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Tungsten in PDB 5xls: Crystal Structure of Uraa in Occluded Conformation

Protein crystallography data

The structure of Crystal Structure of Uraa in Occluded Conformation, PDB code: 5xls was solved by X.Z.Yu, G.H.Yang, C.Y.Yan, N.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.79 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.721, 134.726, 143.452, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 24.7

Tungsten Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Tungsten atom in the Crystal Structure of Uraa in Occluded Conformation (pdb code 5xls). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 24 binding sites of Tungsten where determined in the Crystal Structure of Uraa in Occluded Conformation, PDB code: 5xls:
Jump to Tungsten binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tungsten binding site 1 out of 24 in 5xls

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Tungsten binding site 1 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


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Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:53.3
occ:1.00
W1 A:KEG502 0.0 53.3 1.0
O17 A:KEG502 2.0 47.8 1.0
O1 A:KEG502 2.0 47.1 1.0
O25 A:KEG502 2.0 52.7 1.0
O23 A:KEG502 2.2 49.3 1.0
O27 A:KEG502 2.2 48.2 1.0
O29 A:KEG502 2.6 53.1 1.0
O45 A:KEG502 2.6 51.5 1.0
W9 A:KEG502 3.4 54.2 1.0
O37 A:KEG502 3.4 50.2 1.0
W5 A:KEG502 3.4 53.7 1.0
W3 A:KEG502 3.6 59.9 1.0
W12 A:KEG502 3.7 60.9 1.0
O35 A:KEG502 3.8 49.5 1.0
NE A:ARG265 3.8 49.5 1.0
O39 A:KEG502 3.8 54.3 1.0
NZ A:LYS62 4.0 60.4 1.0
O42 A:KEG502 4.0 51.5 1.0
O21 A:KEG502 4.0 55.9 1.0
NE2 A:HIS264 4.1 48.0 1.0
O5 A:KEG502 4.3 50.7 1.0
CZ A:ARG265 4.3 51.4 1.0
CD A:ARG265 4.4 48.0 1.0
NH1 A:ARG265 4.4 51.5 1.0
O32 A:KEG502 4.5 55.7 1.0
CE A:LYS62 4.5 59.1 1.0
CE1 A:HIS264 4.5 46.9 1.0
CG A:ARG265 4.8 47.0 1.0
O14 A:KEG502 4.9 57.9 1.0
O46 A:KEG502 4.9 55.1 1.0
O33 A:KEG502 5.0 56.5 1.0

Tungsten binding site 2 out of 24 in 5xls

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Tungsten binding site 2 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


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Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:65.7
occ:1.00
W2 A:KEG502 0.0 65.7 1.0
O18 A:KEG502 2.0 56.5 1.0
O2 A:KEG502 2.0 58.4 1.0
O30 A:KEG502 2.1 56.9 1.0
O26 A:KEG502 2.1 55.7 1.0
O24 A:KEG502 2.1 56.9 1.0
O28 A:KEG502 2.2 56.5 1.0
O46 A:KEG502 2.9 55.1 1.0
O40 A:KEG502 3.1 57.5 1.0
W6 A:KEG502 3.4 59.5 1.0
W10 A:KEG502 3.4 60.8 1.0
W4 A:KEG502 3.7 64.0 1.0
O42 A:KEG502 3.7 51.5 1.0
W8 A:KEG502 3.8 61.6 1.0
O36 A:KEG502 3.8 50.6 1.0
O34 A:KEG502 4.1 58.4 1.0
W11 A:KEG502 4.3 83.8 1.0
O19 A:KEG502 4.4 59.4 1.0
O44 A:KEG502 4.4 59.6 1.0
O21 A:KEG502 4.5 55.9 1.0
O38 A:KEG502 4.6 58.4 1.0
O6 A:KEG502 4.7 62.5 1.0
O39 A:KEG502 4.8 54.3 1.0
O10 A:KEG502 4.8 63.8 1.0
W12 A:KEG502 4.9 60.9 1.0
O32 A:KEG502 5.0 55.7 1.0

Tungsten binding site 3 out of 24 in 5xls

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Tungsten binding site 3 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


