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Xenon in PDB 1s56: Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms

Protein crystallography data

The structure of Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms, PDB code: 1s56 was solved by M.Milani, A.Pesce, Y.Ouellet, S.Dewilde, J.Friedman, P.Ascenzi, M.Guertin, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.321, 61.959, 90.747, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 27.7

Other elements in 1s56:

The structure of Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms also contains other interesting chemical elements:

Potassium (K) 1 atom
Iron (Fe) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms (pdb code 1s56). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 8 binding sites of Xenon where determined in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms, PDB code: 1s56:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Xenon binding site 1 out of 8 in 1s56

Go back to Xenon Binding Sites List in 1s56
Xenon binding site 1 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


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 "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe202

b:44.3
occ:1.00
CG1 A:VAL28 3.8 27.9 1.0
CD1 A:LEU66 3.9 26.6 1.0
CG A:PHE62 3.9 31.8 1.0
CD1 A:PHE62 4.0 33.7 1.0
CB A:PHE62 4.1 29.9 1.0
CG2 A:VAL28 4.3 26.2 1.0
CD2 A:LEU102 4.4 17.4 1.0
CG1 A:ILE25 4.4 30.2 1.0
CG2 A:ILE25 4.5 30.5 1.0
XE A:XE207 4.5 60.9 0.3
CD2 A:PHE62 4.6 34.1 1.0
CE1 A:PHE62 4.6 35.8 1.0
CB A:VAL28 4.6 26.4 1.0
CD2 A:LEU98 4.7 21.9 1.0
CB A:ILE25 4.9 30.7 1.0
CD1 A:ILE25 4.9 30.1 1.0
CD1 A:ILE19 5.0 30.4 1.0
CA A:ILE25 5.0 30.7 1.0
CG A:LEU102 5.0 18.5 1.0

Xenon binding site 2 out of 8 in 1s56

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Xenon binding site 2 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


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 "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe203

b:35.6
occ:0.70
CZ A:PHE62 3.2 35.9 1.0
CE2 A:PHE62 3.3 34.7 1.0
C3B A:HEC144 3.6 27.3 1.0
CAB A:HEC144 3.6 28.2 1.0
CZ A:PHE32 3.8 23.8 1.0
C2B A:HEC144 3.8 27.9 1.0
CG1 A:VAL94 4.0 21.3 1.0
NE2 A:GLN58 4.1 20.7 1.0
CMB A:HEC144 4.1 28.1 1.0
CE2 A:PHE32 4.2 23.3 1.0
C4B A:HEC144 4.2 27.5 1.0
CG A:LEU98 4.3 21.9 1.0
XE A:XE207 4.4 60.9 0.3
CBB A:HEC144 4.4 28.4 1.0
CE1 A:PHE32 4.5 24.9 1.0
C1B A:HEC144 4.5 28.2 1.0
CE1 A:PHE62 4.5 35.8 1.0
CD2 A:PHE62 4.6 34.1 1.0
CD1 A:LEU98 4.7 22.0 1.0
NB A:HEC144 4.7 27.5 1.0
CD A:GLN58 4.8 23.5 1.0
CHC A:HEC144 4.8 26.6 1.0
C A:CYN145 4.8 28.8 1.0

Xenon binding site 3 out of 8 in 1s56

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Xenon binding site 3 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


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 "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe207

b:60.9
occ:0.31
CE2 A:PHE62 2.6 34.7 1.0
CD2 A:PHE62 2.8 34.1 1.0
CD2 A:LEU98 3.4 21.9 1.0
CZ A:PHE62 3.5 35.9 1.0
CD2 A:PHE32 3.6 24.0 1.0
CG2 A:VAL29 3.7 25.9 1.0
CE2 A:PHE32 3.8 23.3 1.0
CG A:PHE62 3.8 31.8 1.0
CG A:GLN58 4.0 23.8 1.0
CG A:PHE32 4.1 24.8 1.0
CG A:LEU98 4.1 21.9 1.0
CD A:GLN58 4.3 23.5 1.0
CE1 A:PHE62 4.3 35.8 1.0
XE A:XE203 4.4 35.6 0.7
CZ A:PHE32 4.4 23.8 1.0
CD1 A:PHE62 4.5 33.7 1.0
XE A:XE202 4.5 44.3 1.0
CB A:PHE32 4.6 25.4 1.0
CD1 A:PHE32 4.6 24.8 1.0
NE2 A:GLN58 4.7 20.7 1.0
CB A:PHE62 4.7 29.9 1.0
CD1 A:LEU98 4.8 22.0 1.0
CE1 A:PHE32 4.8 24.9 1.0
OE1 A:GLN58 4.8 26.1 1.0
CB A:VAL29 4.8 26.1 1.0
CA A:VAL29 4.8 25.9 1.0

Xenon binding site 4 out of 8 in 1s56

Go back to Xenon Binding Sites List in 1s56
Xenon binding site 4 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


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 "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe208

b:47.7
occ:0.50
CB A:ALA120 3.6 32.1 1.0
O A:LEU116 3.8 29.6 1.0
C A:LEU116 3.9 29.8 1.0
CB A:LEU116 4.0 28.9 1.0
N A:GLY117 4.3 30.0 1.0
CA A:GLY117 4.5 30.2 1.0
CA A:LEU116 4.5 29.3 1.0
CA A:ALA120 4.8 32.1 1.0

