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Xenon in PDB 3gln: Carbonmonoxy Ngb Under Xenon Pressure

Protein crystallography data

The structure of Carbonmonoxy Ngb Under Xenon Pressure, PDB code: 3gln was solved by T.Moschetti, U.Mueller, J.Schultze, M.Brunori, B.Vallone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.47 / 2.26
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 88.680, 88.680, 109.830, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 25.4

Other elements in 3gln:

The structure of Carbonmonoxy Ngb Under Xenon Pressure also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Carbonmonoxy Ngb Under Xenon Pressure (pdb code 3gln). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 5 binding sites of Xenon where determined in the Carbonmonoxy Ngb Under Xenon Pressure, PDB code: 3gln:
Jump to Xenon binding site number: 1; 2; 3; 4; 5;

Xenon binding site 1 out of 5 in 3gln

Go back to Xenon Binding Sites List in 3gln
Xenon binding site 1 out of 5 in the Carbonmonoxy Ngb Under Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Carbonmonoxy Ngb Under Xenon Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe153

b:61.1
occ:0.40
CMD A:HEM158 3.6 26.8 0.2
OH A:TYR88 3.6 41.4 1.0
CG2 A:VAL71 3.9 28.0 1.0
CD2 A:LEU70 4.2 35.1 1.0
CG A:LYS67 4.4 26.1 0.2
O A:LYS67 4.4 27.3 0.8
CMD A:HEM158 4.4 30.9 0.8
CZ A:TYR88 4.5 42.4 1.0
O A:HOH165 4.6 50.2 1.0
CB A:LYS67 4.6 28.1 0.8
O A:LYS67 4.7 26.3 0.2
CB A:LYS67 4.9 26.0 0.2
CD A:LYS67 4.9 25.6 0.2
CE1 A:TYR88 4.9 43.5 1.0
C2D A:HEM158 5.0 26.8 0.2

Xenon binding site 2 out of 5 in 3gln

Go back to Xenon Binding Sites List in 3gln
Xenon binding site 2 out of 5 in the Carbonmonoxy Ngb Under Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Carbonmonoxy Ngb Under Xenon Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe154

b:47.8
occ:0.40
CD2 A:LEU56 3.1 22.0 1.0
OG A:SER55 3.3 21.3 1.0
CG A:LEU56 3.4 20.1 1.0
N A:ALA29 3.5 16.8 1.0
CA A:ALA29 3.6 18.8 1.0
CD2 A:PHE32 3.7 21.7 1.0
C A:PHE28 3.7 17.9 1.0
O A:PRO52 3.7 24.8 1.0
O A:PHE28 3.9 16.9 1.0
CE2 A:PHE32 3.9 21.2 1.0
CD1 A:LEU56 3.9 19.2 1.0
CE2 A:PHE61 4.2 17.2 1.0
CB A:ALA29 4.2 18.1 1.0
CB A:PHE28 4.3 18.0 1.0
O A:HOH191 4.4 29.2 1.0
CA A:PHE28 4.6 17.6 1.0
C A:PRO52 4.6 24.6 1.0
O A:THR25 4.6 19.6 1.0
CB A:SER55 4.7 22.4 1.0
CZ A:PHE61 4.7 19.9 1.0
N A:LEU56 4.8 22.8 1.0
CB A:LEU56 4.8 22.3 1.0
O A:HOH178 4.9 29.6 1.0
C A:ALA29 4.9 19.2 1.0
CG A:PHE32 4.9 21.7 1.0
CB A:PRO52 5.0 24.7 1.0

Xenon binding site 3 out of 5 in 3gln

Go back to Xenon Binding Sites List in 3gln
Xenon binding site 3 out of 5 in the Carbonmonoxy Ngb Under Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Carbonmonoxy Ngb Under Xenon Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe155

