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Xenon in PDB 2z8a: Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe

Protein crystallography data

The structure of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe, PDB code: 2z8a was solved by J.E.Knapp, W.E.Royer Jr., K.Nienhaus, P.Palladino, G.U.Nienhaus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.30 / 1.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.660, 43.390, 82.290, 90.00, 122.02, 90.00
R / Rfree (%) 14.3 / 16.2

Other elements in 2z8a:

The structure of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe (pdb code 2z8a). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 4 binding sites of Xenon where determined in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe, PDB code: 2z8a:
Jump to Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 in 2z8a

Go back to Xenon Binding Sites List in 2z8a
Xenon binding site 1 out of 4 in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe5504

b:13.8
occ:0.60
CD2 A:LEU1077 3.7 10.7 1.0
CG2 A:VAL1139 3.8 10.9 1.0
CE2 A:PHE1080 3.8 12.5 1.0
CBB A:HEM1147 3.9 16.9 1.0
CA A:VAL1139 3.9 9.4 1.0
CD2 A:PHE1080 4.0 10.5 1.0
N A:VAL1139 4.0 9.0 1.0
CG A:LEU1138 4.1 10.1 1.0
CG2 A:VAL1142 4.3 10.7 1.0
C A:LEU1138 4.3 8.8 1.0
O A:LEU1138 4.3 9.8 1.0
CD2 A:LEU1138 4.4 12.0 1.0
CAB A:HEM1147 4.5 10.3 1.0
CB A:VAL1139 4.5 9.3 1.0
CMB A:HEM1147 4.7 11.6 1.0
CE2 A:PHE1111 4.7 9.8 1.0
CB A:LEU1138 4.7 9.5 1.0
CZ A:PHE1111 4.9 10.3 1.0

Xenon binding site 2 out of 4 in 2z8a

Go back to Xenon Binding Sites List in 2z8a
Xenon binding site 2 out of 4 in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe5505

b:9.9
occ:0.06
CMB A:HEM1147 3.4 11.6 1.0
C2B A:HEM1147 3.4 9.2 1.0
CZ A:PHE1111 3.4 10.3 1.0
CB A:PHE1097 3.6 10.2 1.0
C1B A:HEM1147 3.6 8.7 1.0
CE1 A:PHE1111 3.7 10.8 1.0
CE1 A:HIS1101 3.9 8.3 1.0
CZ A:PHE1080 3.9 13.0 1.0
CHB A:HEM1147 3.9 8.9 1.0
CE2 A:PHE1080 4.1 12.5 1.0
CG1 A:VAL1142 4.1 11.7 1.0
C3B A:HEM1147 4.1 8.8 1.0
CG2 A:VAL1142 4.2 10.7 1.0
ND1 A:HIS1101 4.2 8.5 1.0
CG A:PHE1097 4.2 9.7 1.0
NB A:HEM1147 4.4 8.2 1.0
C4B A:HEM1147 4.6 8.2 1.0
CE2 A:PHE1111 4.6 9.8 1.0
NE2 A:HIS1101 4.7 7.7 1.0
CB A:VAL1142 4.7 9.5 1.0
CD2 A:PHE1097 4.7 11.8 1.0
CA A:PHE1097 4.8 8.9 1.0
C A:PHE1097 4.8 8.7 1.0
O A:PHE1097 4.8 9.5 1.0
CAB A:HEM1147 4.9 10.3 1.0
CD1 A:PHE1097 4.9 12.0 1.0
C4A A:HEM1147 4.9 8.2 1.0

Xenon binding site 3 out of 4 in 2z8a

Go back to Xenon Binding Sites List in 2z8a
Xenon binding site 3 out of 4 in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe5502

b:14.3
occ:0.70
CD2 B:LEU2077 3.6 9.1 1.0
CG2 B:VAL2139 3.8 10.1 1.0
CE2 B:PHE2080 3.9 12.4 1.0
CA B:VAL2139 3.9 8.5 1.0
CD2 B:PHE2080 3.9 10.4 1.0
CBB B:HEM2147 3.9 11.4 1.0
N B:VAL2139 4.0 8.2 1.0
CG B:LEU2138 4.1 8.9 1.0
CG2 B:VAL2142 4.2 10.4 1.0
C B:LEU2138 4.3 8.0 1.0
O B:LEU2138 4.3 8.6 1.0
CD2 B:LEU2138 4.4 10.0 1.0
CB B:VAL2139 4.4 8.7 1.0
CAB B:HEM2147 4.6 9.0 1.0
CE1 B:PHE2111 4.7 10.3 1.0
CB B:LEU2138 4.7 8.7 1.0
CZ B:PHE2111 4.9 10.8 1.0
CMB B:HEM2147 4.9 10.0 1.0
CZ3 B:TRP2135 5.0 10.9 1.0

Xenon binding site 4 out of 4 in 2z8a

Go back to Xenon Binding Sites List in 2z8a
Xenon binding site 4 out of 4 in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe5506

b:11.1
occ:0.04
CZ B:PHE2111 3.3 10.8 1.0
CB B:PHE2097 3.5 10.0 1.0
CE2 B:PHE2111 3.5 10.5 1.0
CMB B:HEM2147 3.5 10.0 1.0
C2B B:HEM2147 3.6 8.5 1.0
C1B B:HEM2147 3.8 8.0 1.0
CE1 B:HIS2101 3.8 8.1 1.0
CZ B:PHE2080 4.0 12.6 1.0
CG1 B:VAL2142 4.0 11.3 1.0
CHB B:HEM2147 4.0 8.3 1.0
ND1 B:HIS2101 4.1 8.7 1.0
C3B B:HEM2147 4.2 8.2 1.0
CE2 B:PHE2080 4.2 12.4 1.0
CG B:PHE2097 4.3 10.5 1.0
CG2 B:VAL2142 4.3 10.4 1.0
NB B:HEM2147 4.4 7.8 1.0
CE1 B:PHE2111 4.4 10.3 1.0
O B:PHE2097 4.5 10.1 1.0
C B:PHE2097 4.5 8.9 1.0
CA B:PHE2097 4.6 8.9 1.0
C4B B:HEM2147 4.6 7.8 1.0
NE2 B:HIS2101 4.7 7.7 1.0
CD2 B:PHE2111 4.8 9.3 1.0
CB B:VAL2142 4.8 9.5 1.0
CD1 B:PHE2097 4.9 12.4 1.0
CAB B:HEM2147 4.9 9.0 1.0
C4A B:HEM2147 5.0 8.4 1.0
CD2 B:PHE2097 5.0 13.6 1.0

Reference:

K.Nienhaus, J.E.Knapp, P.Palladino, W.E.Royer Jr., G.U.Nienhaus. Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis Biochemistry V. 46 14018 2007.
ISSN: ISSN 0006-2960
PubMed: 18001141
DOI: 10.1021/BI7016798
Page generated: Wed Dec 16 02:39:42 2020

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