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Iridium in PDB 5e2d: Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr

Protein crystallography data

The structure of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr, PDB code: 5e2d was solved by B.Maity, K.Fukumori, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.03 / 1.87
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.190, 181.190, 181.190, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Other elements in 5e2d:

The structure of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr also contains other interesting chemical elements:

Cadmium (Cd) 1 atom
Palladium (Pd) 3 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr (pdb code 5e2d). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 6 binding sites of Iridium where determined in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr, PDB code: 5e2d:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6;

Iridium binding site 1 out of 6 in 5e2d

Go back to Iridium Binding Sites List in 5e2d
Iridium binding site 1 out of 6 in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir201

b:40.7
occ:0.40
IR A:IR3205 1.7 37.8 0.2
NE2 A:HIS49 2.1 43.2 1.0
CE1 A:HIS49 2.6 43.6 1.0
IR A:IR3202 2.7 46.1 0.4
CD2 A:HIS49 3.3 43.4 1.0
ND1 A:HIS49 3.9 44.6 1.0
CG A:HIS49 4.2 31.2 1.0
O A:HOH357 4.3 32.8 1.0
CG A:GLU53 4.5 37.5 1.0
CB A:GLU53 4.7 24.5 1.0

Iridium binding site 2 out of 6 in 5e2d

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Iridium binding site 2 out of 6 in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir202

b:46.1
occ:0.40
IR A:IR3205 2.1 37.8 0.2
CE1 A:HIS49 2.6 43.6 1.0
IR A:IR3201 2.7 40.7 0.4
NE2 A:HIS49 2.9 43.2 1.0
ND1 A:HIS49 3.7 44.6 1.0
CD2 A:HIS49 4.1 43.4 1.0
CG A:HIS49 4.5 31.2 1.0

Iridium binding site 3 out of 6 in 5e2d

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Iridium binding site 3 out of 6 in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir203

b:38.3
occ:0.15
CD2 A:PHE128 2.2 47.9 1.0
CE2 A:PHE128 3.0 40.4 1.0
CG A:PHE128 3.2 49.0 1.0
CB A:PHE128 3.5 49.3 1.0
CA A:PHE128 4.0 49.2 1.0
CZ A:PHE128 4.3 39.2 1.0
CE1 A:HIS124 4.3 41.1 1.0
CD1 A:PHE128 4.5 45.8 1.0
O A:HOH338 4.6 36.0 1.0
NE2 A:HIS124 4.6 41.1 1.0
OE1 A:GLN71 4.8 34.8 1.0
CG A:MET68 4.8 26.6 1.0
CE1 A:PHE128 4.9 51.4 1.0
C A:PHE128 4.9 51.5 1.0
O A:PHE128 5.0 38.1 1.0
CB A:MET68 5.0 20.5 1.0

Iridium binding site 4 out of 6 in 5e2d

Go back to Iridium Binding Sites List in 5e2d
Iridium binding site 4 out of 6 in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir204

b:58.3
occ:0.40
CE1 A:HIS114 2.1 54.3 0.5
NE2 A:HIS114 2.7 47.3 0.5
OG A:SER118 3.0 63.5 1.0
NE2 A:HIS114 3.0 53.9 0.5
ND1 A:HIS114 3.1 52.0 0.5
CD2 A:HIS114 3.1 45.5 0.5
SG A:CYS126 3.2 82.3 1.0
PD A:PD211 3.4 54.5 0.6
CB A:CYS126 3.5 59.5 1.0
CE1 A:HIS114 3.9 46.1 0.5
CD2 A:HIS114 4.2 54.9 0.5
CG A:HIS114 4.2 52.6 0.5
CG A:HIS114 4.3 45.5 0.5
CB A:SER118 4.4 62.0 1.0
ND1 A:HIS114 4.7 42.0 0.5
O A:HIS114 4.7 43.3 1.0
CA A:CYS126 4.9 50.5 1.0
CA A:SER118 5.0 55.1 1.0

Iridium binding site 5 out of 6 in 5e2d

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Iridium binding site 5 out of 6 in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir205

b:37.8
occ:0.20
IR A:IR3201 1.7 40.7 0.4
IR A:IR3202 2.1 46.1 0.4
NE2 A:HIS49 2.5 43.2 1.0
CE1 A:HIS49 3.2 43.6 1.0
CD2 A:HIS49 3.6 43.4 1.0
ND1 A:HIS49 4.3 44.6 1.0
CG A:HIS49 4.5 31.2 1.0

Iridium binding site 6 out of 6 in 5e2d

Go back to Iridium Binding Sites List in 5e2d
Iridium binding site 6 out of 6 in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir206

b:33.0
occ:0.20
O A:HOH353 3.4 36.0 1.0

Reference:

B.Maity, K.Fukumori, S.Abe, T.Ueno. Immobilization of Two Organometallic Complexes Into A Single Cage to Construct Protein-Based Microcompartments Chem.Commun.(Camb.) V. 52 5463 2016.
ISSN: ESSN 1364-548X
PubMed: 27021005
DOI: 10.1039/C6CC00679E
Page generated: Sun Dec 13 22:40:21 2020

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