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Cobalt in PDB 3ds7: Structure of An Rna-2'-Deoxyguanosine Complex

Protein crystallography data

The structure of Structure of An Rna-2'-Deoxyguanosine Complex, PDB code: 3ds7 was solved by A.L.Edwards, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.50 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 35.139, 41.830, 64.810, 86.55, 81.16, 89.64
R / Rfree (%) 20 / 25.9

Cobalt Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Cobalt atom in the Structure of An Rna-2'-Deoxyguanosine Complex (pdb code 3ds7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 11 binding sites of Cobalt where determined in the Structure of An Rna-2'-Deoxyguanosine Complex, PDB code: 3ds7:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 11 in 3ds7

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Cobalt binding site 1 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co101

b:1.4
occ:1.00
 CO A:NCO101 0.0 1.4 1.0
N2 A:NCO101 1.9 18.7 1.0
N3 A:NCO101 2.0 16.3 1.0
N4 A:NCO101 2.0 18.1 1.0
N6 A:NCO101 2.0 18.0 1.0
N5 A:NCO101 2.1 14.8 1.0
N1 A:NCO101 2.1 16.0 1.0
O A:HOH1217 3.2 0.2 1.0
O A:HOH1495 3.5 0.4 1.0
O A:HOH1160 3.8 27.6 1.0
O A:HOH1112 4.1 26.8 1.0
OP1 A:U67 4.1 11.5 1.0
O A:HOH1054 4.1 21.5 1.0
O A:HOH1406 4.3 0.7 1.0
O3' A:A66 4.4 12.9 1.0
O A:HOH1463 4.5 46.9 1.0
O A:HOH1231 4.5 45.8 1.0
O A:HOH1628 4.6 88.1 1.0
P A:U67 4.8 16.2 1.0

Cobalt binding site 2 out of 11 in 3ds7

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Cobalt binding site 2 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:30.1
occ:1.00
 CO A:NCO102 0.0 30.1 1.0
N4 A:NCO102 1.9 31.8 1.0
N2 A:NCO102 1.9 34.9 1.0
N3 A:NCO102 2.0 33.1 1.0
N6 A:NCO102 2.0 32.9 1.0
N5 A:NCO102 2.0 33.4 1.0
N1 A:NCO102 2.0 31.7 1.0
O A:HOH1173 3.5 69.3 1.0
O A:HOH1130 3.7 83.8 1.0
O A:HOH1454 3.8 68.7 1.0
OP1 A:G56 3.8 30.7 1.0
O A:HOH1012 3.8 32.9 1.0
O A:HOH1411 3.9 85.7 1.0
OP1 A:G38 4.0 16.1 1.0
O2' B:G257 4.2 21.2 1.0
O A:HOH1113 4.4 23.8 1.0
O A:HOH1396 4.5 45.4 1.0
O A:HOH1209 4.7 35.3 1.0
O3' B:G257 4.8 21.4 1.0
P A:G56 4.8 28.4 1.0
OP2 A:G56 4.8 28.5 1.0
OP2 A:G38 4.9 16.0 1.0
P A:G38 5.0 18.1 1.0

Cobalt binding site 3 out of 11 in 3ds7

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Cobalt binding site 3 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:1.4
occ:1.00
 CO A:NCO103 0.0 1.4 1.0
N4 A:NCO103 1.8 20.4 1.0
N3 A:NCO103 1.9 18.2 1.0
N2 A:NCO103 2.0 19.5 1.0
N5 A:NCO103 2.0 18.9 1.0
N6 A:NCO103 2.1 19.3 1.0
N1 A:NCO103 2.1 19.1 1.0
O A:HOH1313 3.7 36.8 1.0
O4 A:U69 3.9 16.9 1.0
O6 A:G56 4.0 23.2 1.0
O A:HOH1176 4.1 22.2 1.0
O A:HOH1625 4.3 75.7 1.0
O A:HOH1099 4.3 26.4 1.0
O A:HOH1318 4.3 39.9 1.0
O A:HOH1059 4.3 22.6 1.0
O A:HOH1238 4.4 85.0 1.0
OP1 A:C39 4.4 19.0 1.0
N7 A:G56 4.5 24.9 1.0
OP2 A:C39 4.6 22.1 1.0
O6 A:G68 4.8 12.4 1.0
C6 A:G56 4.9 24.4 1.0

