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Uranium in PDB 1jev: Oligo-Peptide Binding Protein (Oppa) Complexed with Kwk

Protein crystallography data

The structure of Oligo-Peptide Binding Protein (Oppa) Complexed with Kwk, PDB code: 1jev 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 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.820, 75.330, 70.440, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 22.6

Uranium Binding Sites:

The binding sites of Uranium atom in the Oligo-Peptide Binding Protein (Oppa) Complexed with Kwk (pdb code 1jev). 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 Kwk, PDB code: 1jev:
Jump to Uranium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Uranium binding site 1 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U518

b:11.6
occ:1.00
O A:HOH527 1.8 12.8 1.0
O A:HOH526 2.0 10.3 1.0
OD2 A:ASP323 2.3 11.5 1.0
O A:HOH597 2.5 12.2 1.0
O A:HOH581 2.5 10.8 1.0
O A:HOH1038 2.6 6.5 0.5
CG A:ASP323 3.2 9.3 1.0
OD1 A:ASP323 3.5 13.1 1.0
O A:HOH1039 3.5 15.0 0.5
O A:HOH818 3.7 24.8 1.0
O A:HOH1041 4.2 20.6 0.5
O A:HOH944 4.3 32.8 1.0
O A:HOH621 4.6 14.1 1.0
CB A:ASP323 4.6 9.3 1.0
O A:HOH800 4.7 24.1 1.0
O A:HOH1031 4.8 54.7 1.0
NZ A:LYS157 4.8 9.8 1.0
O A:HOH722 4.8 19.8 1.0
O A:HOH761 4.8 22.1 1.0

Uranium binding site 2 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U519

b:15.6
occ:1.00
O A:HOH528 1.0 2.1 1.0
O A:HOH529 2.1 20.6 1.0
O A:HOH614 2.4 13.6 1.0
O A:HOH598 2.5 12.3 1.0
O A:HOH666 2.6 16.9 1.0
O A:HOH684 2.6 17.8 1.0
O A:HOH712 3.4 19.2 1.0
O A:HOH723 3.4 19.8 1.0
O A:HOH800 3.6 24.1 1.0
O A:HOH531 3.8 2.1 1.0
O A:HOH860 4.0 27.4 1.0
U A:IUM520 4.2 18.5 1.0
O A:HOH722 4.4 19.8 1.0
O A:HOH592 4.5 12.0 1.0
O A:HOH703 4.5 18.9 1.0
O A:HOH530 4.7 2.1 1.0
O A:HOH988 4.7 36.6 1.0
O A:HOH704 4.8 19.0 1.0
O A:HOH603 4.9 12.9 1.0
O A:HOH611 5.0 13.3 1.0

Uranium binding site 3 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U520

b:18.5
occ:1.00
O A:HOH531 1.1 2.1 1.0
O A:HOH530 1.2 2.1 1.0
O A:HOH684 2.3 17.8 1.0
O A:HOH603 2.5 12.9 1.0
O A:HOH704 2.6 19.0 1.0
O A:HOH982 3.2 35.6 1.0
O A:HOH836 3.5 26.0 1.0
O A:HOH925 3.7 31.2 1.0
O A:HOH528 4.0 2.1 1.0
U A:IUM519 4.2 15.6 1.0
O A:HOH529 4.3 20.6 1.0
OD2 A:ASP459 4.3 35.8 1.0
OD1 A:ASP459 4.3 35.3 1.0
O A:HOH669 4.4 17.0 1.0
O A:HOH860 4.6 27.4 1.0
O A:HOH598 4.6 12.3 1.0
CG A:ASP459 4.6 31.9 1.0
CB A:PRO153 4.7 12.9 1.0
O A:HOH1028 4.7 53.5 1.0
O A:HOH617 4.8 13.9 1.0
O A:HOH666 4.8 16.9 1.0
NH1 A:ARG462 4.9 19.7 1.0
O A:HOH722 4.9 19.8 1.0

Uranium binding site 4 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U521

b:51.2
occ:1.00
O A:HOH934 3.4 32.0 1.0
OD1 A:ASP369 3.6 23.8 1.0
OE2 A:GLU251 3.6 55.3 1.0
CD A:GLU251 4.1 54.8 1.0
CE A:LYS373 4.3 36.1 1.0
CG A:ASP369 4.4 17.7 1.0
CG A:GLU251 4.4 54.2 1.0
OE1 A:GLU251 4.8 56.0 1.0
CG2 A:VAL230 4.8 13.1 1.0
NZ A:LYS373 4.9 40.5 1.0
CB A:ASP369 4.9 16.7 1.0

Uranium binding site 5 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U522

b:14.7
occ:1.00
O A:HOH532 1.2 7.8 1.0
O A:HOH533 1.3 6.9 1.0
OD2 A:ASP362 2.4 11.7 1.0
OD2 A:ASP410 2.4 13.1 1.0
O A:HOH640 2.5 15.2 1.0
CG A:ASP362 3.3 11.2 1.0
CG A:ASP410 3.3 10.8 1.0
OD1 A:ASP410 3.6 12.0 1.0
OD1 A:ASP362 3.8 14.7 1.0
NZ A:LYS281 4.0 28.3 1.0
O A:HOH972 4.1 34.8 1.0
N A:ASP362 4.3 9.1 1.0
CB A:ASP362 4.3 11.2 1.0
O A:HOH727 4.4 20.1 1.0
O A:HOH653 4.5 15.8 1.0
CB A:ASP410 4.7 8.1 1.0
O A:HOH985 4.7 35.8 1.0
CA A:PHE361 4.8 10.9 1.0
O A:HOH987 4.8 36.5 1.0
O A:HOH1027 4.9 52.3 1.0
C A:PHE361 4.9 9.0 1.0
CA A:ASP362 5.0 8.9 1.0

Uranium binding site 6 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U523

b:56.7
occ:0.60
O A:HOH766 2.4 22.4 1.0
OXT A:HIS517 2.9 21.7 1.0
C A:HIS517 3.7 19.2 1.0
O A:HIS517 3.7 22.2 1.0
U A:IUM524 3.9 43.4 0.3
O A:HOH706 4.7 19.1 1.0

Uranium binding site 7 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U524

b:43.4
occ:0.30
U A:IUM523 3.9 56.7 0.6
O A:HOH766 4.0 22.4 1.0
O A:HOH763 4.9 22.2 1.0
O A:HOH871 5.0 28.1 1.0

Uranium binding site 8 out of 8 in 1jev

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


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 Kwk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U525

b:49.4
occ:0.60
OD2 A:ASP11 2.8 37.5 1.0
CG A:ASP11 3.5 28.8 1.0
CB A:ASP11 3.8 22.3 1.0
OD1 A:ASP11 4.4 26.9 1.0
O A:HOH809 4.9 24.4 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: Thu Oct 29 07:03:33 2020

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