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Uranium in PDB 2olb: Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine

Protein crystallography data

The structure of Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine, PDB code: 2olb 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 / 1.40
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 (%) n/a / n/a

Uranium Binding Sites:

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

Uranium binding site 1 out of 8 in 2olb

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Uranium binding site 1 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:9.1
occ:1.00
 U A:IUM518 0.0 9.1 1.0
O2 A:IUM518 1.9 7.6 1.0
O1 A:IUM518 1.9 13.0 1.0
O A:ACT529 2.4 8.3 1.0
OD2 A:ASP323 2.4 9.3 1.0
O A:HOH586 2.4 11.5 1.0
O A:HOH627 2.9 15.1 1.0
C A:ACT529 3.2 11.1 1.0
CG A:ASP323 3.3 9.4 1.0
CH3 A:ACT529 3.4 11.8 1.0
O A:HOH668 3.4 17.5 1.0
OD1 A:ASP323 3.5 9.6 1.0
O A:HOH752 4.1 23.2 1.0
O A:HOH885 4.4 32.3 1.0
OXT A:ACT529 4.4 11.3 1.0
CB A:ASP323 4.7 8.3 1.0
NZ A:LYS157 4.7 8.2 1.0
O A:HOH674 4.9 17.8 1.0
O A:HOH785 5.0 25.1 1.0
O A:HOH590 5.0 12.0 1.0

Uranium binding site 2 out of 8 in 2olb

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Uranium binding site 2 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:13.0
occ:1.00
 U A:IUM519 0.0 13.0 1.0
O A:HOH578 2.1 10.8 1.0
O A:HOH623 2.2 14.8 1.0
O1 A:IUM519 2.2 11.4 1.0
O A:ACT530 2.4 14.5 1.0
O2 A:IUM519 2.5 11.1 1.0
O A:HOH618 2.5 14.4 1.0
C A:ACT530 3.3 13.4 1.0
O A:HOH814 3.3 26.8 1.0
CH3 A:ACT530 3.4 9.6 1.0
O A:HOH776 3.5 24.5 1.0
O1 A:IUM520 3.9 13.4 1.0
U A:IUM520 4.1 13.3 1.0
O A:HOH924 4.2 35.6 1.0
O A:HOH643 4.3 15.8 1.0
O A:HOH785 4.3 25.1 1.0
O A:HOH627 4.5 15.1 1.0
OXT A:ACT530 4.5 11.0 1.0
O A:HOH628 4.6 15.1 1.0
O A:HOH637 4.8 15.6 1.0

Uranium binding site 3 out of 8 in 2olb

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Uranium binding site 3 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:13.3
occ:1.00
 U A:IUM520 0.0 13.3 1.0
O2 A:IUM520 1.8 12.1 1.0
O1 A:IUM520 2.0 13.4 1.0
O1 A:IUM519 2.4 11.4 1.0
O A:HOH628 2.5 15.1 1.0
O A:ACT528 2.6 24.0 1.0
O A:HOH637 2.6 15.6 1.0
CH3 A:ACT528 3.2 10.7 1.0
O A:HOH768 3.3 24.3 1.0
C A:ACT528 3.3 26.5 1.0
O A:HOH701 3.5 19.5 1.0
OD2 A:ASP459 3.7 62.9 1.0
U A:IUM519 4.1 13.0 1.0
O A:HOH623 4.2 14.8 1.0
OXT A:ACT528 4.5 20.2 1.0
O A:ACT530 4.5 14.5 1.0
CG A:ASP459 4.6 44.9 1.0
O A:HOH924 4.6 35.6 1.0
O A:HOH618 4.7 14.4 1.0
CB A:PRO153 4.8 12.3 1.0
O A:HOH785 4.8 25.1 1.0
NH1 A:ARG462 4.9 34.2 1.0
O A:HOH707 4.9 19.7 1.0

Uranium binding site 4 out of 8 in 2olb

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Uranium binding site 4 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:14.5
occ:1.00
 U A:IUM521 0.0 14.5 1.0
O2 A:IUM521 1.8 22.1 1.0
O1 A:IUM521 1.9 15.7 1.0
OE2 A:GLU251 2.3 16.6 1.0
OD2 A:ASP369 2.3 20.8 1.0
O A:HOH613 2.7 13.8 1.0
O A:HOH713 2.9 20.2 1.0
O A:HOH694 3.0 19.2 1.0
CG A:ASP369 3.1 23.2 1.0
OD1 A:ASP369 3.3 22.7 1.0
CD A:GLU251 3.5 22.7 1.0
NZ A:LYS373 4.1 25.9 1.0
CG A:GLU251 4.3 13.8 1.0
OE1 A:GLU251 4.3 17.1 1.0
O A:HOH780 4.5 24.7 1.0
O A:HOH862 4.5 30.3 1.0
CB A:ASP369 4.5 11.7 1.0
O A:HOH932 4.6 36.2 1.0
O A:HOH909 4.6 34.5 1.0
CG2 A:VAL230 4.6 8.4 1.0
CE A:LYS373 4.9 21.6 1.0

