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Uranium in PDB 1jet: Oligo-Peptide Binding Protein (Oppa) Complexed with Kak

Protein crystallography data

The structure of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak, PDB code: 1jet was solved by J.Tame, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.190, 76.040, 70.280, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 25.5

Uranium Binding Sites:

The binding sites of Uranium atom in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak (pdb code 1jet). This binding sites where shown within 5.0 Angstroms radius around Uranium atom.
In total 8 binding sites of Uranium where determined in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak, PDB code: 1jet:
Jump to Uranium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Uranium binding site 1 out of 8 in 1jet

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Uranium binding site 1 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 1 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U518

b:11.2
occ:1.00
 O A:HOH527 2.1 19.9 1.0
O A:HOH526 2.2 13.9 1.0
OD2 A:ASP323 2.4 12.6 1.0
O A:HOH573 2.5 11.2 1.0
O A:HOH1076 2.5 6.2 0.8
O A:HOH811 2.8 29.0 1.0
CG A:ASP323 3.3 9.5 1.0
O A:HOH1081 3.4 12.4 0.8
O A:HOH1045 3.4 57.0 1.0
O A:HOH1077 3.4 8.9 0.8
O A:HOH627 3.4 15.9 1.0
OD1 A:ASP323 3.4 11.8 1.0
O A:HOH849 4.4 31.8 1.0
O A:HOH930 4.5 40.2 1.0
CB A:ASP323 4.7 10.5 1.0
O A:HOH735 4.7 23.5 1.0
O A:HOH1078 4.7 10.2 0.8
NZ A:LYS157 4.8 9.5 1.0
O A:HOH769 4.9 26.8 1.0
O A:HOH666 4.9 18.9 1.0

Uranium binding site 2 out of 8 in 1jet

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Uranium binding site 2 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 2 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U519

b:17.2
occ:1.00
 O A:HOH529 2.3 20.8 1.0
O A:HOH528 2.4 19.4 1.0
O A:HOH617 2.6 15.1 1.0
O A:HOH1079 2.6 10.6 0.8
O A:HOH658 2.7 18.1 1.0
O A:HOH1050 3.1 57.9 1.0
O A:HOH678 3.4 19.6 1.0
O A:HOH1083 3.7 15.2 0.8
O A:HOH666 3.7 18.9 1.0
O A:HOH1088 3.7 23.2 0.8
O A:HOH531 3.9 1.7 1.0
U A:IUM520 4.1 18.4 1.0
O A:HOH811 4.2 29.0 1.0
O A:HOH1016 4.4 50.5 1.0
O A:HOH769 4.4 26.8 1.0
O A:HOH1082 4.6 12.5 0.8
O A:HOH651 4.6 17.9 1.0
O A:HOH695 4.6 20.6 1.0
O A:HOH662 4.7 18.5 1.0
O A:HOH1045 4.9 57.0 1.0

Uranium binding site 3 out of 8 in 1jet

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Uranium binding site 3 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 3 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U520

b:18.4
occ:1.00
 O A:HOH531 1.4 1.7 1.0
O A:HOH530 2.4 20.4 1.0
O A:HOH528 2.5 19.4 1.0
O A:HOH1080 2.6 11.3 0.8
O A:HOH651 2.6 17.9 1.0
O A:HOH662 2.7 18.5 1.0
O A:HOH787 3.4 27.8 1.0
O A:HOH1085 3.4 19.5 0.8
O A:HOH1050 3.4 57.9 1.0
OD2 A:ASP459 3.5 49.4 1.0
O A:HOH1087 3.5 22.9 0.8
O A:HOH749 3.7 24.7 1.0
U A:IUM519 4.1 17.2 1.0
O A:HOH529 4.4 20.8 1.0
O A:HOH1040 4.5 55.2 1.0
CG A:ASP459 4.6 46.9 1.0
O A:HOH1084 4.6 15.9 0.8
O A:HOH1079 4.8 10.6 0.8
O A:HOH658 4.8 18.1 1.0
CB A:PRO153 4.9 12.7 1.0
O A:HOH769 4.9 26.8 1.0
NH1 A:ARG462 4.9 31.2 1.0

