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Iridium in PDB 5jmg: X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days of Soaking)

Enzymatic activity of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days of Soaking)

All present enzymatic activity of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days of Soaking):
3.1.27.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days of Soaking), PDB code: 5jmg 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) 72.27 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.932, 32.652, 72.273, 90.00, 90.28, 90.00
R / Rfree (%) 17.3 / 22.6

Other elements in 5jmg:

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

Iridium binding site 1 out of 6 in 5jmg

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Iridium binding site 1 out of 6 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days 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 Pentachlorocarbonyliridate(III) (4 Days of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir201

b:35.1
occ:0.50
 CL A:CL202 2.0 30.3 0.5
O A:HOH381 2.0 25.8 0.5
C A:CMO203 2.0 33.7 0.5
NE2 A:HIS105 2.3 23.4 1.0
O A:HOH394 2.4 26.4 0.5
O A:HOH392 2.4 25.6 0.5
CE1 A:HIS105 3.1 21.4 1.0
CD2 A:HIS105 3.2 22.3 1.0
O A:CMO203 3.2 31.3 0.5
ND1 A:HIS105 4.2 20.7 1.0
CG A:HIS105 4.3 20.0 1.0
O A:HOH351 4.5 34.9 1.0

Iridium binding site 2 out of 6 in 5jmg

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Iridium binding site 2 out of 6 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days 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 Pentachlorocarbonyliridate(III) (4 Days of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir204

b:47.0
occ:0.40
 C A:CMO205 2.0 26.0 0.4
SD A:MET29 2.6 30.6 1.0
O A:HOH367 2.6 27.2 0.4
O A:HOH409 2.7 30.5 0.4
O A:HOH389 2.8 36.2 1.0
O A:CMO205 3.2 29.1 0.4
CE A:MET29 3.7 28.9 1.0
CG A:MET29 4.0 24.9 1.0
OG A:SER32 4.4 30.7 1.0
O A:HOH318 4.5 45.5 1.0
OD2 A:ASP14 5.0 28.4 1.0

Iridium binding site 3 out of 6 in 5jmg

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Iridium binding site 3 out of 6 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days 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 Pentachlorocarbonyliridate(III) (4 Days of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir206

b:60.8
occ:0.55
 CL A:CL207 2.3 19.3 0.6
N A:LYS1 2.8 50.3 1.0
CA A:LYS1 3.0 49.6 1.0
C A:LYS1 4.0 50.1 1.0
CB A:LYS1 4.1 57.5 1.0
O A:LYS1 4.3 53.6 1.0
N A:GLU2 4.9 40.6 1.0

Iridium binding site 4 out of 6 in 5jmg

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Iridium binding site 4 out of 6 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days 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 Pentachlorocarbonyliridate(III) (4 Days of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir208

b:49.4
occ:0.30
 IR A:IR208 0.0 49.4 0.3
O A:HOH395 2.0 14.2 0.3
ND1 A:HIS119 2.4 22.7 0.5
ND1 A:HIS119 2.5 22.4 0.5
O A:HOH401 2.7 41.1 1.0
CE1 A:HIS119 2.7 25.0 0.5
CG A:HIS119 3.0 22.3 0.5
O A:HOH307 3.2 43.8 1.0
NE2 A:HIS119 3.2 24.3 0.5
CE1 A:HIS119 3.3 22.4 0.5
CG A:HIS119 3.3 21.2 0.5
CD2 A:HIS119 3.4 21.3 0.5
CB A:HIS119 3.7 20.7 0.5
CB A:HIS119 3.7 21.1 0.5
NE2 A:HIS119 4.3 19.9 0.5
CD2 A:HIS119 4.3 21.1 0.5
O A:HOH361 4.5 28.6 1.0
CA A:HIS119 4.9 19.8 0.5
CA A:HIS119 4.9 20.0 0.5
IR A:IR208 5.0 41.1 0.3

Iridium binding site 5 out of 6 in 5jmg

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Iridium binding site 5 out of 6 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days 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 Pentachlorocarbonyliridate(III) (4 Days of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir208

b:41.1
occ:0.30
 IR A:IR208 0.0 41.1 0.3
NE2 A:HIS119 2.3 24.3 0.5
O A:HOH369 2.4 31.2 1.0
CD2 A:HIS119 2.8 21.3 0.5
O A:HOH362 2.8 47.9 1.0
O A:HOH315 2.9 22.9 1.0
OE2 A:GLU111 2.9 14.1 0.3
CE1 A:HIS119 3.5 25.0 0.5
OE1 A:GLU111 3.9 26.4 0.7
OE2 A:GLU111 4.0 28.6 0.7
CG A:HIS119 4.1 22.3 0.5
CD A:GLU111 4.1 25.9 0.7
CD A:GLU111 4.1 14.5 0.3
ND1 A:HIS119 4.4 22.7 0.5
CG2 A:VAL118 4.4 21.6 1.0
O A:HOH384 4.7 25.0 1.0
OE1 A:GLU111 4.9 12.3 0.3
IR A:IR208 5.0 49.4 0.3

Iridium binding site 6 out of 6 in 5jmg

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Iridium binding site 6 out of 6 in the X-Ray Structure of the Complex Between Bovine Pancreatic Ribonuclease and Pentachlorocarbonyliridate(III) (4 Days 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 Pentachlorocarbonyliridate(III) (4 Days of Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir201

b:32.6
occ:0.40
 O B:HOH351 2.0 14.1 0.4
C B:CMO203 2.0 27.0 0.4
O B:HOH380 2.0 18.5 0.4
NE2 B:HIS119 2.2 19.7 0.4
O B:HOH409 2.5 19.8 0.4
CL B:CL202 2.7 24.5 0.6
CD2 B:HIS119 3.0 18.2 0.4
O B:CMO203 3.2 27.8 0.4
O B:HOH380 3.3 28.7 0.6
CE1 B:HIS119 3.3 19.6 0.4
OE1 B:GLU111 3.9 23.5 0.4
CG B:HIS119 4.3 19.0 0.4
ND1 B:HIS119 4.4 18.2 0.4
CG2 B:VAL118 4.5 18.5 1.0
O B:HOH417 4.8 28.2 0.5
O B:HOH388 4.9 26.4 1.0
CL B:CL204 5.0 26.8 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: Mon Aug 12 03:35:47 2024

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