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Uranium in PDB 1b3f: Oligo-Peptide Binding Protein (Oppa) Complexed with Khk

Protein crystallography data

The structure of Oligo-Peptide Binding Protein (Oppa) Complexed with Khk, PDB code: 1b3f was solved by J.R.H.Tame, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.936, 75.892, 70.594, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.7

Uranium Binding Sites:

The binding sites of Uranium atom in the Oligo-Peptide Binding Protein (Oppa) Complexed with Khk (pdb code 1b3f). 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 Khk, PDB code: 1b3f:
Jump to Uranium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Uranium binding site 1 out of 8 in 1b3f

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


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

b:17.6
occ:0.88
O A:HOH609 2.2 22.5 1.0
OD2 A:ASP323 2.3 18.9 1.0
O A:HOH537 2.4 16.4 1.0
CG A:ASP323 3.2 19.1 1.0
OD1 A:ASP323 3.5 19.7 1.0
O A:HOH923 4.2 44.2 1.0
O A:HOH630 4.4 24.2 1.0
CB A:ASP323 4.6 17.9 1.0
NZ A:LYS157 4.8 18.6 1.0
O A:HOH774 4.9 32.4 1.0
O A:HOH705 4.9 28.6 1.0

Uranium binding site 2 out of 8 in 1b3f

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


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

b:22.2
occ:0.84
O A:HOH579 2.4 20.1 1.0
O A:HOH553 2.5 18.0 1.0
O A:HOH620 2.6 23.1 1.0
O A:HOH751 3.7 31.0 1.0
U A:IUM520 4.2 22.5 0.8
O A:HOH774 4.3 32.4 1.0
O A:HOH570 4.4 19.2 1.0
O A:HOH588 4.6 20.7 1.0
O A:HOH896 4.7 40.4 1.0
O A:HOH640 4.7 24.8 1.0

Uranium binding site 3 out of 8 in 1b3f

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


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

b:22.5
occ:0.76
O A:HOH588 2.3 20.7 1.0
O A:HOH651 2.4 25.4 1.0
O A:HOH640 2.5 24.8 1.0
O A:HOH605 2.5 22.3 1.0
OD2 A:ASP459 4.1 43.3 1.0
U A:IUM519 4.2 22.2 0.8
OD1 A:ASP459 4.2 42.0 1.0
CG A:ASP459 4.4 41.5 1.0
O A:HOH659 4.4 25.9 1.0
O A:HOH692 4.6 27.8 1.0
O A:HOH896 4.6 40.4 1.0
O A:HOH553 4.6 18.0 1.0
O A:HOH579 4.6 20.1 1.0
O A:HOH774 4.9 32.4 1.0
O A:HOH746 4.9 30.6 1.0
CB A:PRO153 5.0 22.2 1.0
NH1 A:ARG462 5.0 38.3 1.0

Uranium binding site 4 out of 8 in 1b3f

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


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

b:23.5
occ:0.62
OE2 A:GLU251 2.4 35.6 1.0
O A:HOH617 2.4 23.0 1.0
O A:HOH840 2.6 36.2 1.0
OD1 A:ASP369 3.1 33.1 1.0
CD A:GLU251 3.6 36.5 1.0
CG A:ASP369 4.2 31.9 1.0
NZ A:LYS373 4.3 36.4 1.0
CG A:GLU251 4.3 35.8 1.0
OE1 A:GLU251 4.4 36.8 1.0
CE A:LYS373 4.6 34.6 1.0
CG2 A:VAL230 4.6 21.0 1.0
CB A:ASP369 4.9 28.8 1.0

Uranium binding site 5 out of 8 in 1b3f

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


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

b:22.9
occ:0.89
OD2 A:ASP362 2.4 16.1 1.0
O A:HOH595 2.4 21.1 1.0
OD2 A:ASP410 2.4 17.6 1.0
CG A:ASP362 3.3 19.7 1.0
CG A:ASP410 3.4 20.3 1.0
OD1 A:ASP410 3.8 22.2 1.0
OD1 A:ASP362 3.9 21.3 1.0
NZ A:LYS281 4.1 30.0 1.0
CB A:ASP362 4.3 17.6 1.0
N A:ASP362 4.4 19.8 1.0
O A:HOH633 4.6 24.4 1.0
CB A:ASP410 4.7 18.8 1.0
O A:HOH937 4.8 46.5 1.0
CA A:PHE361 4.9 19.8 1.0

Uranium binding site 6 out of 8 in 1b3f

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


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

b:27.6
occ:0.49
OXT A:HIS517 2.6 24.8 1.0
O A:HIS517 3.2 29.6 1.0
C A:HIS517 3.3 26.3 1.0
U A:IUM524 4.1 31.8 0.5
O A:HOH797 4.7 33.8 1.0
CA A:HIS517 4.8 25.8 1.0

Uranium binding site 7 out of 8 in 1b3f

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


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

b:31.8
occ:0.49
U A:IUM523 4.1 27.6 0.5
O A:HOH805 4.6 34.2 1.0
O A:HOH838 4.9 36.1 1.0

Uranium binding site 8 out of 8 in 1b3f

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


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

b:31.4
occ:0.49
OD2 A:ASP11 2.3 33.1 1.0
CG A:ASP11 3.4 31.6 1.0
CB A:ASP11 3.8 28.6 1.0
OD1 A:ASP11 4.5 31.1 1.0
O A:HOH787 5.0 33.2 1.0

Reference:

S.H.Sleigh, P.R.Seavers, A.J.Wilkinson, J.E.Ladbury, J.R.Tame. Crystallographic and Calorimetric Analysis of Peptide Binding to Oppa Protein. J.Mol.Biol. V. 291 393 1999.
ISSN: ISSN 0022-2836
PubMed: 10438628
DOI: 10.1006/JMBI.1999.2929
Page generated: Wed Dec 16 02:29:18 2020

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