RT404 2.7 57.9 0.4
O2 A:9RT404 2.8 54.5 0.4
C12 A:9RT404 2.8 51.4 0.4
IR1 A:RIR405 3.1 59.0 0.4
C3 A:9RT404 3.1 56.5 0.4
N3 A:9RT404 3.5 58.9 0.4
NE2 A:HIS227 3.6 67.8 0.0
ND1 A:HIS227 3.7 67.5 0.0
C8 A:9RT404 3.7 60.2 0.4
C13 A:9RT404 3.7 55.7 0.4
CD2 A:HIS227 3.8 40.8 0.5
C2 A:9RT404 3.9 57.5 0.4
ND1 A:HIS227 4.0 36.6 0.5
C20 A:RIR405 4.3 57.9 0.4
C25 A:RIR405 4.4 55.6 0.4
C19 A:RIR405 4.4 57.7 0.4
CG A:HIS227 4.5 40.1 0.5
C24 A:RIR405 4.7 54.9 0.4
C21 A:RIR405 4.7 58.8 0.4
CAQ A:95B403 4.7 53.0 1.0
C11 A:9RT404 4.8 63.5 0.4
CD2 A:HIS227 4.8 67.5 0.0
CG A:HIS227 4.8 67.5 0.0
C18 A:RIR405 4.9 57.4 0.4
C9 A:9RT404 5.0 61.1 0.4

Iridium binding site 2 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 2 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir405

b:59.0
occ:0.43
IR1 A:RIR405 0.0 59.0 0.4
NE2 A:HIS227 1.5 67.8 0.0
N3 A:9RT404 1.9 58.9 0.4
N2 A:9RT404 1.9 52.3 0.4
C19 A:RIR405 2.0 57.7 0.4
C20 A:RIR405 2.0 57.9 0.4
C21 A:RIR405 2.0 58.8 0.4
C18 A:RIR405 2.0 57.4 0.4
C17 A:RIR405 2.0 57.1 0.4
CE1 A:HIS227 2.1 67.5 0.0
NE2 A:HIS227 2.2 32.8 0.5
C7 A:9RT404 2.4 57.9 0.4
CD2 A:HIS227 2.5 40.8 0.5
C6 A:9RT404 2.5 62.7 0.4
CD2 A:HIS227 2.8 67.5 0.0
C11 A:9RT404 2.9 63.5 0.4
IR A:IR402 3.1 46.0 0.3
C24 A:RIR405 3.1 54.9 0.4
C25 A:RIR405 3.1 55.6 0.4
C26 A:RIR405 3.1 56.5 0.4
C23 A:RIR405 3.1 57.7 0.4
C22 A:RIR405 3.1 54.3 0.4
ND1 A:HIS227 3.3 67.5 0.0
S1 A:9RT404 3.4 55.7 0.4
CE1 A:HIS227 3.5 38.4 0.5
C8 A:9RT404 3.6 60.2 0.4
CG A:HIS227 3.7 67.5 0.0
O1 A:9RT404 3.7 51.8 0.4
CG A:HIS227 3.8 40.1 0.5
C10 A:9RT404 4.0 64.0 0.4
O2 A:9RT404 4.0 54.5 0.4
C9 A:9RT404 4.2 61.1 0.4
ND1 A:HIS227 4.3 36.6 0.5
OG1 A:THR226 4.6 71.7 1.0
C5 A:9RT404 4.6 58.6 0.4
C4 A:9RT404 4.8 54.7 0.4

Iridium binding site 3 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 3 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir403

b:81.8
occ:0.16
OG1 B:THR226 2.0 99.0 1.0
CB B:THR226 3.4 0.7 1.0
O B:GLY225 4.0 0.9 1.0
N B:THR226 4.1 0.1 1.0
CG2 B:THR226 4.1 0.2 1.0
C B:GLY225 4.1 0.2 1.0
CA B:THR226 4.3 0.5 1.0
CA B:GLY225 5.0 0.1 1.0

Iridium binding site 4 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 4 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir404

b:90.4
occ:0.16
IR B:IR405 2.0 94.5 0.2
O B:THR226 2.9 0.7 1.0
CB B:THR226 3.1 0.7 1.0
OG1 B:THR226 3.7 99.0 1.0
C B:THR226 3.8 0.8 1.0
CG2 B:THR226 3.8 0.2 1.0
CA B:THR226 4.0 0.5 1.0
ND1 B:HIS227 4.5 0.5 1.0

