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Iridium in PDB 5jml: X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)

Enzymatic activity of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)

All present enzymatic activity of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking):
3.1.27.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking), PDB code: 5jml was solved by M.Caterino, A.A.Petruk, A.Vergara, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.59 / 2.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.592, 32.388, 72.595, 90.00, 89.97, 90.00
R / Rfree (%) 22.6 / 29.4

Other elements in 5jml:

The structure of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) (pdb code 5jml). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 10 binding sites of Iridium where determined in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking), PDB code: 5jml:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 10 in 5jml

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Iridium binding site 1 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir201

b:39.5
occ:1.00
 O A:HOH326 2.0 20.5 1.0
O A:O202 2.0 20.0 1.0
O A:HOH318 2.0 27.8 1.0
C A:CMO204 2.0 52.9 1.0
NE2 A:HIS105 2.3 30.4 1.0
CL A:CL203 2.3 35.4 1.0
CD2 A:HIS105 3.2 28.8 1.0
CE1 A:HIS105 3.2 30.4 1.0
O A:CMO204 3.2 47.9 1.0
CG A:HIS105 4.3 30.7 1.0
ND1 A:HIS105 4.3 30.5 1.0
CG2 A:THR78 4.9 31.2 1.0

Iridium binding site 2 out of 10 in 5jml

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Iridium binding site 2 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir205

b:41.0
occ:0.50
 C A:CMO206 2.0 32.3 0.5
O A:HOH334 2.0 35.7 0.5
O A:HOH328 2.0 36.4 0.5
O A:HOH332 2.0 31.1 0.5
SD A:MET29 2.3 37.9 1.0
O A:CMO206 3.2 29.8 0.5
CG A:MET29 3.6 33.5 1.0
CE A:MET29 3.6 36.2 1.0
OD2 A:ASP14 4.6 50.4 1.0
CB A:MET29 4.8 32.7 1.0
CA A:MET29 5.0 32.0 1.0

Iridium binding site 3 out of 10 in 5jml

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Iridium binding site 3 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir207

b:31.3
occ:0.50
 O A:HOH302 2.0 20.2 1.0
O A:HOH323 2.0 22.4 0.5
O A:HOH325 2.0 27.0 0.5
O A:HOH313 2.0 29.1 1.0
NE2 A:HIS119 2.3 29.4 0.5
CD2 A:HIS119 2.7 31.9 0.5
CE1 A:HIS119 3.4 31.0 0.5
OE2 A:GLU111 3.6 36.9 1.0
CG A:HIS119 3.9 31.1 0.5
ND1 A:HIS119 4.2 31.8 0.5
CD A:GLU111 4.2 34.9 1.0
CG2 A:VAL118 4.5 33.4 1.0
OE1 A:GLU111 4.6 33.5 1.0

Iridium binding site 4 out of 10 in 5jml

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Iridium binding site 4 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir207

b:41.3
occ:0.50
 O A:HOH325 2.0 32.5 0.5
O A:HOH323 2.0 28.1 0.5
O A:HOH327 2.0 38.1 1.0
NE2 A:HIS119 2.3 32.7 0.5
CE1 A:HIS119 3.2 31.7 0.5
CD2 A:HIS119 3.2 31.8 0.5
IR A:IR208 4.0 49.6 0.3
ND1 A:HIS119 4.3 31.8 0.5
ND1 A:HIS119 4.4 32.3 0.5
CG A:HIS119 4.4 31.8 0.5
O A:HOH305 4.5 22.2 1.0
CE1 A:HIS119 4.9 31.0 0.5

Iridium binding site 5 out of 10 in 5jml

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Iridium binding site 5 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir208

b:49.6
occ:0.30
 O A:HOH305 2.0 22.2 1.0
O A:HOH323 2.5 28.1 0.5
NE2 A:GLN11 2.5 55.8 1.0
NE2 A:HIS12 2.7 23.3 1.0
NZ A:LYS41 3.0 66.0 1.0
CE1 A:HIS12 3.5 24.4 1.0
CD A:GLN11 3.7 54.3 1.0
CD2 A:HIS12 3.8 23.0 1.0
O A:HOH327 4.0 38.1 1.0
IR A:IR207 4.0 41.3 0.5
NE2 A:HIS119 4.2 32.7 0.5
CD2 A:HIS119 4.2 31.8 0.5
OE1 A:GLN11 4.3 60.2 1.0
CE A:LYS41 4.4 60.7 1.0
CB A:GLN11 4.4 43.5 1.0
CG A:GLN11 4.6 49.2 1.0
OD1 A:ASN44 4.7 32.1 1.0
ND1 A:HIS12 4.7 24.8 1.0
CE1 A:HIS119 4.8 31.7 0.5
N A:PHE120 4.9 30.8 1.0
CG A:HIS12 4.9 23.6 1.0
CG A:HIS119 5.0 31.8 0.5

