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Xenon in PDB 3c9i: Structure of P22 Tail-Needle GP26 Bound to Xenon Gas

Protein crystallography data

The structure of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas, PDB code: 3c9i was solved by G.Cingolani, A.S.Olia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.539, 114.531, 172.045, 90.00, 91.01, 90.00
R / Rfree (%) 23.4 / 26.9

Other elements in 3c9i:

The structure of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Xenon atom in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas (pdb code 3c9i). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 14 binding sites of Xenon where determined in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas, PDB code: 3c9i:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 14 in 3c9i

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Xenon binding site 1 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1234

b:59.9
occ:1.00
CG2 A:ILE1045 3.7 27.1 1.0
CD1 C:ILE1045 3.7 23.1 1.0
CG2 C:ILE1045 3.7 33.0 1.0
CB C:ILE1045 3.9 35.6 1.0
CB A:ILE1045 4.1 26.1 1.0
CD1 A:ILE1045 4.2 48.8 1.0
CD1 B:ILE1045 4.2 41.6 1.0
CG2 B:VAL1042 4.2 28.1 1.0
CG2 A:VAL1042 4.2 35.2 1.0
CG2 B:ILE1045 4.3 38.3 1.0
CA B:VAL1042 4.4 24.4 1.0
CG1 C:VAL1042 4.4 33.1 1.0
CB B:ILE1045 4.4 36.9 1.0
CA A:VAL1042 4.4 31.2 1.0
CA C:VAL1042 4.4 34.4 1.0
CG1 C:ILE1045 4.4 39.3 1.0
CG2 C:VAL1042 4.5 31.7 1.0
O C:VAL1042 4.6 35.0 1.0
CG1 A:VAL1042 4.7 28.7 1.0
CB B:VAL1042 4.7 25.2 1.0
CB C:VAL1042 4.7 31.2 1.0
CB A:VAL1042 4.7 34.3 1.0
CG1 B:VAL1042 4.7 19.1 1.0
O B:VAL1042 4.8 37.2 1.0
CG1 A:ILE1045 4.8 29.3 1.0
O A:VAL1042 4.8 37.2 1.0
CG1 B:ILE1045 4.9 33.1 1.0

Xenon binding site 2 out of 14 in 3c9i

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Xenon binding site 2 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1235

b:34.1
occ:1.00
CB A:ALA1108 3.9 31.6 1.0
CB C:ALA1108 3.9 13.1 1.0
CB B:ALA1108 3.9 21.8 1.0
CG2 C:VAL1105 4.2 31.7 1.0
CG1 B:VAL1105 4.4 9.1 1.0
CG1 A:VAL1105 4.5 20.0 1.0
CA C:VAL1105 4.6 28.0 1.0
CG2 B:VAL1105 4.6 27.2 1.0
CG2 A:VAL1105 4.6 24.5 1.0
CA A:VAL1105 4.6 16.0 1.0
CG1 C:VAL1105 4.7 29.1 1.0
CB C:VAL1105 4.7 22.9 1.0
CA B:VAL1105 4.8 29.7 1.0
CB A:VAL1105 4.8 24.3 1.0
CB B:VAL1105 4.9 24.9 1.0
O A:VAL1105 4.9 30.7 1.0

Xenon binding site 3 out of 14 in 3c9i

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Xenon binding site 3 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe3

b:39.4
occ:1.00
CB A:ALA1129 3.6 37.0 1.0
CB C:ALA1129 3.7 15.0 1.0
CB B:ALA1129 3.8 18.6 1.0
CG2 C:VAL1126 4.3 21.2 1.0
CA C:VAL1126 4.6 21.3 1.0
CA B:VAL1126 4.6 23.9 1.0
CG2 B:VAL1126 4.6 21.1 1.0
CG2 A:VAL1126 4.6 23.3 1.0
CG1 B:VAL1126 4.6 18.6 1.0
CA A:VAL1126 4.7 22.6 1.0
CG1 A:VAL1126 4.7 18.7 1.0
CG1 C:VAL1126 4.8 21.4 1.0
CB C:VAL1126 4.8 18.6 1.0
O C:VAL1126 4.9 34.9 1.0
CB B:VAL1126 4.9 25.0 1.0
CB A:VAL1126 4.9 29.1 1.0
O B:VAL1126 4.9 27.1 1.0
O A:VAL1126 5.0 26.9 1.0

Xenon binding site 4 out of 14 in 3c9i

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Xenon binding site 4 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe5

b:33.8
occ:1.00
CD1 A:LEU1155 4.0 21.4 1.0
CD1 B:LEU1155 4.1 28.2 1.0
CD1 C:LEU1155 4.2 17.3 1.0
CG1 A:VAL1141 4.3 37.2 1.0
CD2 B:LEU1151 4.3 35.2 1.0
CD2 A:LEU1151 4.4 18.8 1.0
CG1 C:VAL1141 4.5 21.0 1.0
CG1 B:VAL1141 4.5 37.6 1.0
CG C:LEU1155 4.6 31.9 1.0
CD2 C:LEU1151 4.7 22.1 1.0
CG A:LEU1155 4.7 28.6 1.0
CG2 A:VAL1141 4.7 21.2 1.0
CG B:LEU1155 4.7 33.5 1.0
CB A:VAL1141 4.8 38.1 1.0
CD2 C:LEU1155 4.9 33.4 1.0
CD1 A:LEU1151 4.9 45.8 1.0
CD1 C:LEU1151 4.9 36.3 1.0
CG2 B:VAL1141 5.0 48.2 1.0
CB B:VAL1141 5.0 48.4 1.0

Xenon binding site 5 out of 14 in 3c9i

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Xenon binding site 5 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe6

b:31.6
occ:1.00
CG A:TYR1161 3.9 29.9 1.0
CG C:TYR1161 3.9 22.5 1.0
CG B:TYR1161 3.9 23.9 1.0
CG2 A:VAL1169 4.0 20.3 1.0
CD2 B:TYR1161 4.0 25.0 1.0
CD1 A:TYR1161 4.0 27.5 1.0
CD2 C:TYR1161 4.1 19.4 1.0
CB A:TYR1161 4.1 33.4 1.0
CG2 C:VAL1169 4.1 35.6 1.0
CB C:TYR1161 4.1 27.2 1.0
CG2 B:VAL1169 4.1 24.6 1.0
CD2 A:TYR1161 4.1 31.1 1.0
CD1 C:TYR1161 4.1 25.6 1.0
CB B:TYR1161 4.2 21.7 1.0
CD1 B:TYR1161 4.2 19.9 1.0
CB C:VAL1169 4.3 31.1 1.0
CB B:VAL1169 4.4 26.6 1.0
CE2 B:TYR1161 4.4 16.5 1.0
CE1 A:TYR1161 4.5 33.1 1.0
CB A:VAL1169 4.5 26.3 1.0
CE2 C:TYR1161 4.5 25.7 1.0
CE2 A:TYR1161 4.6 31.2 1.0
CG1 C:VAL1169 4.6 27.2 1.0
CE1 C:TYR1161 4.6 28.2 1.0
CE1 B:TYR1161 4.7 27.2 1.0
CZ A:TYR1161 4.7 35.5 1.0
CG1 B:VAL1169 4.7 22.1 1.0
CZ B:TYR1161 4.8 29.8 1.0
CZ C:TYR1161 4.8 28.1 1.0
CG1 A:VAL1169 5.0 18.3 1.0

Xenon binding site 6 out of 14 in 3c9i

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Xenon binding site 6 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe7

b:96.2
occ:1.00
CG2 C:ILE1208 3.6 43.6 1.0
CG2 B:ILE1208 3.6 30.6 1.0
CD1 A:ILE1208 3.7 41.0 1.0
CD1 C:ILE1205 3.7 67.9 1.0
CG1 C:ILE1205 3.9 59.2 1.0
O B:HOH1494 4.0 48.3 1.0
CB C:ILE1208 4.1 38.5 1.0
CD1 B:ILE1208 4.1 30.0 1.0
CG2 A:ILE1208 4.2 45.7 1.0
CD1 A:ILE1205 4.2 44.6 1.0
CB A:ILE1208 4.5 39.2 1.0
CD1 B:ILE1205 4.5 31.0 1.0
CG2 A:ILE1205 4.5 40.4 1.0
CB B:ILE1208 4.5 43.3 1.0
CG1 C:ILE1208 4.5 43.0 1.0
CG2 B:ILE1205 4.6 29.4 1.0
CG1 A:ILE1208 4.7 34.4 1.0
CG1 B:ILE1208 4.9 41.6 1.0
CB C:ILE1205 4.9 57.6 1.0

Xenon binding site 7 out of 14 in 3c9i

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Xenon binding site 7 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe4

b:74.0
occ:1.00
CB C:TYR1140 3.6 32.9 1.0
CB A:TYR1140 3.7 29.1 1.0
CD2 C:LEU1136 3.7 24.9 1.0
CB B:TYR1140 3.8 25.4 1.0
CG A:TYR1140 3.9 26.9 1.0
CD1 A:TYR1140 3.9 25.5 1.0
CG C:TYR1140 4.0 28.8 1.0
CD2 C:TYR1140 4.1 26.2 1.0
CB C:LEU1136 4.2 27.4 1.0
CD2 A:LEU1136 4.2 30.8 1.0
CG B:TYR1140 4.3 21.3 1.0
CD1 B:LEU1136 4.3 29.3 1.0
CB B:LEU1136 4.3 34.6 1.0
CG C:LEU1136 4.3 28.9 1.0
CB A:LEU1136 4.4 36.1 1.0
CD2 B:TYR1140 4.4 24.2 1.0
CD2 B:LEU1136 4.4 28.1 1.0
CD1 C:LEU1136 4.4 26.7 1.0
CD1 A:LEU1136 4.5 46.5 1.0
CG B:LEU1136 4.6 34.1 1.0
CG A:LEU1136 4.6 38.8 1.0
CD2 A:TYR1140 4.8 25.0 1.0
CE1 A:TYR1140 4.8 24.8 1.0
CD1 C:TYR1140 4.9 31.4 1.0
O C:LEU1136 4.9 30.6 1.0
O B:LEU1136 4.9 28.6 1.0
CA C:TYR1140 4.9 36.1 1.0

