Atomistry » Iridium » PDB 5e1u-7onm » 5jmg
Atomistry »
  Iridium »
    PDB 5e1u-7onm »
      5jmg »

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

Go back to Iridium Binding Sites List in 5jmg
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

Go back to Iridium Binding Sites List in 5jmg
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

Go back to Iridium Binding Sites List in 5jmg
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

Go back to Iridium Binding Sites List in 5jmg
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

Go back to Iridium Binding Sites List in 5jmg
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

Go back to Iridium Binding Sites List in 5jmg
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: Sun Dec 13 22:40:23 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy