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Uranium in PDB 1t9h: The Crystal Structure of Yloq, A Circularly Permuted Gtpase.

Protein crystallography data

The structure of The Crystal Structure of Yloq, A Circularly Permuted Gtpase., PDB code: 1t9h was solved by V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Cladiere, A.A.Antson, M.N.Isupov, S.J.Seror, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.50 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 47.970, 47.970, 279.890, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.8

Other elements in 1t9h:

The structure of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Zinc (Zn) 1 atom

Uranium Binding Sites:

The binding sites of Uranium atom in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase. (pdb code 1t9h). This binding sites where shown within 5.0 Angstroms radius around Uranium atom.
In total 8 binding sites of Uranium where determined in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase., PDB code: 1t9h:
Jump to Uranium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Uranium binding site 1 out of 8 in 1t9h

Go back to Uranium Binding Sites List in 1t9h
Uranium binding site 1 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 1 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U401

b:24.9
occ:1.00
U A:IUM401 0.0 24.9 1.0
O1 A:IUM401 1.8 20.8 1.0
O2 A:IUM401 1.8 24.3 1.0
O A:HOH436 2.3 19.6 1.0
O A:HOH424 2.3 16.9 1.0
CH3 A:ACT417 2.6 11.3 1.0
OXT A:ACT417 2.9 19.7 1.0
C A:ACT417 3.2 16.7 1.0
O2 A:IUM407 3.9 27.4 1.0
U A:IUM408 4.1 24.6 1.0
O A:HOH479 4.1 30.5 1.0
U A:IUM407 4.1 28.7 1.0
O1 A:IUM408 4.3 19.0 1.0
O A:HOH437 4.4 19.9 1.0
O A:ACT417 4.4 18.7 1.0
O2 A:IUM408 4.5 25.5 1.0
OD1 A:ASP108 4.9 20.7 1.0
O A:HOH453 4.9 25.4 1.0
O1 A:IUM407 5.0 26.6 1.0

Uranium binding site 2 out of 8 in 1t9h

Go back to Uranium Binding Sites List in 1t9h
Uranium binding site 2 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 2 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U402

b:23.5
occ:1.00
U A:IUM402 0.0 23.5 1.0
O2 A:IUM402 1.8 21.4 1.0
O1 A:IUM402 1.8 21.4 1.0
O A:HOH419 2.1 12.2 1.0
OXT A:ACT416 2.3 16.6 1.0
O A:HOH420 2.4 13.1 1.0
OE2 A:GLU105 2.4 17.3 1.0
OE1 A:GLU105 2.6 15.5 1.0
CD A:GLU105 2.9 16.6 1.0
C A:ACT416 3.3 16.5 1.0
O A:ACT416 3.4 21.6 1.0
U A:IUM408 3.8 24.6 1.0
O A:HOH434 4.1 20.3 1.0
O A:HOH465 4.2 27.3 1.0
U A:IUM403 4.2 24.7 1.0
O1 A:IUM408 4.2 19.0 1.0
O2 A:IUM408 4.3 25.5 1.0
CG A:GLU105 4.4 15.8 1.0
O2 A:IUM403 4.4 27.2 1.0
NH1 A:ARG246 4.5 21.7 1.0
CD A:PRO111 4.6 16.6 1.0
CG A:PRO243 4.6 20.5 1.0
CH3 A:ACT416 4.7 15.8 1.0
O1 A:IUM403 4.7 22.7 1.0
OH A:TYR142 4.8 17.6 1.0
O A:HOH440 4.9 20.4 1.0
CE2 A:TYR142 5.0 18.8 1.0