Xenon binding site 8 out of 14 in 3c9i

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Xenon binding site 8 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe8

b:33.3
occ:1.00
CG2 E:ILE1045 3.8 24.1 1.0
CD1 E:ILE1045 3.8 13.9 1.0
CG2 F:ILE1045 3.8 21.9 1.0
CD1 F:ILE1045 3.9 22.1 1.0
CD1 D:ILE1045 4.0 25.3 1.0
CB E:ILE1045 4.0 22.9 1.0
CG2 D:ILE1045 4.0 16.1 1.0
CB F:ILE1045 4.1 25.1 1.0
CB D:ILE1045 4.2 23.7 1.0
CG1 F:VAL1042 4.4 22.4 1.0
CA F:VAL1042 4.4 18.8 1.0
CA D:VAL1042 4.5 23.4 1.0
CG1 E:VAL1042 4.5 14.2 1.0
CA E:VAL1042 4.5 24.1 1.0
CG1 E:ILE1045 4.5 24.8 1.0
CG1 D:VAL1042 4.6 23.1 1.0
CG2 D:VAL1042 4.6 28.8 1.0
CG2 F:VAL1042 4.6 18.1 1.0
CG2 E:VAL1042 4.6 29.9 1.0
CG1 F:ILE1045 4.6 21.7 1.0
O F:VAL1042 4.7 23.3 1.0
O D:VAL1042 4.7 15.5 1.0
CG1 D:ILE1045 4.7 17.7 1.0
CB F:VAL1042 4.7 19.9 1.0
CB D:VAL1042 4.8 28.9 1.0
CB E:VAL1042 4.8 23.3 1.0
O E:VAL1042 4.8 23.0 1.0

Xenon binding site 9 out of 14 in 3c9i

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Xenon binding site 9 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe9

b:32.7
occ:1.00
CB D:ALA1108 3.8 18.7 1.0
CB F:ALA1108 3.9 30.6 1.0
CB E:ALA1108 4.0 19.1 1.0
CG2 D:VAL1105 4.2 22.8 1.0
CG2 F:VAL1105 4.3 33.8 1.0
CG2 E:VAL1105 4.5 14.5 1.0
CG1 F:VAL1105 4.5 25.3 1.0
CA F:VAL1105 4.6 15.4 1.0
CG1 E:VAL1105 4.6 23.6 1.0
CA D:VAL1105 4.6 29.5 1.0
CA E:VAL1105 4.6 21.1 1.0
CB F:VAL1105 4.7 15.6 1.0
CG1 D:VAL1105 4.7 17.9 1.0
CB D:VAL1105 4.8 25.0 1.0
CB E:VAL1105 4.8 25.2 1.0

Xenon binding site 10 out of 14 in 3c9i

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Xenon binding site 10 out of 14 in the Structure of P22 Tail-Needle GP26 Bound to Xenon Gas


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Structure of P22 Tail-Needle GP26 Bound to Xenon Gas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe11

b:0.4
occ:1.00
CD2 F:LEU1136 3.6 41.8 1.0
CB D:TYR1140 3.7 35.1 1.0
CD2 E:LEU1136 3.7 12.4 1.0
CB F:TYR1140 3.9 26.4 1.0
CB E:TYR1140 3.9 30.4 1.0
CD2 D:TYR1140 4.0 28.8 1.0
CG D:TYR1140 4.0 32.7 1.0
CB D:LEU1136 4.1 40.3 1.0
CD1 E:TYR1140 4.1 35.5 1.0
CG F:TYR1140 4.2 25.1 1.0
CG E:TYR1140 4.2 34.8 1.0
CD2 F:TYR1140 4.3 27.5 1.0
CB E:LEU1136 4.3 34.0 1.0
CD1 F:LEU1136 4.3 40.8 1.0
CG F:LEU1136 4.3 45.2 1.0
CB F:LEU1136 4.3 41.1 1.0
CG E:LEU1136 4.3 30.7 1.0
O D:LEU1136 4.3 79.0 1.0
CD1 E:LEU1136 4.3 36.5 1.0
CD1 D:LEU1136 4.5 34.0 1.0
C D:LEU1136 4.7 57.6 1.0
CG D:LEU1136 4.7 39.0 1.0
O F:LEU1136 4.7 33.2 1.0
CA D:LEU1136 4.8 58.4 1.0
O E:LEU1136 4.8 68.0 1.0
CD2 D:LEU1136 4.8 52.2 1.0
CE2 D:TYR1140 4.8 25.2 1.0
CD1 D:TYR1140 5.0 36.4 1.0

Reference:

A.S.Olia, S.Casjens, G.Cingolani. Structural Plasticity of the Phage P22 Tail Needle GP26 Probed with Xenon Gas. Protein Sci. V. 18 537 2009.
ISSN: ISSN 0961-8368
PubMed: 19241380
DOI: 10.1002/PRO.53
Page generated: Wed Dec 16 02:39:44 2020

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