b:29.4
occ:0.53
XE A:XE155 0.0 29.4 0.5
XE A:XE155 1.1 20.9 0.2
CG2 A:VAL140 3.8 34.0 1.0
CA A:TYR137 4.0 31.4 1.0
CD1 A:TYR137 4.0 26.2 1.0
CB A:VAL140 4.2 35.9 1.0
CD2 A:LEU113 4.2 19.7 1.0
CB A:TYR137 4.3 30.5 1.0
N A:TYR137 4.3 32.4 1.0
CD2 A:LEU136 4.4 32.6 1.0
CG A:LEU136 4.4 34.2 1.0
CG1 A:VAL140 4.5 33.4 1.0
CG2 A:ILE72 4.5 26.5 1.0
CG1 A:ILE72 4.6 28.1 1.0
CZ3 A:TRP133 4.6 23.2 1.0
C A:LEU136 4.6 33.4 1.0
O A:LEU136 4.6 34.0 1.0
CG A:TYR137 4.6 28.5 1.0
CB A:ALA75 4.7 35.1 1.0
CB A:ILE72 4.9 29.4 1.0
CA A:ILE72 5.0 29.4 1.0
CE3 A:TRP133 5.0 22.6 1.0
CE1 A:TYR137 5.0 26.5 1.0

Xenon binding site 4 out of 5 in 3gln

Go back to Xenon Binding Sites List in 3gln
Xenon binding site 4 out of 5 in the Carbonmonoxy Ngb Under Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Carbonmonoxy Ngb Under Xenon Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe155

b:20.9
occ:0.25
XE A:XE155 0.0 20.9 0.2
XE A:XE155 1.1 29.4 0.5
CZ3 A:TRP133 3.6 23.2 1.0
CD2 A:LEU136 3.6 32.6 1.0
CG A:LEU136 3.9 34.2 1.0
CG2 A:ILE72 4.0 26.5 1.0
CE3 A:TRP133 4.1 22.6 1.0
CD2 A:LEU113 4.2 19.7 1.0
CA A:TYR137 4.4 31.4 1.0
N A:TYR137 4.4 32.4 1.0
CG2 A:VAL140 4.4 34.0 1.0
CB A:ALA75 4.6 35.1 1.0
CG1 A:ILE72 4.6 28.1 1.0
CB A:TYR137 4.6 30.5 1.0
C A:LEU136 4.7 33.4 1.0
CB A:ILE72 4.7 29.4 1.0
CB A:LEU136 4.7 34.9 1.0
CD1 A:TYR137 4.7 26.2 1.0
CH2 A:TRP133 4.7 20.9 1.0
CA A:ILE72 4.8 29.4 1.0
O A:LEU136 4.9 34.0 1.0
O A:ILE72 5.0 31.3 1.0

Xenon binding site 5 out of 5 in 3gln

Go back to Xenon Binding Sites List in 3gln
Xenon binding site 5 out of 5 in the Carbonmonoxy Ngb Under Xenon Pressure


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Carbonmonoxy Ngb Under Xenon Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe156

b:26.8
occ:0.40
CMC A:HEM158 3.2 29.7 0.2
CG1 A:VAL109 3.7 19.4 1.0
CD1 A:ILE72 3.8 30.6 1.0
CAC A:HEM158 4.0 32.7 0.8
CMC A:HEM158 4.1 31.0 0.8
C3C A:HEM158 4.1 31.0 0.8
C2C A:HEM158 4.1 30.7 0.8
CE1 A:TYR137 4.1 26.5 1.0
CG1 A:VAL68 4.2 24.8 1.0
CG1 A:ILE72 4.2 28.1 1.0
C2C A:HEM158 4.3 29.3 0.2
CBC A:HEM158 4.3 29.7 0.2
CD1 A:LEU27 4.4 24.7 1.0
CAC A:HEM158 4.4 29.6 0.2
CD1 A:TYR137 4.6 26.2 1.0
CD2 A:LEU113 4.6 19.7 1.0
C3C A:HEM158 4.7 29.0 0.2
CB A:LEU113 4.8 19.4 1.0
CD1 A:LEU113 4.9 20.2 1.0
C1C A:HEM158 4.9 29.6 0.8
C4C A:HEM158 4.9 33.0 0.8
O A:VAL109 5.0 18.8 1.0

Reference:

T.Moschetti, U.Mueller, J.Schulze, M.Brunori, B.Vallone. The Structure of Neuroglobin at High Xe and Kr Pressure Reveals Partial Conservation of Globin Internal Cavities. Biophys. J. V. 97 1700 2009.
ISSN: ESSN 1542-0086
PubMed: 19751675
DOI: 10.1016/J.BPJ.2009.05.059
Page generated: Wed Dec 16 02:39:47 2020

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