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Xenon in PDB 1j52: Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon

Protein crystallography data

The structure of Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon, PDB code: 1j52 was solved by E.C.Liong, G.N.Phillips Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 1.90
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 91.580, 91.580, 45.970, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 20.5

Other elements in 1j52:

The structure of Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon also contains other interesting chemical elements:

Iron (Fe) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon (pdb code 1j52). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 4 binding sites of Xenon where determined in the Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon, PDB code: 1j52:
Jump to Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 in 1j52

Go back to Xenon Binding Sites List in 1j52
Xenon binding site 1 out of 4 in the Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe157

b:24.4
occ:0.86
CG A:HIS93 3.7 14.2 1.0
CD2 A:HIS93 3.7 14.5 1.0
C3B A:HEM154 3.9 12.4 1.0
ND1 A:HIS93 4.0 13.6 1.0
C4B A:HEM154 4.0 12.7 1.0
NE2 A:HIS93 4.1 14.2 1.0
CZ A:PHE138 4.1 20.7 1.0
C2B A:HEM154 4.1 12.9 1.0
CD2 A:LEU104 4.2 16.1 1.0
CE1 A:HIS93 4.2 13.9 1.0
CB A:HIS93 4.3 14.0 1.0
NB A:HEM154 4.3 12.8 1.0
CAB A:HEM154 4.3 12.8 1.0
C1B A:HEM154 4.3 12.9 1.0
CB A:LEU89 4.5 18.7 1.0
CHC A:HEM154 4.5 12.7 1.0
O A:LEU89 4.5 16.3 1.0
CD1 A:ILE142 4.6 20.1 1.0
CD1 A:LEU104 4.6 16.8 1.0
CE1 A:PHE138 4.7 21.6 1.0
CMB A:HEM154 4.8 12.7 1.0
CD2 A:LEU89 4.8 21.8 1.0
CD1 A:LEU89 4.8 21.5 1.0
CG1 A:ILE142 4.9 19.0 1.0
C A:LEU89 4.9 16.1 1.0
CG A:LEU89 5.0 20.5 1.0

Xenon binding site 2 out of 4 in 1j52

Go back to Xenon Binding Sites List in 1j52
Xenon binding site 2 out of 4 in the Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe158

b:44.0
occ:0.35
CD1 A:PHE138 2.9 20.4 1.0
CE1 A:PHE138 2.9 21.6 1.0
OG A:SER108 3.4 17.1 1.0
CBB A:HEM154 3.8 13.2 1.0
O A:LEU104 3.8 16.0 1.0
CG A:ARG139 4.1 22.0 1.0
CAB A:HEM154 4.2 12.8 1.0
CG A:PHE138 4.2 19.3 1.0
CG2 A:ILE107 4.2 12.8 1.0
CZ A:PHE138 4.2 20.7 1.0
CD2 A:LEU135 4.3 14.5 1.0
CB A:LEU104 4.5 15.4 1.0
C A:LEU104 4.6 15.7 1.0
CD A:ARG139 4.6 16.5 1.0
CB A:SER108 4.6 14.2 1.0
O A:LEU135 4.7 14.4 1.0
CA A:LEU104 4.8 15.7 1.0
CB A:PHE138 4.9 16.5 1.0
N A:SER108 4.9 13.7 1.0
CA A:SER108 4.9 13.7 1.0
CB A:LEU135 5.0 13.9 1.0

Xenon binding site 3 out of 4 in 1j52

Go back to Xenon Binding Sites List in 1j52
Xenon binding site 3 out of 4 in the Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe159

b:38.9
occ:0.37
O A:ALA134 3.1 13.4 1.0
O A:HOH200 3.3 14.0 1.0
ND1 A:HIS82 3.7 18.0 1.0
CB A:PHE138 3.7 16.5 1.0
CE1 A:HIS82 3.7 18.2 1.0
N A:PHE138 3.9 13.9 1.0
CG2 A:ILE75 4.0 14.9 1.0
CA A:PHE138 4.0 14.7 1.0
C A:ALA134 4.1 13.2 1.0
CD2 A:LEU137 4.2 15.8 1.0
CD2 A:LEU76 4.2 14.3 1.0
CH2 A:TRP7 4.2 15.4 1.0
CG A:LEU137 4.3 16.4 1.0
CB A:LEU137 4.5 14.7 1.0
CA A:ALA134 4.6 12.2 1.0
CG A:PHE138 4.7 19.3 1.0
C A:LEU137 4.7 13.7 1.0
CB A:ALA134 4.7 12.7 1.0
CD2 A:PHE138 4.8 20.1 1.0
CZ3 A:TRP7 4.9 15.2 1.0
NE2 A:HIS82 4.9 18.3 1.0
CG A:HIS82 5.0 17.5 1.0

Xenon binding site 4 out of 4 in 1j52

Go back to Xenon Binding Sites List in 1j52
Xenon binding site 4 out of 4 in the Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Recombinant Sperm Whale Myoglobin in the Presence of 7ATM Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe160

b:37.4
occ:0.26
CG1 A:VAL68 3.4 11.8 1.0
CG2 A:ILE28 3.5 13.7 1.0
CB A:VAL68 3.7 12.1 1.0
CG A:LEU29 3.8 14.4 1.0
O A:GLY25 3.8 13.5 1.0
CB A:ILE28 3.9 13.2 1.0
CD2 A:LEU29 3.9 15.5 1.0
CD2 A:LEU69 3.9 17.5 1.0
O A:GLY65 4.0 12.8 1.0
CG A:LEU69 4.0 16.8 1.0
CA A:GLY25 4.1 12.9 1.0
CA A:GLY65 4.2 12.7 1.0
C A:GLY25 4.4 13.7 1.0
CG2 A:VAL68 4.4 12.3 1.0
N A:LEU29 4.5 13.7 1.0
CD1 A:LEU29 4.5 14.5 1.0
C A:GLY65 4.6 12.9 1.0
CD1 A:ILE28 4.6 13.2 1.0
CD1 A:ILE107 4.6 13.2 1.0
N A:LEU69 4.7 12.8 1.0
CG1 A:ILE28 4.8 13.0 1.0
CD1 A:LEU69 4.9 16.6 1.0
CB A:LEU29 4.9 14.5 1.0
CA A:VAL68 4.9 12.5 1.0
C A:ILE28 4.9 13.1 1.0
CA A:ILE28 5.0 12.9 1.0
C A:VAL68 5.0 12.8 1.0

Reference:

W.Radding, E.C.Liong, G.N.Phillips Jr.. Internal Cavities in Myoglobin: Implications For Protein Action To Be Published.
Page generated: Wed Dec 16 02:39:20 2020

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