Uranium binding site 3 out of 8 in 1t9h

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Uranium binding site 3 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 3 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U403

b:24.7
occ:1.00
U A:IUM403 0.0 24.7 1.0
O2 A:IUM403 1.8 27.2 1.0
O1 A:IUM403 1.8 22.7 1.0
O A:HOH422 2.1 13.2 1.0
O A:ACT416 2.2 21.6 1.0
O A:HOH440 2.3 20.4 1.0
O A:HOH419 2.5 12.2 1.0
OXT A:ACT418 2.5 20.5 1.0
C A:ACT416 3.5 16.5 1.0
U A:IUM406 3.8 25.0 1.0
C A:ACT418 3.8 23.2 1.0
U A:IUM408 3.8 24.6 1.0
OXT A:ACT416 3.9 16.6 1.0
U A:IUM404 4.0 25.1 1.0
O1 A:IUM404 4.1 26.5 1.0
O1 A:IUM408 4.1 19.0 1.0
O2 A:IUM406 4.1 25.1 1.0
O A:HOH463 4.2 28.2 1.0
U A:IUM402 4.2 23.5 1.0
O A:HOH465 4.3 27.3 1.0
O2 A:IUM408 4.3 25.5 1.0
O2 A:IUM402 4.4 21.4 1.0
O1 A:IUM406 4.4 29.5 1.0
NH2 A:ARG246 4.5 22.3 1.0
CH3 A:ACT418 4.5 23.9 1.0
O A:ACT418 4.6 23.0 1.0
CH3 A:ACT416 4.6 15.8 1.0
O2 A:IUM404 4.7 25.1 1.0
O1 A:IUM402 4.7 21.4 1.0
O A:HOH425 4.8 18.0 1.0
O A:HOH420 4.8 13.1 1.0
OXT A:ACT417 4.9 19.7 1.0

Uranium binding site 4 out of 8 in 1t9h

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Uranium binding site 4 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 4 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U404

b:25.1
occ:1.00
U A:IUM404 0.0 25.1 1.0
O2 A:IUM404 1.8 25.1 1.0
O1 A:IUM404 1.8 26.5 1.0
O A:HOH425 2.3 18.0 1.0
O A:HOH422 2.4 13.2 1.0
O A:ACT418 2.6 23.0 1.0
OXT A:ACT418 2.7 20.5 1.0
C A:ACT418 3.0 23.2 1.0
U A:IUM406 3.7 25.0 1.0
U A:IUM405 3.9 25.5 1.0
U A:IUM403 4.0 24.7 1.0
O2 A:IUM403 4.1 27.2 1.0
O1 A:IUM406 4.2 29.5 1.0
O1 A:IUM405 4.2 27.2 1.0
O2 A:IUM405 4.4 26.1 1.0
O2 A:IUM406 4.4 25.1 1.0
O A:HOH463 4.5 28.2 1.0
CH3 A:ACT418 4.5 23.9 1.0
O1 A:IUM403 4.7 22.7 1.0
O A:HOH440 4.7 20.4 1.0

Uranium binding site 5 out of 8 in 1t9h

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Uranium binding site 5 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 5 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U405

b:25.5
occ:1.00
U A:IUM405 0.0 25.5 1.0
O1 A:IUM405 1.8 27.2 1.0
O2 A:IUM405 1.8 26.1 1.0
O A:HOH425 2.1 18.0 1.0
U A:IUM404 3.9 25.1 1.0
U A:IUM406 4.0 25.0 1.0
O2 A:IUM404 4.3 25.1 1.0
O1 A:IUM404 4.4 26.5 1.0
O1 A:IUM406 4.4 29.5 1.0
O2 A:IUM406 4.4 25.1 1.0
O A:HOH422 4.9 13.2 1.0

Uranium binding site 6 out of 8 in 1t9h

Go back to Uranium Binding Sites List in 1t9h
Uranium binding site 6 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 6 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U406