Iridium binding site 5 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 5 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir405

b:94.5
occ:0.21
IR B:IR404 2.0 90.4 0.2
O B:THR226 2.8 0.7 1.0
ND1 B:HIS227 3.1 0.5 1.0
CE1 B:HIS227 3.4 0.5 1.0
C B:THR226 4.0 0.8 1.0
CG B:HIS227 4.2 0.7 1.0
CB B:THR226 4.5 0.7 1.0
NE2 B:HIS227 4.5 0.5 1.0
CA B:THR226 4.8 0.5 1.0
CB B:HIS227 4.9 0.1 1.0
N B:HIS227 5.0 0.8 1.0

Iridium binding site 6 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 6 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ir402

b:52.8
occ:0.17
C4 C:9RT405 1.4 42.7 0.6
C5 C:9RT405 1.5 41.6 0.6
S1 C:9RT405 1.9 43.8 0.6
N2 C:9RT405 2.0 38.2 0.6
C6 C:9RT405 2.5 36.7 0.6
O1 C:9RT405 2.6 41.7 0.6
C3 C:9RT405 2.6 39.7 0.6
C12 C:9RT405 2.7 38.0 0.6
O2 C:9RT405 3.2 43.8 0.6
CE1 C:HIS227 3.3 70.0 1.0
C7 C:9RT405 3.5 33.6 0.6
C2 C:9RT405 3.5 36.8 0.6
NE2 C:HIS227 3.5 68.8 1.0
C13 C:9RT405 3.5 34.6 0.6
IR1 C:RIR406 3.8 43.6 0.6
ND1 C:HIS227 4.1 74.1 1.0
N3 C:9RT405 4.1 28.2 0.6
C8 C:9RT405 4.3 33.1 0.6
CD2 C:HIS227 4.5 70.8 1.0
CG C:HIS227 4.8 73.5 1.0
C1 C:9RT405 4.9 38.9 0.6
C20 C:RIR406 5.0 49.3 0.6
C19 C:RIR406 5.0 45.6 0.6

Iridium binding site 7 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 7 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ir403

b:66.0
occ:0.44
ND1 C:HIS227 2.3 74.1 1.0
CE1 C:HIS227 3.0 70.0 1.0
CG C:HIS227 3.4 73.5 1.0
CB C:HIS227 3.8 67.0 1.0
NE2 C:HIS227 4.2 68.8 1.0
CD2 C:HIS227 4.3 70.8 1.0

Iridium binding site 8 out of 8 in 5od5

Go back to Iridium Binding Sites List in 5od5
Iridium binding site 8 out of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ir406

b:43.6
occ:0.63
IR1 C:RIR406 0.0 43.6 0.6
C18 C:RIR406 2.0 49.1 0.6
C17 C:RIR406 2.0 49.7 0.6
N2 C:9RT405 2.0 38.2 0.6
C21 C:RIR406 2.0 53.3 0.6
C19 C:RIR406 2.0 45.6 0.6
C20 C:RIR406 2.0 49.3 0.6
N3 C:9RT405 2.1 28.2 0.6
NE2 C:HIS227 2.2 68.8 1.0
C6 C:9RT405 2.8 36.7 0.6
C7 C:9RT405 2.8 33.6 0.6
C11 C:9RT405 3.1 35.4 0.6
C22 C:RIR406 3.1 54.4 0.6
C26 C:RIR406 3.1 51.1 0.6
C25 C:RIR406 3.2 44.8 0.6
CD2 C:HIS227 3.2 70.8 1.0
C23 C:RIR406 3.2 53.2 0.6
C24 C:RIR406 3.2 52.9 0.6
CE1 C:HIS227 3.2 70.0 1.0
S1 C:9RT405 3.4 43.8 0.6
O1 C:9RT405 3.5 41.7 0.6
IR C:IR402 3.8 52.8 0.2
O2 C:9RT405 4.0 43.8 0.6
C8 C:9RT405 4.2 33.1 0.6
ND1 C:HIS227 4.3 74.1 1.0
CG C:HIS227 4.3 73.5 1.0
C10 C:9RT405 4.4 35.3 0.6
C5 C:9RT405 4.7 41.6 0.6
C9 C:9RT405 4.8 33.1 0.6

Reference:

A.D.J.Raines, J.E.Clarke, E.Blagova, E.J.Dodson, K.S.Wilson, A.K.Duhme-Klair. Redox-Switchable Siderophore Anchor Enables Reversible Artificial Metalloenzyme Assembly Nat Catal 2018.
DOI: 10.1038/S41929-018-0124-3
Page generated: Mon Aug 12 03:37:26 2024

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