Uranium binding site 4 out of 8 in 1jet

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Uranium binding site 4 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 4 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U521

b:27.7
occ:1.00
 OE2 A:GLU251 3.0 42.4 1.0
O A:HOH721 3.4 22.8 1.0
O A:HOH855 3.4 32.3 1.0
OD1 A:ASP369 3.5 38.8 1.0
O A:HOH533 3.7 43.4 1.0
CD A:GLU251 3.7 38.0 1.0
O A:HOH1003 3.7 48.6 1.0
O A:HOH848 3.8 31.7 1.0
CG A:ASP369 4.1 29.4 1.0
CG A:GLU251 4.3 34.2 1.0
O A:HOH937 4.4 41.1 1.0
O A:HOH1037 4.4 53.9 1.0
O A:HOH868 4.4 33.6 1.0
OE1 A:GLU251 4.5 38.9 1.0
CB A:ASP369 4.6 24.4 1.0
OD2 A:ASP369 4.7 31.2 1.0
CG2 A:VAL230 4.7 13.4 1.0
O A:HOH532 4.8 72.7 1.0

Uranium binding site 5 out of 8 in 1jet

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Uranium binding site 5 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 5 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U522

b:17.4
occ:1.00
 O A:HOH535 1.8 14.3 1.0
O A:HOH534 2.3 21.4 1.0
OD2 A:ASP362 2.3 11.5 1.0
OD2 A:ASP410 2.5 14.1 1.0
O A:HOH621 2.7 15.5 1.0
CG A:ASP362 3.3 15.1 1.0
CG A:ASP410 3.3 11.9 1.0
OD1 A:ASP410 3.5 13.4 1.0
OD1 A:ASP362 3.8 17.7 1.0
NZ A:LYS281 3.9 35.3 1.0
O A:HOH943 4.2 42.0 1.0
N A:ASP362 4.2 10.5 1.0
CB A:ASP362 4.3 12.2 1.0
O A:HOH782 4.3 27.4 1.0
O A:HOH693 4.6 20.6 1.0
CB A:ASP410 4.7 11.7 1.0
CA A:PHE361 4.8 12.0 1.0
CA A:ASP362 4.9 11.2 1.0
C A:PHE361 4.9 11.1 1.0

Uranium binding site 6 out of 8 in 1jet

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Uranium binding site 6 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 6 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U523

b:48.2
occ:0.80
 O A:HOH595 2.4 12.5 1.0
OXT A:HIS517 2.8 21.6 1.0
O A:HOH1009 3.3 49.6 1.0
O A:HIS517 3.5 25.2 1.0
C A:HIS517 3.6 23.1 1.0
O A:HOH912 3.8 38.2 1.0
U A:IUM524 3.9 52.0 0.6
O A:HOH946 4.0 42.2 1.0
O A:HOH987 4.2 46.2 1.0
O A:HOH986 4.4 46.1 1.0
O A:HOH1064 4.4 65.4 1.0
O A:HOH962 4.7 44.1 1.0
O A:HOH698 4.7 21.0 1.0

Uranium binding site 7 out of 8 in 1jet

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Uranium binding site 7 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 7 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U524

b:52.0
occ:0.60
 O A:HOH938 3.2 41.5 1.0
O A:HOH946 3.3 42.2 1.0
O A:HOH987 3.7 46.2 1.0
O A:HOH1009 3.9 49.6 1.0
U A:IUM523 3.9 48.2 0.8
O A:HOH595 4.2 12.5 1.0
O A:HOH739 4.6 23.9 1.0
O A:HOH982 4.8 46.0 1.0
O A:HOH962 4.8 44.1 1.0
O A:HOH822 4.9 29.7 1.0

Uranium binding site 8 out of 8 in 1jet

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Uranium binding site 8 out of 8 in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kak


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 8 of Oligo-Peptide Binding Protein (Oppa) Complexed with Kak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U525

b:49.6
occ:1.00
 OD2 A:ASP11 3.1 33.0 1.0
O A:HOH982 3.7 46.0 1.0
CG A:ASP11 3.7 26.8 1.0
CB A:ASP11 3.8 22.0 1.0
O A:HOH1047 4.0 57.5 1.0
O A:HOH1089 4.0 25.1 0.8
O A:HOH753 4.7 25.1 1.0
OD1 A:ASP11 4.7 29.5 1.0
O A:HOH987 5.0 46.2 1.0

Reference:

J.R.Tame, S.H.Sleigh, A.J.Wilkinson, J.E.Ladbury. The Role of Water in Sequence-Independent Ligand Binding By An Oligopeptide Transporter Protein. Nat.Struct.Biol. V. 3 998 1996.
ISSN: ISSN 1072-8368
PubMed: 8946852
DOI: 10.1038/NSB1296-998
Page generated: Wed Dec 16 02:29:34 2020

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