b:25.0
occ:1.00
U A:IUM406 0.0 25.0 1.0
O2 A:IUM406 1.8 25.1 1.0
O1 A:IUM406 1.8 29.5 1.0
O A:ACT417 2.2 18.7 1.0
O A:HOH422 2.3 13.2 1.0
O A:HOH440 2.4 20.4 1.0
O A:HOH425 2.4 18.0 1.0
C A:ACT417 3.1 16.7 1.0
OXT A:ACT417 3.4 19.7 1.0
U A:IUM404 3.7 25.1 1.0
U A:IUM403 3.8 24.7 1.0
O2 A:IUM403 3.9 27.2 1.0
U A:IUM405 4.0 25.5 1.0
O1 A:IUM404 4.1 26.5 1.0
O2 A:IUM404 4.2 25.1 1.0
O A:HOH463 4.3 28.2 1.0
O1 A:IUM408 4.4 19.0 1.0
CH3 A:ACT417 4.4 11.3 1.0
U A:IUM408 4.4 24.6 1.0
O1 A:IUM405 4.4 27.2 1.0
O2 A:IUM405 4.4 26.1 1.0
O1 A:IUM403 4.4 22.7 1.0
OXT A:ACT418 4.8 20.5 1.0
O2 A:IUM408 5.0 25.5 1.0

Uranium binding site 7 out of 8 in 1t9h

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Uranium binding site 7 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 7 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U407

b:28.7
occ:1.00
U A:IUM407 0.0 28.7 1.0
O2 A:IUM407 1.8 27.4 1.0
O1 A:IUM407 1.8 26.6 1.0
O A:HOH436 2.1 19.6 1.0
O A:HOH453 2.3 25.4 1.0
OD1 A:ASP108 2.4 20.7 1.0
OD2 A:ASP108 2.5 24.7 1.0
O A:HOH451 2.6 25.8 1.0
CG A:ASP108 2.9 19.5 1.0
O A:HOH449 3.9 23.4 1.0
O2 A:IUM401 4.0 24.3 1.0
O A:HOH607 4.0 45.6 1.0
U A:IUM401 4.1 24.9 1.0
O A:HOH503 4.2 33.7 1.0
O A:HOH437 4.3 19.9 1.0
CB A:ASP108 4.4 19.9 1.0
O A:HOH479 4.4 30.5 1.0
O A:HOH509 4.7 33.5 1.0
O A:HOH424 4.9 16.9 1.0
O1 A:IUM401 5.0 20.8 1.0

Uranium binding site 8 out of 8 in 1t9h

Go back to Uranium Binding Sites List in 1t9h
Uranium binding site 8 out of 8 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 8 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U408

b:24.6
occ:1.00
U A:IUM408 0.0 24.6 1.0
O1 A:IUM408 1.8 19.0 1.0
O2 A:IUM408 1.8 25.5 1.0
O A:HOH420 2.2 13.1 1.0
OXT A:ACT417 2.3 19.7 1.0
O A:HOH419 2.4 12.2 1.0
O A:HOH424 2.4 16.9 1.0
O A:HOH440 2.4 20.4 1.0
C A:ACT417 3.5 16.7 1.0
U A:IUM402 3.8 23.5 1.0
U A:IUM403 3.8 24.7 1.0
O2 A:IUM402 4.0 21.4 1.0
O A:ACT417 4.0 18.7 1.0
U A:IUM401 4.1 24.9 1.0
O2 A:IUM403 4.1 27.2 1.0
O A:HOH465 4.2 27.3 1.0
O2 A:IUM406 4.2 25.1 1.0
O A:HOH479 4.2 30.5 1.0
O2 A:IUM401 4.3 24.3 1.0
U A:IUM406 4.4 25.0 1.0
O1 A:IUM402 4.4 21.4 1.0
O1 A:IUM403 4.4 22.7 1.0
O A:HOH434 4.5 20.3 1.0
CH3 A:ACT417 4.6 11.3 1.0
O1 A:IUM401 4.6 20.8 1.0
O A:HOH437 4.7 19.9 1.0
O A:HOH422 4.7 13.2 1.0

Reference:

V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Cladiere, A.A.Antson, M.N.Isupov, S.J.Seror, A.J.Wilkinson. The Crystal Structure of Yloq, A Circularly Permuted Gtpase Essential For Bacillus Subtilis Viability. J.Mol.Biol. V. 340 767 2004.
ISSN: ISSN 0022-2836
PubMed: 15223319
DOI: 10.1016/J.JMB.2004.05.029
Page generated: Thu Oct 29 07:03:37 2020

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