Xenon binding site 5 out of 8 in 1s56

Go back to Xenon Binding Sites List in 1s56
Xenon binding site 5 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe201

b:40.9
occ:1.00
CD2 B:LEU102 3.8 34.7 1.0
CG B:PHE62 4.0 27.0 1.0
CD1 B:PHE62 4.1 28.1 1.0
CB B:PHE62 4.2 26.2 1.0
CD1 B:LEU98 4.3 30.5 1.0
CG1 B:ILE25 4.4 33.3 1.0
CD1 B:ILE19 4.4 27.5 1.0
CD1 B:LEU66 4.4 24.4 1.0
CD1 B:ILE115 4.5 26.7 1.0
CD2 B:PHE62 4.5 28.5 1.0
CG2 B:ILE25 4.5 34.0 1.0
CG1 B:VAL28 4.6 33.9 1.0
CE1 B:PHE62 4.6 28.8 1.0
CG2 B:ILE115 4.8 26.8 1.0
CB B:ILE25 4.9 34.0 1.0
CB B:VAL28 4.9 33.9 1.0
CA B:ILE25 5.0 33.9 1.0
CE2 B:PHE62 5.0 28.7 1.0

Xenon binding site 6 out of 8 in 1s56

Go back to Xenon Binding Sites List in 1s56
Xenon binding site 6 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe204

b:50.5
occ:0.50
CZ B:PHE62 3.3 28.8 1.0
CZ B:PHE32 3.5 32.9 1.0
CBB B:HEM144 3.5 36.7 1.0
CG1 B:VAL94 3.6 30.4 1.0
C3B B:HEM144 3.7 32.5 1.0
CAB B:HEM144 3.8 35.2 1.0
CE2 B:PHE62 3.8 28.7 1.0
OE1 B:GLN58 4.0 33.7 1.0
C2B B:HEM144 4.0 32.5 1.0
CE1 B:PHE32 4.0 33.7 1.0
CD2 B:LEU98 4.2 30.5 1.0
CE2 B:PHE32 4.3 32.6 1.0
C4B B:HEM144 4.3 30.8 1.0
CMB B:HEM144 4.3 33.1 1.0
CE1 B:PHE62 4.4 28.8 1.0
CD B:GLN58 4.5 30.4 1.0
C1B B:HEM144 4.6 31.6 1.0
CHC B:HEM144 4.8 30.4 1.0
NB B:HEM144 4.8 30.2 1.0
CG2 B:ILE119 4.9 36.1 1.0
NE2 B:GLN58 5.0 30.6 1.0
CB B:LEU98 5.0 32.2 1.0

Xenon binding site 7 out of 8 in 1s56

Go back to Xenon Binding Sites List in 1s56
Xenon binding site 7 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe205

b:31.2
occ:0.50
N B:ALA120 3.4 37.8 1.0
CG2 B:ILE119 3.6 36.1 1.0
CA B:ALA120 3.6 38.4 1.0
CB B:ILE119 3.6 36.1 1.0
C B:ILE119 3.6 36.9 1.0
O B:LEU116 3.8 27.9 1.0
CZ B:PHE91 3.9 33.6 1.0
CB B:ALA120 4.0 38.4 1.0
O B:ILE119 4.0 37.5 1.0
CE2 B:PHE91 4.2 33.6 1.0
CB B:ALA95 4.2 29.9 1.0
CA B:ILE119 4.2 36.1 1.0
CA B:LEU116 4.3 27.9 1.0
CD2 B:LEU116 4.5 26.1 1.0
C B:LEU116 4.5 28.4 1.0
CBB B:HEM144 4.6 36.7 1.0
CB B:LEU116 4.7 27.7 1.0
CA B:ALA95 4.8 30.1 1.0
CE1 B:PHE91 4.8 33.1 1.0
N B:ILE119 4.9 35.0 1.0
C B:ALA120 4.9 38.9 1.0
CG1 B:ILE119 4.9 37.0 1.0

Xenon binding site 8 out of 8 in 1s56

Go back to Xenon Binding Sites List in 1s56
Xenon binding site 8 out of 8 in the Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Crystal Structure of "Truncated" Hemoglobin N (Hbn) From Mycobacterium Tuberculosis, Soaked with Xe Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe206

b:39.4
occ:0.50
CB B:ALA120 3.0 38.4 1.0
O B:LEU116 3.3 27.9 1.0
C B:LEU116 3.8 28.4 1.0
CB B:LEU116 4.1 27.7 1.0
CA B:ALA120 4.4 38.4 1.0
N B:GLY117 4.4 29.5 1.0
CA B:GLY117 4.5 30.1 1.0
CA B:LEU116 4.6 27.9 1.0
N B:ALA120 5.0 37.8 1.0

Reference:

M.Milani, A.Pesce, Y.Ouellet, S.Dewilde, J.Friedman, P.Ascenzi, M.Guertin, M.Bolognesi. Heme-Ligand Tunneling in Group I Truncated Hemoglobins J.Biol.Chem. V. 279 21520 2004.
ISSN: ISSN 0021-9258
PubMed: 15016811
DOI: 10.1074/JBC.M401320200
Page generated: Wed Dec 16 02:39:24 2020

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