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Xenon in PDB 3gk9: Crystal Structure of Murine Ngb Under Xe Pressure

Protein crystallography data

The structure of Crystal Structure of Murine Ngb Under Xe Pressure, PDB code: 3gk9 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) 25.60 / 1.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 88.830, 88.830, 110.926, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 21.1

Other elements in 3gk9:

The structure of Crystal Structure of Murine Ngb Under Xe Pressure also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of Murine Ngb Under Xe Pressure (pdb code 3gk9). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 6 binding sites of Xenon where determined in the Crystal Structure of Murine Ngb Under Xe Pressure, PDB code: 3gk9:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6;

Xenon binding site 1 out of 6 in 3gk9

Go back to Xenon Binding Sites List in 3gk9
Xenon binding site 1 out of 6 in the Crystal Structure of Murine Ngb Under Xe Pressure


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 Murine Ngb Under Xe Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe152

b:20.0
occ:0.40
XE A:XE152 0.0 20.0 0.4
XE A:XE152 1.2 19.1 0.1
CE A:LYS67 3.9 14.3 1.0
O A:HOH214 4.1 32.9 1.0
NZ A:LYS67 4.3 14.2 1.0
OD2 A:ASP63 4.8 21.3 1.0
CB A:ASP63 4.8 13.0 1.0
CG A:ASP63 5.0 16.4 1.0

Xenon binding site 2 out of 6 in 3gk9

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Xenon binding site 2 out of 6 in the Crystal Structure of Murine Ngb Under Xe Pressure


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 Murine Ngb Under Xe Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe152

b:19.1
occ:0.15
XE A:XE152 0.0 19.1 0.1
XE A:XE152 1.2 20.0 0.4
CE A:LYS67 3.8 14.3 1.0
NZ A:LYS67 4.6 14.2 1.0
CG A:LYS67 4.7 14.3 1.0
CD A:LYS67 4.8 14.4 1.0
CB A:ASP63 4.8 13.0 1.0
O A:HOH214 4.9 32.9 1.0
CG A:ASP63 5.0 16.4 1.0

Xenon binding site 3 out of 6 in 3gk9

Go back to Xenon Binding Sites List in 3gk9
Xenon binding site 3 out of 6 in the Crystal Structure of Murine Ngb Under Xe Pressure


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 Murine Ngb Under Xe Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe153

b:14.8
occ:0.48
O A:HOH240 1.7 15.2 0.3
OG A:SER55 3.3 12.6 1.0
CD2 A:LEU56 3.5 15.4 1.0
CG A:LEU56 3.6 14.5 1.0
N A:ALA29 3.7 9.8 1.0
CD2 A:PHE32 3.7 10.7 1.0
CA A:ALA29 3.7 10.4 1.0
C A:PHE28 3.8 9.9 1.0
O A:PHE28 3.9 10.0 1.0
CE2 A:PHE32 3.9 13.5 1.0
O A:PRO52 4.0 14.1 1.0
CD1 A:LEU56 4.0 16.3 1.0
O A:HOH166 4.1 29.2 1.0
CE2 A:PHE61 4.2 12.9 1.0
CB A:PHE28 4.3 10.1 1.0
CB A:ALA29 4.3 9.7 1.0
CZ A:PHE61 4.4 14.8 1.0
CA A:PHE28 4.6 10.2 1.0
C A:PRO52 4.7 14.6 1.0
CB A:PRO52 4.7 15.7 1.0
CB A:SER55 4.7 12.0 1.0
O A:THR25 4.8 10.8 1.0
CG A:PHE32 4.9 9.8 1.0
CA A:PRO52 5.0 15.0 1.0
O A:HOH161 5.0 15.3 1.0

Xenon binding site 4 out of 6 in 3gk9

Go back to Xenon Binding Sites List in 3gk9
Xenon binding site 4 out of 6 in the Crystal Structure of Murine Ngb Under Xe Pressure


