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Uranium in PDB 2rkm: Structure of Oppa Complexed with Lys-Lys

Protein crystallography data

The structure of Structure of Oppa Complexed with Lys-Lys, PDB code: 2rkm was solved by S.H.Sleigh, 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) 20.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.470, 77.150, 71.590, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.9

Uranium Binding Sites:

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

Uranium binding site 1 out of 8 in 2rkm

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Uranium binding site 1 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:9.4
occ:0.87
 U A:IUM518 0.0 9.4 0.9
O1 A:IUM518 1.9 11.7 1.0
O2 A:IUM518 1.9 13.3 1.0
OD2 A:ASP323 2.4 11.2 1.0
O A:HOH2049 2.4 13.2 1.0
O A:HOH2026 2.4 11.4 1.0
O A:HOH2141 2.7 18.5 1.0
CG A:ASP323 3.3 11.2 1.0
OD1 A:ASP323 3.5 11.6 1.0
O A:HOH2241 4.2 23.6 1.0
O A:HOH2060 4.5 13.7 1.0
O A:HOH2068 4.5 14.5 1.0
CB A:ASP323 4.7 11.5 1.0
NZ A:LYS157 4.8 9.8 1.0

Uranium binding site 2 out of 8 in 2rkm

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Uranium binding site 2 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:10.3
occ:0.81
 U A:IUM519 0.0 10.3 0.8
O1 A:IUM519 1.9 12.3 1.0
O2 A:IUM519 2.0 14.4 1.0
O A:HOH2080 2.3 15.2 1.0
O A:HOH2032 2.4 11.9 1.0
O A:HOH2171 2.4 19.8 1.0
O A:HOH2065 2.6 14.2 1.0
O A:HOH2124 2.7 17.9 1.0
O1 A:IUM520 4.0 15.5 1.0
U A:IUM520 4.2 12.4 0.9
O A:HOH2030 4.5 11.5 1.0
O A:HOH2233 4.6 22.9 1.0
O A:HOH2093 4.6 16.2 1.0
O A:HOH2064 4.9 14.1 1.0

Uranium binding site 3 out of 8 in 2rkm

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Uranium binding site 3 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:12.4
occ:0.89
 U A:IUM520 0.0 12.4 0.9
O2 A:IUM520 1.7 12.8 1.0
O1 A:IUM520 1.7 15.5 1.0
O A:HOH2093 2.4 16.2 1.0
O A:HOH2097 2.4 16.3 1.0
O A:HOH2080 2.4 15.2 1.0
O A:HOH2154 2.6 19.1 1.0
O A:HOH2064 2.7 14.1 1.0
O1 A:IUM519 4.1 12.3 1.0
U A:IUM519 4.2 10.3 0.8
OD1 A:ASP459 4.4 42.6 1.0
OD2 A:ASP459 4.5 43.2 1.0
O A:HOH2178 4.5 20.3 1.0
O A:HOH2110 4.5 17.2 1.0
O A:HOH2032 4.7 11.9 1.0
CG A:ASP459 4.7 40.4 1.0
O A:HOH2065 4.7 14.2 1.0
CB A:PRO153 4.8 15.3 1.0
O A:HOH2166 4.9 19.7 1.0
NH1 A:ARG462 4.9 31.6 1.0

Uranium binding site 4 out of 8 in 2rkm

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Uranium binding site 4 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:14.3
occ:0.89
 U A:IUM521 0.0 14.3 0.9
O1 A:IUM521 1.5 11.7 1.0
O2 A:IUM521 1.6 13.4 1.0
OD2 A:ASP369 2.2 19.9 1.0
OE2 A:GLU251 2.3 20.8 1.0
O A:HOH2047 2.4 12.7 1.0
O A:HOH2111 2.6 17.2 1.0
O A:HOH2295 2.6 26.4 1.0
CG A:ASP369 3.2 20.5 1.0
OD1 A:ASP369 3.5 25.0 1.0
CD A:GLU251 3.5 22.8 1.0
NZ A:LYS373 3.8 22.6 1.0
O A:HOH2244 4.3 23.9 1.0
OE1 A:GLU251 4.3 20.3 1.0
CG A:GLU251 4.3 19.3 1.0
O A:HOH2195 4.5 21.1 1.0
CB A:ASP369 4.6 14.6 1.0
CG2 A:VAL230 4.7 11.7 1.0
O A:HOH2285 4.7 26.0 1.0