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Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:59.9
occ:1.00
W3 A:KEG502 0.0 59.9 1.0
O21 A:KEG502 2.0 55.9 1.0
O5 A:KEG502 2.0 50.7 1.0
O31 A:KEG502 2.1 55.3 1.0
O37 A:KEG502 2.1 50.2 1.0
O25 A:KEG502 2.2 52.7 1.0
O33 A:KEG502 2.2 56.5 1.0
O29 A:KEG502 2.5 53.1 1.0
O34 A:KEG502 3.4 58.4 1.0
W4 A:KEG502 3.4 64.0 1.0
W12 A:KEG502 3.5 60.9 1.0
W1 A:KEG502 3.6 53.3 1.0
O38 A:KEG502 3.7 58.4 1.0
O1 A:KEG502 3.8 47.1 1.0
W7 A:KEG502 3.8 58.8 1.0
NZ A:LYS62 3.8 60.4 1.0
O39 A:KEG502 4.2 54.3 1.0
O46 A:KEG502 4.5 55.1 1.0
O19 A:KEG502 4.6 59.4 1.0
O45 A:KEG502 4.6 51.5 1.0
O17 A:KEG502 4.6 47.8 1.0
O23 A:KEG502 4.7 49.3 1.0
O41 A:KEG502 5.0 59.2 1.0
O6 A:KEG502 5.0 62.5 1.0

Tungsten binding site 4 out of 24 in 5xls

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Tungsten binding site 4 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


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Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:64.0
occ:1.00
W4 A:KEG502 0.0 64.0 1.0
O21 A:KEG502 2.0 55.9 1.0
O6 A:KEG502 2.0 62.5 1.0
O34 A:KEG502 2.1 58.4 1.0
O26 A:KEG502 2.1 55.7 1.0
O38 A:KEG502 2.1 58.4 1.0
O31 A:KEG502 2.2 55.3 1.0
O46 A:KEG502 2.9 55.1 1.0
W3 A:KEG502 3.4 59.9 1.0
W12 A:KEG502 3.5 60.9 1.0
O33 A:KEG502 3.6 56.5 1.0
W2 A:KEG502 3.7 65.7 1.0
W8 A:KEG502 3.7 61.6 1.0
O25 A:KEG502 3.8 52.7 1.0
O2 A:KEG502 3.9 58.4 1.0
O37 A:KEG502 3.9 50.2 1.0
O30 A:KEG502 4.0 56.9 1.0
O19 A:KEG502 4.4 59.4 1.0
O28 A:KEG502 4.5 56.5 1.0
O18 A:KEG502 4.6 56.5 1.0
O10 A:KEG502 4.7 63.8 1.0
O29 A:KEG502 4.8 53.1 1.0
W10 A:KEG502 4.9 60.8 1.0
O41 A:KEG502 4.9 59.2 1.0
O39 A:KEG502 5.0 54.3 1.0

Tungsten binding site 5 out of 24 in 5xls

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Tungsten binding site 5 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 5 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:53.7
occ:1.00
W5 A:KEG502 0.0 53.7 1.0
O17 A:KEG502 2.0 47.8 1.0
O7 A:KEG502 2.0 52.8 1.0
O39 A:KEG502 2.1 54.3 1.0
O35 A:KEG502 2.1 49.5 1.0
O23 A:KEG502 2.2 49.3 1.0
O32 A:KEG502 2.5 55.7 1.0
O29 A:KEG502 2.6 53.1 1.0
O43 A:KEG502 3.1 54.4 1.0
W1 A:KEG502 3.4 53.3 1.0
W9 A:KEG502 3.5 54.2 1.0
W7 A:KEG502 3.6 58.8 1.0
CE A:LYS109 3.7 58.4 1.0
W11 A:KEG502 3.7 83.8 1.0
O19 A:KEG502 3.9 59.4 1.0
O13 A:KEG502 4.0 59.3 1.0
O27 A:KEG502 4.0 48.2 1.0
NE2 A:HIS264 4.1 48.0 1.0
O25 A:KEG502 4.1 52.7 1.0
NZ A:LYS109 4.2 59.6 1.0
O42 A:KEG502 4.2 51.5 1.0
CE1 A:HIS264 4.4 46.9 1.0
O45 A:KEG502 4.6 51.5 1.0
O33 A:KEG502 4.9 56.5 1.0
W6 A:KEG502 5.0 59.5 1.0
CD A:LYS109 5.0 57.2 1.0