Iridium binding site 6 out of 10 in 5jml

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Iridium binding site 6 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir209

b:69.1
occ:0.60
 N A:LYS1 2.3 62.4 1.0
CL A:CL210 2.5 33.1 0.6
CA A:LYS1 3.6 59.5 1.0
O A:LYS1 3.8 47.8 1.0
C A:LYS1 4.0 52.7 1.0
CB A:LYS1 4.8 63.5 1.0

Iridium binding site 7 out of 10 in 5jml

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Iridium binding site 7 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir201

b:41.7
occ:0.50
 C B:CMO202 2.0 43.6 0.5
O B:HOH301 2.0 35.3 0.5
O B:HOH314 2.0 28.2 0.5
O B:HOH325 2.0 40.8 0.5
O B:HOH323 2.0 34.8 0.5
NE2 B:HIS119 2.2 28.0 0.5
CE1 B:HIS119 3.0 28.0 0.5
O B:CMO202 3.2 41.1 0.5
CD2 B:HIS119 3.3 28.0 0.5
O B:HOH327 3.8 18.9 1.0
ND1 B:HIS119 4.1 27.3 0.5
IR B:IR207 4.2 40.3 0.3
CG B:HIS119 4.3 27.6 0.5
O B:HOH311 5.0 25.9 1.0

Iridium binding site 8 out of 10 in 5jml

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Iridium binding site 8 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir201

b:38.5
occ:0.50
 NE2 B:HIS119 1.8 27.6 0.5
O B:HOH301 2.0 24.9 0.5
O B:HOH314 2.0 22.3 0.5
O B:HOH325 2.0 22.4 0.5
O B:HOH323 2.0 24.6 0.5
CE1 B:HIS119 2.7 27.7 0.5
CD2 B:HIS119 2.9 26.1 0.5
ND1 B:HIS119 3.9 27.3 0.5
CG B:HIS119 4.0 26.7 0.5
CG2 B:VAL118 4.6 25.7 1.0

Iridium binding site 9 out of 10 in 5jml

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Iridium binding site 9 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir203

b:41.3
occ:1.00
 C B:CMO206 2.0 42.2 1.0
O B:HOH320 2.0 19.4 1.0
CL B:CL204 2.2 30.2 1.0
NE2 B:HIS105 2.2 30.7 1.0
O B:HOH329 2.5 28.0 1.0
CL B:CL205 2.6 50.9 1.0
CD2 B:HIS105 3.0 29.2 1.0
O B:CMO206 3.2 37.8 1.0
CE1 B:HIS105 3.4 29.9 1.0
CG B:HIS105 4.2 28.6 1.0
ND1 B:HIS105 4.4 30.9 1.0
CG2 B:THR78 4.6 26.1 1.0

Iridium binding site 10 out of 10 in 5jml

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Iridium binding site 10 out of 10 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Penthachlorocarbonyliridate(III) (2 Months of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir207

b:40.3
occ:0.30
 O B:HOH327 2.1 18.9 1.0
NE2 B:GLN11 2.5 32.6 1.0
O B:HOH323 2.5 34.8 0.5
NE2 B:HIS12 2.7 29.6 1.0
O B:HOH311 3.0 25.9 1.0
NZ B:LYS41 3.1 54.8 1.0
CE1 B:HIS12 3.5 29.4 1.0
CD B:GLN11 3.7 34.3 1.0
CD2 B:HIS12 3.8 29.1 1.0
O B:HOH325 3.9 40.8 0.5
IR B:IR201 4.2 41.7 0.5
OE1 B:GLN11 4.4 38.0 1.0
CB B:GLN11 4.4 27.9 1.0
CE B:LYS41 4.5 50.1 1.0
CG B:GLN11 4.6 30.2 1.0
C B:CMO202 4.7 43.6 0.5
ND1 B:HIS12 4.7 29.2 1.0
OD1 B:ASN44 4.7 28.2 1.0
CG B:HIS12 4.8 27.9 1.0
NE2 B:HIS119 4.9 28.0 0.5
CD2 B:HIS119 5.0 28.0 0.5

Reference:

M.Caterino, A.A.Petruk, A.Vergara, G.Ferraro, D.Marasco, F.Doctorovich, D.A.Estrin, A.Merlino. Mapping the Protein-Binding Sites For Iridium(III)-Based Co-Releasing Molecules. Dalton Trans V. 45 12206 2016.
ISSN: ESSN 1477-9234
PubMed: 27411388
DOI: 10.1039/C6DT01685E
Page generated: Sun Dec 13 22:40:25 2020

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