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 Murine Ngb Under Xe Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe154

b:15.6
occ:0.45
XE A:XE154 0.0 15.6 0.5
XE A:XE154 0.8 12.6 0.3
CA A:TYR137 3.9 18.7 1.0
CG2 A:VAL140 3.9 21.4 1.0
CD1 A:TYR137 4.0 17.4 1.0
N A:TYR137 4.1 19.6 1.0
CG A:LEU136 4.2 19.8 1.0
CB A:TYR137 4.2 18.8 1.0
CD2 A:LEU113 4.4 17.4 1.0
CB A:VAL140 4.4 20.1 1.0
CG1 A:ILE72 4.4 17.4 1.0
CG2 A:ILE72 4.4 17.8 1.0
C A:LEU136 4.4 19.4 1.0
CD2 A:LEU136 4.5 18.6 1.0
O A:LEU136 4.5 18.4 1.0
CB A:ALA75 4.5 20.4 1.0
CZ3 A:TRP133 4.5 16.4 1.0
CG A:TYR137 4.6 18.2 1.0
CE3 A:TRP133 4.8 17.0 1.0
CB A:ILE72 4.8 16.8 1.0
CG1 A:VAL140 4.9 17.6 1.0
CA A:ILE72 4.9 17.4 1.0
CB A:LEU136 4.9 19.2 1.0
CE1 A:TYR137 5.0 19.1 1.0

Xenon binding site 5 out of 6 in 3gk9

Go back to Xenon Binding Sites List in 3gk9
Xenon binding site 5 out of 6 in the Crystal Structure of Murine Ngb Under Xe Pressure


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 Murine Ngb Under Xe Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe154

b:12.6
occ:0.35
XE A:XE154 0.0 12.6 0.3
XE A:XE154 0.8 15.6 0.5
CZ3 A:TRP133 3.7 16.4 1.0
CG A:LEU136 3.9 19.8 1.0
CG2 A:ILE72 3.9 17.8 1.0
CD2 A:LEU136 4.0 18.6 1.0
CE3 A:TRP133 4.0 17.0 1.0
CD2 A:LEU113 4.2 17.4 1.0
CA A:TYR137 4.2 18.7 1.0
N A:TYR137 4.2 19.6 1.0
CG1 A:ILE72 4.4 17.4 1.0
CG2 A:VAL140 4.5 21.4 1.0
CB A:TYR137 4.5 18.8 1.0
CD1 A:TYR137 4.5 17.4 1.0
CB A:ALA75 4.5 20.4 1.0
CB A:ILE72 4.6 16.8 1.0
C A:LEU136 4.6 19.4 1.0
CB A:LEU136 4.6 19.2 1.0
CA A:ILE72 4.8 17.4 1.0
O A:LEU136 4.8 18.4 1.0
CH2 A:TRP133 4.9 16.8 1.0

Xenon binding site 6 out of 6 in 3gk9

Go back to Xenon Binding Sites List in 3gk9
Xenon binding site 6 out of 6 in the Crystal Structure of Murine Ngb Under Xe Pressure


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 Murine Ngb Under Xe Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe155

b:18.7
occ:0.38
CBB A:HEM200 2.9 4.9 0.2
CD1 A:ILE72 3.6 15.2 1.0
CE1 A:TYR137 3.8 19.1 1.0
CG1 A:ILE72 3.9 17.4 1.0
CMC A:HEM200 4.0 18.6 0.8
CG1 A:VAL109 4.0 15.3 1.0
CBC A:HEM200 4.1 21.3 0.8
CAB A:HEM200 4.1 6.2 0.2
CG1 A:VAL68 4.2 14.9 1.0
CD1 A:TYR137 4.2 17.4 1.0
CD2 A:LEU113 4.4 17.4 1.0
CD1 A:LEU27 4.4 14.8 1.0
CD1 A:LEU113 4.5 18.4 1.0
CB A:LEU113 4.5 12.8 1.0
CG A:LEU113 4.7 14.9 1.0
CZ A:TYR137 4.9 17.6 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 02:39:48 2020

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