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Uranium in PDB 3l0o: Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima

Protein crystallography data

The structure of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima, PDB code: 3l0o was solved by A.Canals, I.Uson, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.55 / 2.35
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 139.000, 139.000, 150.000, 90.00, 90.00, 90.00
R / Rfree (%) 26.8 / 29.7

Other elements in 3l0o:

The structure of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Uranium Binding Sites:

The binding sites of Uranium atom in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima (pdb code 3l0o). This binding sites where shown within 5.0 Angstroms radius around Uranium atom.
In total 7 binding sites of Uranium where determined in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima, PDB code: 3l0o:
Jump to Uranium binding site number: 1; 2; 3; 4; 5; 6; 7;

Uranium binding site 1 out of 7 in 3l0o

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Uranium binding site 1 out of 7 in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 1 of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U428

b:58.5
occ:1.00
U A:IUM428 0.0 58.5 1.0
O1 A:IUM428 2.4 79.5 1.0
O2 A:IUM428 2.4 91.8 1.0
OD1 A:ASP84 2.8 50.8 1.0
OD1 A:ASP77 2.9 40.8 1.0
OD2 A:ASP77 2.9 36.0 1.0
OD2 A:ASP84 3.1 54.6 1.0
CG A:ASP77 3.2 38.2 1.0
CG A:ASP84 3.3 52.8 1.0
OG A:SER82 4.7 48.4 1.0
CB A:ASP77 4.7 37.2 1.0
CB A:ASP84 4.8 53.8 1.0
CB A:GLU76 4.8 39.1 1.0
CG A:ARG74 4.8 37.2 1.0
N A:ASP84 4.9 55.3 1.0
NE A:ARG74 4.9 54.2 1.0

Uranium binding site 2 out of 7 in 3l0o

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Uranium binding site 2 out of 7 in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 2 of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U429

b:0.4
occ:1.00
U A:IUM429 0.0 0.4 1.0
O2 A:IUM429 2.4 0.0 1.0
O1 A:IUM429 2.4 0.0 1.0
OD1 A:ASP40 3.5 41.3 1.0
OD2 A:ASP40 3.8 41.7 1.0
CG A:ASP40 4.1 38.5 1.0
NH2 A:ARG37 4.1 46.6 1.0
NE A:ARG37 4.6 45.9 1.0
CZ A:ARG37 4.8 46.8 1.0

Uranium binding site 3 out of 7 in 3l0o

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Uranium binding site 3 out of 7 in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 3 of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U430

b:25.9
occ:1.00
U A:IUM430 0.0 25.9 1.0
O1 A:IUM430 2.4 36.2 1.0
O2 A:IUM430 2.4 39.3 1.0
OE1 A:GLU14 2.5 28.3 1.0
OE2 A:GLU14 2.8 30.4 1.0
CD A:GLU14 3.0 29.9 1.0
O A:HOH504 3.1 15.7 1.0
O A:HOH483 4.2 49.5 1.0
NZ A:LYS38 4.5 34.7 1.0
CG A:GLU14 4.6 34.4 1.0
CD A:LYS38 4.7 31.6 1.0
CG A:LYS38 4.8 33.8 1.0
CE A:LYS38 4.9 33.3 1.0
CB A:ARG39 5.0 36.3 1.0

Uranium binding site 4 out of 7 in 3l0o

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Uranium binding site 4 out of 7 in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 4 of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U428

b:0.6
occ:0.50
U B:IUM428 0.0 0.6 0.5
O1 B:IUM428 2.4 0.7 0.5
O2 B:IUM428 2.4 56.7 0.5
OG B:SER350 3.6 49.9 1.0
CB B:GLN352 3.7 60.1 1.0
N B:GLN352 3.8 58.9 1.0
NE2 B:GLN352 4.1 63.7 1.0
CG B:GLN352 4.2 61.7 1.0
N B:ARG351 4.2 54.2 1.0
CA B:GLN352 4.4 59.9 1.0
OE1 B:GLU396 4.5 60.9 1.0
CB B:SER350 4.6 50.8 1.0
CD B:GLN352 4.7 63.7 1.0
CA B:SER350 4.8 50.9 1.0
C B:ARG351 4.8 57.7 1.0
CB B:ARG351 4.8 56.8 1.0
C B:SER350 4.8 52.5 1.0
CA B:ARG351 4.9 56.5 1.0
OE2 B:GLU396 4.9 58.3 1.0

Uranium binding site 5 out of 7 in 3l0o

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Uranium binding site 5 out of 7 in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 5 of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U429

b:63.4
occ:1.00
U B:IUM429 0.0 63.4 1.0
O2 B:IUM429 2.4 0.6 1.0
O1 B:IUM429 2.5 74.1 1.0
OD2 B:ASP222 2.9 41.7 1.0
OE1 B:GLU219 3.0 45.4 1.0
O A:HOH447 3.2 49.9 1.0
O B:HOH468 3.2 43.4 1.0
OE2 B:GLU219 3.3 46.7 1.0
CD B:GLU219 3.4 45.2 1.0
CG B:ASP222 3.8 42.0 1.0
NZ B:LYS193 4.0 42.5 1.0
CG2 B:THR189 4.1 35.3 1.0
OH A:TYR147 4.3 43.4 1.0
NE A:ARG371 4.4 44.0 1.0
OD1 B:ASP222 4.4 46.4 1.0
CB B:THR189 4.6 35.0 1.0
CB B:ASP222 4.7 41.6 1.0
CG B:GLU219 4.7 43.9 1.0
CD A:ARG371 4.8 37.4 1.0
CZ A:ARG371 4.9 45.0 1.0
CE2 A:TYR147 4.9 32.2 1.0

Uranium binding site 6 out of 7 in 3l0o

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Uranium binding site 6 out of 7 in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 6 of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U430

b:0.4
occ:0.50
U B:IUM430 0.0 0.4 0.5
O1 B:IUM430 2.4 0.9 0.5
O2 B:IUM430 2.4 1.0 0.5
OE2 B:GLU373 3.4 58.2 1.0
CD B:GLU373 3.9 57.2 1.0
OE1 B:GLU373 4.0 58.2 1.0
CB B:ARG371 4.1 53.6 1.0
CG B:ARG371 4.8 54.3 1.0
CA B:ARG371 4.9 53.3 1.0
CG B:GLU373 4.9 55.4 1.0

Uranium binding site 7 out of 7 in 3l0o

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Uranium binding site 7 out of 7 in the Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 7 of Structure of Rna-Free Rho Transcription Termination Factor From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U431

b:0.9
occ:0.50
U B:IUM431 0.0 0.9 0.5
O1 B:IUM431 2.4 0.3 0.5
O2 B:IUM431 2.4 53.8 0.5
OD2 B:ASP77 2.8 80.2 1.0
OD1 B:ASP84 3.2 95.6 1.0
CG B:ASP77 3.6 80.0 1.0
OD1 B:ASP77 3.7 80.6 1.0
CG B:ARG74 3.8 88.0 1.0
CB B:ARG74 4.2 86.9 1.0
CD B:ARG74 4.3 90.1 1.0
NE B:ARG74 4.4 91.5 1.0
CG B:ASP84 4.4 94.7 1.0
OG B:SER82 4.5 87.3 1.0
N B:ASP84 4.7 92.8 1.0
CG B:GLU76 4.8 84.4 1.0
CB B:ASP77 4.9 79.9 1.0
OD2 B:ASP84 5.0 94.9 1.0

Reference:

A.Canals, I.Uson, M.Coll. The Structure of Rna-Free Rho Termination Factor Indicates A Dynamic Mechanism of Transcript Capture J.Mol.Biol. V. 400 16 2010.
ISSN: ISSN 0022-2836
PubMed: 20452362
DOI: 10.1016/J.JMB.2010.05.004
Page generated: Wed Dec 16 02:29:47 2020

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