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Cobalt in PDB 4fe5: Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine

Protein crystallography data

The structure of Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fe5 was solved by C.D.Stoddard, J.J.Trausch, J.Widmann, J.Marcano, R.Knight, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.247, 35.250, 41.833, 90.00, 90.75, 90.00
R / Rfree (%) 19.6 / 22.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine (pdb code 4fe5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fe5:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 4fe5

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Cobalt binding site 1 out of 6 in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co104

b:16.8
occ:1.00
 CO B:NCO104 0.0 16.8 1.0
N1 B:NCO104 2.0 18.5 1.0
N2 B:NCO104 2.0 20.2 1.0
N6 B:NCO104 2.0 17.5 1.0
N4 B:NCO104 2.0 17.6 1.0
N3 B:NCO104 2.0 17.6 1.0
N5 B:NCO104 2.0 16.2 1.0
O B:HOH798 3.4 0.3 1.0
O B:HOH380 3.9 23.3 1.0
O B:HOH442 3.9 24.3 1.0
O B:HOH370 3.9 32.0 1.0
O B:HOH809 4.0 20.8 1.0
O B:HOH582 4.1 36.3 1.0
OP1 B:U67 4.1 13.2 1.0
O3' B:A66 4.4 12.7 1.0
O B:HOH414 4.5 23.2 1.0
P B:U67 4.9 11.7 1.0
O B:HOH553 5.0 33.5 1.0

Cobalt binding site 2 out of 6 in 4fe5

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Cobalt binding site 2 out of 6 in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co105

b:13.7
occ:1.00
 CO B:NCO105 0.0 13.7 1.0
N2 B:NCO105 2.0 15.6 1.0
N1 B:NCO105 2.0 14.2 1.0
N3 B:NCO105 2.0 15.1 1.0
N5 B:NCO105 2.0 14.6 1.0
N6 B:NCO105 2.0 14.9 1.0
N4 B:NCO105 2.0 13.7 1.0
OP2 B:A66 3.8 17.6 1.0
O B:HOH303 3.9 17.0 1.0
O B:HOH468 4.0 22.4 1.0
O6 B:G32 4.0 11.2 1.0
O6 B:G31 4.1 12.2 1.0
O B:HOH344 4.2 20.5 1.0
O B:HOH367 4.2 16.6 1.0
O B:HOH812 4.2 25.0 1.0
O B:HOH308 4.2 16.8 1.0
O B:HOH321 4.3 17.4 1.0
O B:HOH399 4.3 18.9 1.0
N7 B:G31 4.4 11.9 1.0
O B:HOH519 4.7 23.9 1.0
C6 B:G31 4.9 11.1 1.0
O B:HOH309 5.0 14.5 1.0

Cobalt binding site 3 out of 6 in 4fe5

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Cobalt binding site 3 out of 6 in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co106

b:19.1
occ:1.00
 CO B:NCO106 0.0 19.1 1.0
N4 B:NCO106 2.0 19.9 1.0
N2 B:NCO106 2.0 21.5 1.0
N6 B:NCO106 2.0 19.6 1.0
N3 B:NCO106 2.0 21.2 1.0
N1 B:NCO106 2.0 19.1 1.0
N5 B:NCO106 2.0 21.5 1.0
O B:HOH578 3.7 41.0 1.0
O B:HOH404 3.7 31.6 1.0
O B:HOH586 3.8 52.5 1.0
OP1 B:G38 3.8 13.2 1.0
O B:HOH473 3.9 25.6 1.0
O B:HOH324 4.0 17.9 1.0
O B:HOH429 4.2 20.3 1.0
OP1 B:G56 4.2 20.2 1.0
O B:HOH824 4.2 61.1 1.0
O B:HOH612 4.8 45.0 1.0
P B:G38 4.9 12.1 1.0
OP2 B:G56 4.9 17.8 1.0
OP2 B:G38 5.0 13.5 1.0
O B:HOH382 5.0 21.5 1.0

Cobalt binding site 4 out of 6 in 4fe5

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Cobalt binding site 4 out of 6 in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co107

b:22.4
occ:1.00
 CO B:NCO107 0.0 22.4 1.0
N5 B:NCO107 2.0 24.3 1.0
N1 B:NCO107 2.0 23.5 1.0
N6 B:NCO107 2.0 23.1 1.0
N4 B:NCO107 2.0 24.2 1.0
N3 B:NCO107 2.0 22.5 1.0
N2 B:NCO107 2.0 22.6 1.0
O B:HOH425 3.8 24.3 1.0
O B:HOH756 4.0 0.9 1.0
O6 B:G38 4.1 11.9 1.0
OP2 B:G37 4.1 14.7 1.0
O B:HOH489 4.1 28.8 1.0
O B:HOH343 4.1 21.3 1.0
O B:HOH400 4.1 23.1 1.0
N7 B:G38 4.2 12.4 1.0
O B:HOH657 4.2 42.4 1.0
N7 B:G37 4.3 12.7 1.0
O B:HOH688 4.6 45.5 1.0
O B:HOH539 4.6 41.8 1.0
O B:HOH455 4.7 22.7 1.0
C6 B:G38 4.9 13.2 1.0
C5 B:G38 4.9 11.5 1.0
C8 B:G37 4.9 12.3 1.0

Cobalt binding site 5 out of 6 in 4fe5

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Cobalt binding site 5 out of 6 in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co108

b:16.6
occ:1.00
 CO B:NCO108 0.0 16.6 1.0
N6 B:NCO108 2.0 17.7 1.0
N3 B:NCO108 2.0 17.7 1.0
N2 B:NCO108 2.0 17.4 1.0
N1 B:NCO108 2.0 16.4 1.0
N5 B:NCO108 2.0 17.6 1.0
N4 B:NCO108 2.0 18.1 1.0
O B:HOH514 3.3 46.2 1.0
O B:HOH355 3.9 29.9 1.0
O B:HOH475 3.9 31.2 1.0
O B:HOH314 4.0 21.3 1.0
O B:HOH328 4.1 22.6 1.0
O4 B:U69 4.1 13.2 1.0
O B:HOH329 4.1 19.6 1.0
O6 B:G56 4.2 16.4 1.0
O B:HOH304 4.3 16.9 1.0
O B:HOH387 4.3 28.6 1.0
OP2 B:C39 4.4 14.3 1.0
OP1 B:C39 4.4 12.5 1.0
N7 B:G56 4.6 14.5 1.0
O6 B:G68 4.9 13.2 1.0
P B:C39 4.9 13.0 1.0

Cobalt binding site 6 out of 6 in 4fe5

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Cobalt binding site 6 out of 6 in the Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co109

b:28.3
occ:0.64
 CO B:NCO109 0.0 28.3 0.6
N2 B:NCO109 2.0 28.5 0.6
N1 B:NCO109 2.0 28.5 0.6
N3 B:NCO109 2.0 28.6 0.6
N5 B:NCO109 2.0 27.6 0.6
N6 B:NCO109 2.0 28.8 0.6
N4 B:NCO109 2.0 27.1 0.6
OP1 B:G72 4.2 12.5 1.0
O B:HOH602 4.3 64.6 1.0
OP2 B:A73 4.8 18.6 1.0

Reference:

R.T.Batey, S.D.Gilbert, R.K.Montange. Structure of A Natural Guanine-Responsive Riboswitch Complexed with the Metabolite Hypoxanthine. Nature V. 432 411 2004.
ISSN: ISSN 0028-0836
PubMed: 15549109
DOI: 10.1038/NATURE03037
Page generated: Tue Jul 30 17:04:35 2024

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