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Iridium in PDB 4nht: X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days)

Enzymatic activity of X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days)

All present enzymatic activity of X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days), PDB code: 4nht was solved by A.A.Petruk, D.E.Bikiel, A.Vergara, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.52 / 1.65
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.583, 78.583, 37.118, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.8

Other elements in 4nht:

The structure of X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days) also contains other interesting chemical elements:

Chlorine (Cl) 22 atoms
Sodium (Na) 1 atom

Iridium Binding Sites:

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

Iridium binding site 1 out of 5 in 4nht

Go back to Iridium Binding Sites List in 4nht
Iridium binding site 1 out of 5 in the X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days)


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 Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir1001

b:46.5
occ:0.80
 IR A:2T81001 0.0 46.5 0.8
C A:2T81001 1.9 42.6 0.5
CL2 A:2T81001 2.3 39.9 0.8
CL4 A:2T81001 2.3 41.0 0.8
CL3 A:2T81001 2.4 41.5 0.8
CL1 A:2T81001 2.4 42.4 0.8
NE2 A:HIS15 2.4 34.1 1.0
O A:2T81001 3.0 43.1 0.5
CE1 A:HIS15 3.2 34.3 1.0
CD2 A:HIS15 3.6 31.2 1.0
ND1 A:HIS15 4.4 34.8 1.0
CG A:HIS15 4.6 32.9 1.0
OD1 A:ASP87 4.8 32.4 1.0
OG1 A:THR89 5.0 31.4 1.0

Iridium binding site 2 out of 5 in 4nht

Go back to Iridium Binding Sites List in 4nht
Iridium binding site 2 out of 5 in the X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days)


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 Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir1002

b:44.2
occ:0.47
 IR A:2T81002 0.0 44.2 0.5
C A:2T81002 1.8 39.5 0.5
CL2 A:2T81002 2.3 38.9 0.5
O2 A:2T81002 2.3 38.8 0.5
CL4 A:2T81002 2.4 38.9 0.5
CL3 A:2T81002 2.4 38.3 0.5
CL1 A:2T81002 2.4 37.6 0.5
O A:2T81002 2.9 40.9 0.5
OG A:SER24 4.3 23.8 1.0
CG2 A:VAL120 4.4 22.9 1.0
O A:HOH1165 4.6 41.8 1.0

Iridium binding site 3 out of 5 in 4nht

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Iridium binding site 3 out of 5 in the X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days)


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 Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir1003

b:43.0
occ:0.70
 IR A:2T81003 0.0 43.0 0.7
OD1 A:ASP18 2.3 36.0 1.0
CL2 A:2T81003 2.3 38.5 0.7
CL4 A:2T81003 2.3 37.6 0.7
CL1 A:2T81003 2.4 36.9 0.7
O2 A:2T81003 2.4 35.8 0.7
CL3 A:2T81003 2.4 37.3 0.7
CG A:ASP18 3.0 33.6 1.0
OD2 A:ASP18 3.1 34.6 1.0
CB A:ASP18 4.5 30.9 1.0
NZ A:LYS13 4.9 36.1 1.0

Iridium binding site 4 out of 5 in 4nht

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Iridium binding site 4 out of 5 in the X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days)


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 Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir1004

b:27.7
occ:0.39
 IR A:2T81004 0.0 27.7 0.4
C A:2T81004 1.9 22.3 0.4
CL2 A:2T81004 2.3 19.8 0.4
O2 A:2T81004 2.3 19.0 0.4
CL4 A:2T81004 2.3 20.6 0.4
CL3 A:2T81004 2.3 17.8 0.4
CL1 A:2T81004 2.3 20.4 0.4
O A:2T81004 3.0 26.6 0.4
O A:HOH1177 3.5 19.6 0.6
O A:ALA107 4.2 20.1 1.0
NE1 A:TRP63 4.2 23.1 1.0
CB A:ASN59 4.7 24.3 1.0
OD1 A:ASN59 4.8 34.8 1.0
CD1 A:TRP62 4.9 32.7 1.0
O A:HOH1112 4.9 62.2 1.0
CD1 A:TRP63 4.9 22.1 1.0

Iridium binding site 5 out of 5 in 4nht

Go back to Iridium Binding Sites List in 4nht
Iridium binding site 5 out of 5 in the X-Ray Structure of the Complex Between Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days)


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 Hen Egg White Lysozyme and Pentachlorocarbonyliridate(III) (6 Days) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir1005

b:36.1
occ:0.29
 IR A:2T81005 0.0 36.1 0.3
C A:2T81005 1.9 33.6 0.3
CL2 A:2T81005 2.3 32.9 0.3
O2 A:2T81005 2.3 32.9 0.3
CL4 A:2T81005 2.3 33.5 0.3
CL3 A:2T81005 2.4 33.0 0.3
CL1 A:2T81005 2.4 32.8 0.3
O A:2T81005 3.0 34.7 0.3
CB A:ASN46 4.4 26.0 1.0
OD1 A:ASN46 4.5 26.9 1.0
CG A:ASN46 4.5 24.2 1.0
OG1 A:THR47 4.7 39.8 1.0
O A:HOH1169 4.7 47.3 1.0

Reference:

A.A.Petruk, A.Vergara, D.Marasco, D.E.Bikiel, F.Doctorovich, D.A.Estrin, A.Merlino. Interaction Between Proteins and Ir Based Co Releasing Molecules: Mechanism of Adduct Formation and Co Release To Be Published.
Page generated: Mon Aug 12 03:27:30 2024

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