Uranium binding site 5 out of 8 in 2olb

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Uranium binding site 5 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:14.8
occ:1.00
 U A:IUM522 0.0 14.8 1.0
O1 A:IUM522 1.6 11.1 1.0
O2 A:IUM522 2.0 18.2 1.0
OD2 A:ASP362 2.3 11.8 1.0
OD2 A:ASP410 2.5 13.6 1.0
O A:HOH688 3.0 18.9 1.0
CG A:ASP362 3.3 11.2 1.0
CG A:ASP410 3.3 10.3 1.0
OD1 A:ASP410 3.5 13.7 1.0
OD1 A:ASP362 3.8 16.6 1.0
NZ A:LYS281 4.2 30.3 1.0
O A:HOH964 4.3 38.2 1.0
N A:ASP362 4.3 7.9 1.0
O A:HOH844 4.3 29.0 1.0
CB A:ASP362 4.4 11.5 1.0
O A:HOH698 4.6 19.4 1.0
CB A:ASP410 4.7 9.8 1.0
CA A:PHE361 4.8 8.1 1.0
C A:PHE361 4.9 9.5 1.0

Uranium binding site 6 out of 8 in 2olb

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Uranium binding site 6 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:22.3
occ:1.00
 O A:HOH673 2.0 17.7 1.0
O A:HOH813 2.2 26.7 1.0
O A:HOH782 2.5 24.9 1.0
OXT A:HIS517 2.6 15.2 1.0
O A:HIS517 2.8 22.2 1.0
C A:HIS517 3.1 18.1 1.0
U A:IUM524 4.0 28.4 1.0
O A:HOH1058 4.2 51.5 1.0
O A:HOH891 4.2 32.9 1.0
O A:HOH959 4.3 37.7 1.0
O A:HOH830 4.4 28.4 1.0
CA A:HIS517 4.6 16.9 1.0
O A:HOH696 4.7 19.3 1.0
O A:HOH827 4.9 28.2 1.0
CD2 A:HIS517 4.9 17.8 1.0
O A:HOH955 4.9 37.5 1.0

Uranium binding site 7 out of 8 in 2olb

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Uranium binding site 7 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:28.4
occ:1.00
 O A:HOH782 2.5 24.9 1.0
O A:HOH718 2.8 20.6 1.0
O A:HOH880 3.4 31.9 1.0
O A:HOH959 3.5 37.7 1.0
O A:HOH1058 3.9 51.5 1.0
U A:IUM523 4.0 22.3 1.0
O A:HOH891 4.1 32.9 1.0
O A:HOH830 4.4 28.4 1.0
O A:HOH813 4.5 26.7 1.0
O A:HOH736 4.7 21.9 1.0
O A:HOH827 4.9 28.2 1.0

Uranium binding site 8 out of 8 in 2olb

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Uranium binding site 8 out of 8 in the Oligopeptide Binding Protein (Oppa) Complexed with Tri- Lysine


Mono view


Stereo pair view

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

b:27.2
occ:1.00
 OD2 A:ASP11 2.6 24.8 1.0
OXT A:ACT531 2.7 22.3 1.0
O A:ACT531 3.3 35.1 1.0
C A:ACT531 3.4 32.0 1.0
CG A:ASP11 3.5 22.6 1.0
CB A:ASP11 3.7 14.4 1.0
OD1 A:ASP11 4.6 23.0 1.0
CH3 A:ACT531 4.8 19.1 1.0
O A:HOH718 4.9 20.6 1.0
O A:HOH823 5.0 27.9 1.0

Reference:

J.R.Tame, E.J.Dodson, G.Murshudov, C.F.Higgins, A.J.Wilkinson. The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands. Structure V. 3 1395 1995.
ISSN: ISSN 0969-2126
PubMed: 8747465
DOI: 10.1016/S0969-2126(01)00276-3
Page generated: Wed Dec 16 02:29:40 2020

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