Atomistry » Cobalt » PDB 4fe5-4j0b » 4fe5
Atomistry »
  Cobalt »
    PDB 4fe5-4j0b »
      4fe5 »

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

Go back to Cobalt Binding Sites List in 4fe5
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

Go back to Cobalt Binding Sites List in 4fe5
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

Go back to Cobalt Binding Sites List in 4fe5
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

Go back to Cobalt Binding Sites List in 4fe5
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

Go back to Cobalt Binding Sites List in 4fe5
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

Go back to Cobalt Binding Sites List in 4fe5
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: Sun Jul 13 19:43:14 2025

Last articles

Mg in 4DR3
Mg in 4DR1
Mg in 4DPG
Mg in 4DQP
Mg in 4DQQ
Mg in 4DPM
Mg in 4DPV
Mg in 4DQI
Mg in 4DOB
Mg in 4DOC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy