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Xenon in PDB 2b2j: Ammonium Transporter Amt-1 From A. Fulgidus (Xe)

Protein crystallography data

The structure of Ammonium Transporter Amt-1 From A. Fulgidus (Xe), PDB code: 2b2j was solved by S.L.A.Andrade, A.Dickmanns, R.Ficner, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 1.85
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 111.460, 111.460, 135.578, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 22.1

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Xenon atom in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe) (pdb code 2b2j). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 15 binding sites of Xenon where determined in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe), PDB code: 2b2j:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 15 in 2b2j

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Xenon binding site 1 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1001

b:38.4
occ:0.60
CD1 A:ILE103 3.8 21.1 1.0
CZ3 A:TRP201 3.8 23.5 1.0
CG1 A:VAL99 4.0 25.1 1.0
CG1 A:ILE103 4.0 22.6 1.0
CE1 A:HIS305 4.0 27.9 1.0
CH2 A:TRP201 4.1 22.3 1.0
CE A:MET19 4.1 15.3 1.0
CG2 A:VAL23 4.1 18.5 1.0
CD2 A:LEU197 4.2 20.5 1.0
XE A:XE1002 4.2 57.0 0.5
CD1 A:LEU197 4.6 21.0 1.0
NE2 A:HIS305 4.6 29.9 1.0
CE3 A:TRP201 4.7 23.6 1.0
ND1 A:HIS305 4.8 27.2 1.0
CE1 A:HIS157 4.9 26.6 1.0
CG A:LEU197 4.9 21.1 1.0

Xenon binding site 2 out of 15 in 2b2j

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Xenon binding site 2 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1002

b:57.0
occ:0.50
NE2 A:HIS305 3.4 29.9 1.0
CD2 A:PHE26 3.6 20.4 1.0
OH A:TYR27 3.7 18.4 1.0
O A:HOH1040 3.7 37.6 1.0
CE2 A:PHE26 3.8 20.1 1.0
CE1 A:TYR27 3.9 18.8 1.0
CZ A:TYR27 3.9 19.4 1.0
CD1 A:LEU197 4.0 21.0 1.0
CE1 A:HIS305 4.1 27.9 1.0
XE A:XE1001 4.2 38.4 0.6
CG2 A:VAL23 4.2 18.5 1.0
CG1 A:VAL23 4.3 19.0 1.0
CD2 A:HIS305 4.5 27.7 1.0
CG A:PHE26 4.5 20.6 1.0
CG1 A:ILE103 4.6 22.6 1.0
CD1 A:TYR27 4.7 16.4 1.0
CB A:VAL23 4.7 20.8 1.0
CD1 A:ILE254 4.8 23.1 1.0
CE2 A:TYR27 4.8 19.8 1.0
CZ A:PHE26 4.9 18.6 1.0
CG2 A:ILE103 4.9 23.4 1.0
CA A:VAL23 5.0 20.4 1.0

Xenon binding site 3 out of 15 in 2b2j

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Xenon binding site 3 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1003

b:40.5
occ:0.80
O A:ALA194 3.5 22.3 1.0
CG1 A:ILE254 3.6 25.1 1.0
CE3 A:TRP198 3.9 28.1 1.0
O A:VAL250 4.0 27.7 1.0
CB A:ALA194 4.1 20.4 1.0
CB A:ALA253 4.1 28.1 1.0
C A:ALA194 4.2 21.3 1.0
CD1 A:ILE254 4.2 23.1 1.0
CB A:TRP198 4.3 24.4 1.0
CA A:ALA194 4.4 20.3 1.0
CB A:VAL250 4.4 26.9 1.0
CD1 A:LEU257 4.5 20.6 1.0
N A:TRP198 4.6 22.3 1.0
N A:ILE254 4.6 26.3 1.0
CA A:VAL250 4.6 26.7 1.0
CG1 A:VAL250 4.7 25.1 1.0
CD2 A:TRP198 4.7 27.4 1.0
C A:VAL250 4.8 27.4 1.0
CZ3 A:TRP198 4.8 27.0 1.0
CA A:TRP198 4.8 23.6 1.0
CG A:TRP198 4.9 27.9 1.0
CB A:ILE254 4.9 26.1 1.0
C A:ALA253 5.0 28.7 1.0
CA A:ILE254 5.0 26.5 1.0