Tungsten binding site 6 out of 24 in 5xls

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Tungsten binding site 6 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 6 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:59.5
occ:1.00
W6 A:KEG502 0.0 59.5 1.0
O18 A:KEG502 2.0 56.5 1.0
O8 A:KEG502 2.0 56.2 1.0
O40 A:KEG502 2.1 57.5 1.0
O24 A:KEG502 2.1 56.9 1.0
O36 A:KEG502 2.2 50.6 1.0
O42 A:KEG502 2.4 51.5 1.0
O32 A:KEG502 2.5 55.7 1.0
W11 A:KEG502 2.9 83.8 1.0
O13 A:KEG502 3.2 59.3 1.0
NZ A:LYS109 3.3 59.6 1.0
W2 A:KEG502 3.4 65.7 1.0
W9 A:KEG502 3.7 54.2 1.0
W10 A:KEG502 3.7 60.8 1.0
O39 A:KEG502 3.7 54.3 1.0
O30 A:KEG502 3.8 56.9 1.0
O28 A:KEG502 4.2 56.5 1.0
O11 A:KEG502 4.2 47.5 1.0
O44 A:KEG502 4.3 59.6 1.0
O19 A:KEG502 4.4 59.4 1.0
O45 A:KEG502 4.5 51.5 1.0
O17 A:KEG502 4.6 47.8 1.0
CE A:LYS109 4.6 58.4 1.0
O46 A:KEG502 4.6 55.1 1.0
O35 A:KEG502 4.6 49.5 1.0
O12 A:KEG502 4.8 49.4 1.0
W5 A:KEG502 5.0 53.7 1.0
O43 A:KEG502 5.0 54.4 1.0
W8 A:KEG502 5.0 61.6 1.0

Tungsten binding site 7 out of 24 in 5xls

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Tungsten binding site 7 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 7 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:58.8
occ:1.00
W7 A:KEG502 0.0 58.8 1.0
O9 A:KEG502 2.0 55.7 1.0
O19 A:KEG502 2.0 59.4 1.0
O41 A:KEG502 2.1 59.2 1.0
O33 A:KEG502 2.1 56.5 1.0
O43 A:KEG502 2.2 54.4 1.0
O39 A:KEG502 2.6 54.3 1.0
O29 A:KEG502 2.6 53.1 1.0
O34 A:KEG502 3.4 58.4 1.0
W8 A:KEG502 3.4 61.6 1.0
W5 A:KEG502 3.6 53.7 1.0
W11 A:KEG502 3.6 83.8 1.0
W3 A:KEG502 3.8 59.9 1.0
O44 A:KEG502 4.0 59.6 1.0
O7 A:KEG502 4.1 52.8 1.0
O25 A:KEG502 4.3 52.7 1.0
O32 A:KEG502 4.5 55.7 1.0
O5 A:KEG502 4.6 50.7 1.0
O17 A:KEG502 4.7 47.8 1.0
O21 A:KEG502 4.7 55.9 1.0
O23 A:KEG502 4.7 49.3 1.0
O31 A:KEG502 4.9 55.3 1.0

Tungsten binding site 8 out of 24 in 5xls

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Tungsten binding site 8 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


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Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 8 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:61.6
occ:1.00
W8 A:KEG502 0.0 61.6 1.0
O19 A:KEG502 1.9 59.4 1.0
O10 A:KEG502 2.0 63.8 1.0
O34 A:KEG502 2.1 58.4 1.0
O30 A:KEG502 2.1 56.9 1.0
O41 A:KEG502 2.1 59.2 1.0
O44 A:KEG502 2.2 59.6 1.0
W11 A:KEG502 3.2 83.8 1.0
W7 A:KEG502 3.4 58.8 1.0
O40 A:KEG502 3.4 57.5 1.0
O33 A:KEG502 3.6 56.5 1.0
O43 A:KEG502 3.7 54.4 1.0
W4 A:KEG502 3.7 64.0 1.0
W2 A:KEG502 3.8 65.7 1.0
O39 A:KEG502 3.8 54.3 1.0
O26 A:KEG502 4.1 55.7 1.0
O2 A:KEG502 4.3 58.4 1.0
O6 A:KEG502 4.5 62.5 1.0
O9 A:KEG502 4.6 55.7 1.0
O18 A:KEG502 4.7 56.5 1.0
O21 A:KEG502 4.7 55.9 1.0
O24 A:KEG502 4.9 56.9 1.0
O31 A:KEG502 4.9 55.3 1.0
O29 A:KEG502 4.9 53.1 1.0
W6 A:KEG502 5.0 59.5 1.0