Uranium binding site 5 out of 8 in 2rkm

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Uranium binding site 5 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:15.1
occ:0.89
 U A:IUM522 0.0 15.1 0.9
O1 A:IUM522 1.3 5.1 1.0
O2 A:IUM522 1.3 6.3 1.0
OD2 A:ASP362 2.4 12.6 1.0
OD2 A:ASP410 2.4 15.0 1.0
O A:HOH2142 2.4 18.5 1.0
CG A:ASP362 3.3 13.7 1.0
CG A:ASP410 3.4 15.2 1.0
OD1 A:ASP410 3.6 17.5 1.0
OD1 A:ASP362 3.8 12.9 1.0
O A:HOH2290 4.1 26.1 1.0
O A:HOH2455 4.2 34.4 1.0
NZ A:LYS281 4.2 20.6 1.0
O A:HOH2453 4.3 34.3 1.0
N A:ASP362 4.4 12.5 1.0
CB A:ASP362 4.4 11.2 1.0
O A:HOH2454 4.5 34.4 1.0
O A:HOH2197 4.6 21.1 1.0
CB A:ASP410 4.7 12.1 1.0
CA A:PHE361 4.9 13.4 1.0

Uranium binding site 6 out of 8 in 2rkm

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Uranium binding site 6 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:14.9
occ:0.67
 U A:IUM523 0.0 14.9 0.7
O1 A:IUM523 1.5 14.5 1.0
O2 A:IUM523 1.6 14.9 1.0
O A:HOH2462 2.2 34.8 1.0
OXT A:HIS517 2.6 20.4 1.0
O A:HIS517 2.9 23.2 1.0
C A:HIS517 3.1 21.2 1.0
U A:IUM524 4.2 15.3 0.6
O2 A:IUM524 4.2 27.4 1.0
O A:HOH2277 4.4 25.7 1.0
CA A:HIS517 4.6 20.7 1.0
O A:HOH2211 4.7 21.9 1.0

Uranium binding site 7 out of 8 in 2rkm

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Uranium binding site 7 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:15.3
occ:0.62
 U A:IUM524 0.0 15.3 0.6
O2 A:IUM524 1.9 27.4 1.0
O1 A:IUM524 1.9 26.6 1.0
O A:HOH2143 2.5 18.6 1.0
O A:HOH2277 2.5 25.7 1.0
O A:HOH2293 2.7 26.3 1.0
O A:HOH2462 2.8 34.8 1.0
O2 A:IUM523 4.0 14.9 1.0
O A:HOH2314 4.0 27.6 1.0
U A:IUM523 4.2 14.9 0.7
O A:HOH2448 4.3 34.0 1.0
O1 A:IUM525 4.6 21.2 1.0
O1 A:IUM523 4.9 14.5 1.0

Uranium binding site 8 out of 8 in 2rkm

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Uranium binding site 8 out of 8 in the Structure of Oppa Complexed with Lys-Lys


Mono view


Stereo pair view

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

b:17.1
occ:0.62
 U A:IUM525 0.0 17.1 0.6
O1 A:IUM525 1.8 21.2 1.0
O A:HOH2470 2.1 35.5 1.0
O A:HOH2145 2.3 18.7 1.0
O A:HOH2213 2.5 21.9 1.0
OD2 A:ASP11 2.5 23.5 1.0
CG A:ASP11 3.5 22.1 1.0
O A:HOH2314 3.6 27.6 1.0
CB A:ASP11 3.9 20.1 1.0
O1 A:IUM524 4.3 26.6 1.0
OD1 A:ASP11 4.5 21.1 1.0
O A:HOH2350 4.6 29.2 1.0
O A:HOH2143 4.9 18.6 1.0

Reference:

S.H.Sleigh, J.R.Tame, E.J.Dodson, A.J.Wilkinson. Peptide Binding in Oppa, the Crystal Structures of the Periplasmic Oligopeptide Binding Protein in the Unliganded Form and in Complex with Lysyllysine. Biochemistry V. 36 9747 1997.
ISSN: ISSN 0006-2960
PubMed: 9245406
DOI: 10.1021/BI970457U
Page generated: Fri Oct 11 11:00:01 2024

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