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Xenon in PDB 2w6w: Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon

Protein crystallography data

The structure of Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon, PDB code: 2w6w was solved by A.E.Miele, F.Draghi, F.Renzi, G.Sciara, K.A.Johnson, B.Vallone, M.Brunori, C.Savino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.99
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 90.626, 90.626, 45.505, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 20.5

Other elements in 2w6w:

The structure of Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon also contains other interesting chemical elements:

Iron (Fe) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon (pdb code 2w6w). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 4 binding sites of Xenon where determined in the Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon, PDB code: 2w6w:
Jump to Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 in 2w6w

Go back to Xenon Binding Sites List in 2w6w
Xenon binding site 1 out of 4 in the Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1155

b:19.2
occ:0.50
CD2 A:PHE138 3.0 14.3 0.3
CE2 A:PHE138 3.4 14.6 0.3
OG A:SER108 3.5 8.9 1.0
CBB A:HEM1154 3.8 10.6 1.0
CAB A:HEM1154 3.9 9.7 1.0
CG A:ARG139 4.0 9.8 1.0
O A:LEU104 4.0 9.4 1.0
CG A:PHE138 4.0 12.6 0.3
CG2 A:ILE107 4.3 7.6 1.0
CB A:LEU104 4.5 9.8 1.0
CD2 A:LEU135 4.5 9.2 1.0
CB A:PHE138 4.5 11.2 1.0
CD A:ARG139 4.6 9.4 1.0
CZ A:PHE138 4.6 13.4 0.3
O A:LEU135 4.6 9.2 1.0
C A:LEU104 4.8 9.5 1.0
CB A:SER108 4.8 8.2 1.0
CD2 A:LEU104 4.9 9.7 1.0
CA A:LEU104 4.9 9.8 1.0
CB A:LEU135 5.0 8.8 1.0

Xenon binding site 2 out of 4 in 2w6w

Go back to Xenon Binding Sites List in 2w6w
Xenon binding site 2 out of 4 in the Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1156

b:13.8
occ:0.90
CG A:HIS93 3.7 8.6 1.0
CD2 A:HIS93 3.8 8.4 1.0
C3B A:HEM1154 3.9 9.7 1.0
ND1 A:HIS93 3.9 8.1 1.0
C4B A:HEM1154 4.0 9.7 1.0
CD2 A:LEU104 4.0 9.7 1.0
NE2 A:HIS93 4.0 8.4 1.0
CE1 A:HIS93 4.1 8.7 1.0
C2B A:HEM1154 4.1 9.8 1.0
NB A:HEM1154 4.3 9.5 1.0
CB A:HIS93 4.3 8.7 1.0
CAB A:HEM1154 4.3 9.7 1.0
CZ A:PHE138 4.3 13.4 0.3
C1B A:HEM1154 4.3 9.8 1.0
CD1 A:LEU104 4.4 10.3 1.0
CHC A:HEM1154 4.4 9.6 1.0
CD1 A:ILE142 4.5 12.0 1.0
CB A:LEU89 4.5 9.3 1.0
CD2 A:LEU89 4.6 10.0 1.0
O A:LEU89 4.6 9.0 1.0
CMB A:HEM1154 4.8 9.4 1.0
CE2 A:PHE138 4.8 14.6 0.3
CG1 A:ILE142 4.8 11.0 1.0
CG A:LEU104 4.9 9.7 1.0
C A:LEU89 4.9 9.0 1.0
CG A:LEU89 4.9 10.0 1.0

Xenon binding site 3 out of 4 in 2w6w

Go back to Xenon Binding Sites List in 2w6w
Xenon binding site 3 out of 4 in the Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1157

b:12.7
occ:0.40
CG A:LEU29 3.7 9.2 1.0
CG1 A:VAL68 3.8 6.0 1.0
CG2 A:ILE28 3.8 8.3 1.0
CD2 A:LEU69 3.9 6.5 1.0
CD2 A:LEU29 3.9 9.2 1.0
CG A:LEU69 3.9 6.6 1.0
O A:GLY25 3.9 7.1 1.0
CB A:VAL68 3.9 5.9 1.0
CB A:ILE28 4.0 8.0 1.0
O A:GLY65 4.1 6.7 1.0
CA A:GLY25 4.2 7.2 1.0
CA A:GLY65 4.3 7.0 1.0
CD1 A:LEU29 4.4 9.0 1.0
N A:LEU29 4.4 8.6 1.0
C A:GLY25 4.5 7.3 1.0
CD1 A:ILE107 4.6 8.5 1.0
CD1 A:LEU69 4.7 6.5 1.0
C A:GLY65 4.7 6.7 1.0
CG2 A:VAL68 4.7 5.8 1.0
N A:LEU69 4.7 6.0 1.0
CB A:LEU29 4.8 9.0 1.0
CD1 A:ILE28 4.8 7.5 1.0
C A:ILE28 4.9 8.3 1.0
CA A:LEU29 5.0 9.1 1.0

Xenon binding site 4 out of 4 in 2w6w

Go back to Xenon Binding Sites List in 2w6w
Xenon binding site 4 out of 4 in the Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Crystal Structure of Recombinant Sperm Whale Myoglobin Under 1ATM of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1158

b:16.7
occ:0.40
O A:ALA134 3.2 8.1 1.0
O A:HOH2090 3.3 10.9 1.0
CE1 A:HIS82 3.6 10.9 1.0
ND1 A:HIS82 3.6 10.9 1.0
N A:PHE138 3.8 10.1 1.0
CB A:PHE138 3.8 11.2 1.0
CG2 A:ILE75 3.9 7.0 1.0
CA A:PHE138 4.0 10.6 1.0
CH2 A:TRP7 4.1 8.1 1.0
C A:ALA134 4.2 8.2 1.0
CD2 A:LEU137 4.2 9.8 1.0
CD2 A:LEU76 4.4 6.5 1.0
CG A:LEU137 4.4 9.8 1.0
CB A:LEU137 4.5 9.7 1.0
C A:LEU137 4.6 9.9 1.0
CG A:PHE138 4.6 12.6 0.3
CA A:ALA134 4.6 8.0 1.0
NE2 A:HIS82 4.7 10.9 1.0
CB A:ALA134 4.8 7.9 1.0
CZ3 A:TRP7 4.8 8.0 1.0
CG A:HIS82 4.8 10.8 1.0
CD1 A:PHE138 4.9 14.2 0.3

Reference:

C.Savino, A.E.Miele, F.Draghi, K.A.Johnson, G.Sciara, M.Brunori, B.Vallone. Pattern of Cavities in Globins: the Case of Human Hemoglobin. Biopolymers V. 91 1097 2009.
ISSN: ISSN 0006-3525
PubMed: 19365817
DOI: 10.1002/BIP.21201
Page generated: Wed Dec 16 02:39:39 2020

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