Tungsten binding site 9 out of 24 in 5xls

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Tungsten binding site 9 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


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Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 9 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:54.2
occ:1.00
W9 A:KEG502 0.0 54.2 1.0
O17 A:KEG502 2.0 47.8 1.0
O11 A:KEG502 2.0 47.5 1.0
O42 A:KEG502 2.1 51.5 1.0
O35 A:KEG502 2.2 49.5 1.0
O27 A:KEG502 2.2 48.2 1.0
O45 A:KEG502 2.5 51.5 1.0
O32 A:KEG502 2.6 55.7 1.0
O36 A:KEG502 3.2 50.6 1.0
W1 A:KEG502 3.4 53.3 1.0
W5 A:KEG502 3.5 53.7 1.0
W6 A:KEG502 3.7 59.5 1.0
O39 A:KEG502 3.7 54.3 1.0
NZ A:LYS109 3.7 59.6 1.0
NE2 A:HIS264 3.7 48.0 1.0
W10 A:KEG502 3.7 60.8 1.0
O23 A:KEG502 3.9 49.3 1.0
NH1 A:ARG265 3.9 51.5 1.0
CE A:LYS109 3.9 58.4 1.0
O18 A:KEG502 3.9 56.5 1.0
NE A:ARG265 4.0 49.5 1.0
O25 A:KEG502 4.1 52.7 1.0
O12 A:KEG502 4.2 49.4 1.0
CD2 A:HIS264 4.3 47.0 1.0
CZ A:ARG265 4.4 51.4 1.0
O29 A:KEG502 4.5 53.1 1.0
O8 A:KEG502 4.6 56.2 1.0
W11 A:KEG502 4.7 83.8 1.0
CD A:LYS109 4.8 57.2 1.0
CE1 A:HIS264 4.9 46.9 1.0
O46 A:KEG502 4.9 55.1 1.0
O13 A:KEG502 4.9 59.3 1.0
W12 A:KEG502 4.9 60.9 1.0

Tungsten binding site 10 out of 24 in 5xls

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Tungsten binding site 10 out of 24 in the Crystal Structure of Uraa in Occluded Conformation


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 10 of Crystal Structure of Uraa in Occluded Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W502

b:60.8
occ:1.00
W10 A:KEG502 0.0 60.8 1.0
O12 A:KEG502 2.0 49.4 1.0
O46 A:KEG502 2.1 55.1 1.0
O18 A:KEG502 2.1 56.5 1.0
O42 A:KEG502 2.2 51.5 1.0
O28 A:KEG502 2.2 56.5 1.0
O36 A:KEG502 2.2 50.6 1.0
O45 A:KEG502 2.5 51.5 1.0
W12 A:KEG502 3.3 60.9 1.0
W2 A:KEG502 3.4 65.7 1.0
NH1 A:ARG265 3.4 51.5 1.0
W6 A:KEG502 3.7 59.5 1.0
W9 A:KEG502 3.7 54.2 1.0
O24 A:KEG502 3.8 56.9 1.0
O26 A:KEG502 3.9 55.7 1.0
O14 A:KEG502 3.9 57.9 1.0
O25 A:KEG502 4.2 52.7 1.0
O11 A:KEG502 4.2 47.5 1.0
O38 A:KEG502 4.3 58.4 1.0
O21 A:KEG502 4.3 55.9 1.0
O27 A:KEG502 4.6 48.2 1.0
O17 A:KEG502 4.7 47.8 1.0
CZ A:ARG265 4.7 51.4 1.0
O32 A:KEG502 4.7 55.7 1.0
W4 A:KEG502 4.9 64.0 1.0

Reference:

X.Yu, G.Yang, C.Yan, J.L.Baylon, J.Jiang, H.Fan, G.Lu, K.Hasegawa, H.Okumura, T.Wang, E.Tajkhorshid, S.Li, N.Yan. Dimeric Structure of the Uracil:Proton Symporter Uraa Provides Mechanistic Insights Into the SLC4/23/26 Transporters Cell Res. V. 27 1020 2017.
ISSN: ISSN 1748-7838
PubMed: 28621327
DOI: 10.1038/CR.2017.83
Page generated: Wed Dec 16 02:35:27 2020

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