Xenon binding site 4 out of 15 in 2b2j

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Xenon binding site 4 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1004

b:43.6
occ:0.45
CG2 A:THR223 3.5 29.6 1.0
CD2 A:PHE202 3.6 27.6 1.0
ND2 A:ASN224 3.6 29.0 1.0
CE2 A:PHE202 3.7 28.1 1.0
N A:PHE202 3.9 25.7 1.0
CG A:PHE202 3.9 27.6 1.0
O A:TRP198 3.9 27.5 1.0
OD1 A:ASN224 4.0 28.6 1.0
CG A:ASN224 4.0 29.3 1.0
CZ A:PHE202 4.0 27.8 1.0
CB A:THR223 4.0 27.1 1.0
NE1 A:TRP198 4.0 28.8 1.0
CA A:PHE202 4.0 27.3 1.0
CD1 A:TRP198 4.0 29.5 1.0
C A:TRP201 4.0 24.6 1.0
CB A:TRP201 4.1 23.2 1.0
CD1 A:PHE202 4.1 27.6 1.0
CE1 A:PHE202 4.2 28.3 1.0
O A:TRP201 4.3 26.1 1.0
N A:ASN224 4.5 27.9 1.0
CB A:PHE202 4.6 27.4 1.0
CA A:TRP201 4.7 23.7 1.0
C A:THR223 4.7 26.7 1.0
O A:VAL220 4.7 31.8 1.0
CD2 A:LEU257 4.7 19.3 1.0
CA A:ASN224 4.8 26.7 1.0
CG A:TRP201 5.0 24.9 1.0
OG1 A:THR223 5.0 28.6 1.0

Xenon binding site 5 out of 15 in 2b2j

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Xenon binding site 5 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1005

b:44.6
occ:0.60
CD1 A:LEU104 3.7 31.3 1.0
CD2 A:LEU120 3.8 30.5 1.0
CD1 A:PHE117 3.8 30.1 1.0
CG A:LEU120 3.9 31.4 1.0
CE1 A:PHE117 4.0 31.7 1.0
CD2 A:LEU104 4.4 33.7 1.0
CB A:LEU120 4.5 31.1 1.0
CG A:LEU104 4.5 33.2 1.0
CD1 A:ILE108 4.6 29.8 1.0
N A:SER121 4.7 33.4 1.0
CG2 A:ILE108 4.7 29.6 1.0
CG2 A:VAL167 4.7 31.4 1.0
O A:PHE117 4.8 31.1 1.0
CG1 A:VAL167 4.8 32.4 1.0
CA A:SER121 4.8 33.4 1.0
CB A:LEU104 4.9 29.7 1.0
XE A:XE1006 4.9 37.8 0.8
CG A:PHE117 5.0 31.0 1.0
CB A:SER121 5.0 34.2 1.0

Xenon binding site 6 out of 15 in 2b2j

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Xenon binding site 6 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1006

b:37.8
occ:0.80
CD2 A:LEU369 3.5 40.5 1.0
CB A:ALA112 3.8 34.7 1.0
CA A:PHE117 3.8 32.7 1.0
N A:PHE117 3.8 34.4 1.0
C A:SER116 4.0 34.3 1.0
CG2 A:ILE108 4.0 29.6 1.0
CB A:SER116 4.1 34.4 1.0
CD2 A:LEU120 4.1 30.5 1.0
CB A:LEU369 4.2 40.6 1.0
O A:SER116 4.2 34.6 1.0
CB A:PHE117 4.3 31.4 1.0
O A:LEU369 4.3 38.0 1.0
CG A:LEU369 4.4 39.5 1.0
O A:LYS113 4.5 30.5 1.0
CA A:LEU369 4.5 40.0 1.0
CD1 A:ILE108 4.6 29.8 1.0
CA A:SER116 4.7 34.1 1.0
CB A:LEU120 4.8 31.1 1.0
C A:LEU369 4.8 38.2 1.0
CB A:ILE108 4.8 30.1 1.0
XE A:XE1005 4.9 44.6 0.6
CD1 A:LEU369 4.9 40.4 1.0
CA A:ALA112 4.9 35.0 1.0
CD1 A:ILE171 5.0 38.2 1.0

Xenon binding site 7 out of 15 in 2b2j

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Xenon binding site 7 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1007

b:68.6
occ:0.50
CG1 A:ILE49 3.2 39.5 1.0
CD1 A:ILE49 3.3 38.5 1.0
OG A:SER121 3.3 39.8 1.0
OG1 A:THR50 3.5 33.8 1.0
CD2 A:LEU125 3.5 42.1 1.0
O A:SER121 3.8 33.5 1.0
CG1 A:ILE101 3.9 36.0 1.0
CB A:ILE49 3.9 36.8 1.0
N A:THR50 4.0 32.4 1.0
C A:SER121 4.0 33.0 1.0
CD1 A:LEU53 4.0 33.1 1.0
C A:ILE49 4.1 34.5 1.0
CG A:LEU125 4.1 41.1 1.0
CA A:THR50 4.2 32.0 1.0
CB A:SER121 4.2 34.2 1.0
N A:ALA122 4.2 32.4 1.0
CA A:ALA122 4.3 33.0 1.0
O A:ILE49 4.3 35.7 1.0
CB A:LEU125 4.4 38.8 1.0
CB A:THR50 4.5 32.7 1.0
O A:SER46 4.6 29.0 1.0
CD1 A:ILE101 4.6 38.2 1.0
CA A:ILE49 4.6 35.1 1.0
CA A:SER121 4.7 33.4 1.0
CG2 A:ILE101 4.8 36.5 1.0
CB A:ILE101 4.8 34.0 1.0
CG A:LEU53 5.0 33.1 1.0

Xenon binding site 8 out of 15 in 2b2j

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Xenon binding site 8 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1008

b:70.3
occ:0.60
CD1 A:ILE295 3.4 45.7 1.0
CH2 A:TRP302 3.9 33.5 1.0
CD1 A:PHE289 4.0 52.8 1.0
CE1 A:PHE289 4.0 53.4 1.0
CZ2 A:TRP302 4.1 33.6 1.0
CZ3 A:TRP302 4.1 34.7 1.0
CD1 A:LEU165 4.3 33.6 1.0
CA A:ARG290 4.3 44.5 1.0
CB A:ARG290 4.4 45.0 1.0
CD2 A:LEU165 4.4 35.0 1.0
O A:HOH1055 4.4 49.2 1.0
CE2 A:TRP302 4.6 33.8 1.0
CE3 A:TRP302 4.7 33.7 1.0
CG1 A:ILE295 4.8 45.3 1.0
N A:ARG290 4.8 46.4 1.0
CD2 A:TRP302 4.9 33.4 1.0
CG A:LEU165 5.0 34.8 1.0

Xenon binding site 9 out of 15 in 2b2j

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Xenon binding site 9 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1009

b:50.8
occ:0.50
CE2 A:PHE44 3.1 33.1 1.0
CD2 A:PHE44 3.3 32.1 1.0
CZ A:PHE44 3.7 32.9 1.0
CE A:MET17 3.8 17.6 1.0
CG A:PHE44 4.0 30.6 1.0
CB A:PRO21 4.2 21.0 1.0
CD2 A:LEU47 4.2 26.3 1.0
CG A:PRO21 4.2 21.4 1.0
CE1 A:PHE44 4.3 36.2 1.0
CD1 A:PHE44 4.4 33.8 1.0
CD A:PRO21 4.5 20.9 1.0
CB A:PHE44 4.8 29.1 1.0
CA A:PHE44 5.0 26.3 1.0

Xenon binding site 10 out of 15 in 2b2j

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Xenon binding site 10 out of 15 in the Ammonium Transporter Amt-1 From A. Fulgidus (Xe)


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Ammonium Transporter Amt-1 From A. Fulgidus (Xe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1010

b:53.3
occ:0.50
O A:HOH1067 3.5 34.4 1.0
N A:PHE89 4.1 34.6 1.0
CB A:PHE89 4.2 33.7 1.0
O A:GLU85 4.2 53.0 1.0
CA A:PHE89 4.2 32.4 1.0
CG A:LEU88 4.3 32.4 1.0
CD2 A:LEU88 4.4 30.6 1.0
CD2 A:LEU210 4.4 31.6 1.0
CB A:LEU88 4.4 34.5 1.0
CG2 A:ILE9 4.6 24.6 1.0
CD1 A:PHE89 4.7 34.1 1.0
C A:LEU88 4.7 36.8 1.0
CG1 A:ILE9 4.8 26.4 1.0
OE2 A:GLU85 4.8 71.1 1.0
CB A:LEU210 4.8 30.9 1.0
CG A:PHE89 4.9 34.5 1.0
O A:LEU210 4.9 32.6 1.0
CD1 A:LEU210 5.0 33.3 1.0

Reference:

S.L.Andrade, A.Dickmanns, R.Ficner, O.Einsle. Crystal Structure of the Archaeal Ammonium Transporter Amt-1 From Archaeoglobus Fulgidus Proc.Natl.Acad.Sci.Usa V. 102 14994 2005.
ISSN: ISSN 0027-8424
PubMed: 16214888
DOI: 10.1073/PNAS.0506254102
Page generated: Wed Dec 16 02:39:35 2020

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