Cobalt binding site 4 out of 11 in 3ds7

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Cobalt binding site 4 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co104

b:1.4
occ:1.00
 CO A:NCO104 0.0 1.4 1.0
N5 A:NCO104 1.9 15.8 1.0
N1 A:NCO104 2.0 16.3 1.0
N6 A:NCO104 2.1 15.1 1.0
N2 A:NCO104 2.1 13.7 1.0
N3 A:NCO104 2.1 13.5 1.0
N4 A:NCO104 2.2 14.1 1.0
OP2 A:A66 3.9 22.4 1.0
O A:HOH1045 4.0 22.9 1.0
O6 A:G32 4.0 19.4 1.0
O A:HOH1021 4.0 28.4 1.0
O A:HOH1031 4.2 16.2 1.0
O6 A:G31 4.2 11.5 1.0
O A:HOH1006 4.2 12.5 1.0
O A:HOH1032 4.3 14.8 1.0
N7 A:G31 4.3 15.0 1.0
O A:HOH1196 4.4 27.6 1.0
O A:HOH1150 4.5 26.8 1.0
O A:HOH1017 4.9 17.9 1.0
C6 A:G31 4.9 14.4 1.0
O4 A:U30 4.9 15.6 1.0
C6 A:G32 5.0 17.7 1.0
C5 A:G31 5.0 14.9 1.0

Cobalt binding site 5 out of 11 in 3ds7

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Cobalt binding site 5 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co105

b:76.0
occ:1.00
 CO A:NCO105 0.0 76.0 1.0
N5 A:NCO105 1.9 76.3 1.0
N4 A:NCO105 1.9 76.7 1.0
N3 A:NCO105 2.0 77.0 1.0
N2 A:NCO105 2.0 76.5 1.0
N6 A:NCO105 2.0 76.6 1.0
N1 A:NCO105 2.0 76.3 1.0
O A:HOH1329 3.5 75.8 1.0
O A:HOH1290 3.9 34.9 1.0

Cobalt binding site 6 out of 11 in 3ds7

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Cobalt binding site 6 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co301

b:1.4
occ:1.00
 CO B:NCO301 0.0 1.4 1.0
N6 B:NCO301 2.0 18.8 1.0
N2 B:NCO301 2.0 20.2 1.0
N3 B:NCO301 2.0 18.4 1.0
N5 B:NCO301 2.0 17.9 1.0
N4 B:NCO301 2.0 21.1 1.0
N1 B:NCO301 2.2 18.4 1.0
O B:HOH1105 3.9 27.9 1.0
N5 B:NCO306 3.9 41.2 1.0
O B:HOH1190 4.0 25.1 1.0
OP1 B:U267 4.1 16.3 1.0
O B:HOH1319 4.2 25.1 1.0
O3' B:A266 4.4 17.3 1.0
O B:HOH1070 4.4 27.4 1.0
O B:HOH1530 4.6 31.5 1.0
P B:U267 4.9 17.2 1.0

Cobalt binding site 7 out of 11 in 3ds7

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Cobalt binding site 7 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co302

b:9.9
occ:1.00
 CO B:NCO302 0.0 9.9 1.0
N2 B:NCO302 2.0 23.0 1.0
N3 B:NCO302 2.0 21.8 1.0
N4 B:NCO302 2.0 20.2 1.0
N6 B:NCO302 2.0 21.2 1.0
N1 B:NCO302 2.1 20.3 1.0
N5 B:NCO302 2.1 22.1 1.0
OP1 B:G238 3.8 13.4 1.0
OP1 B:G256 3.8 32.4 1.0
O B:HOH1046 3.9 36.7 1.0
O B:HOH1245 3.9 34.6 1.0
O B:HOH1408 4.0 51.1 1.0
O B:HOH1505 4.0 0.4 1.0
O B:HOH1255 4.1 31.2 1.0
O B:HOH1041 4.1 26.0 1.0
O B:HOH1367 4.3 37.8 1.0
O B:HOH1500 4.4 47.0 1.0
O A:HOH1164 4.7 27.2 1.0
O B:HOH1114 4.8 23.0 1.0
P B:G238 4.9 17.8 1.0
OP2 B:G238 4.9 14.5 1.0
P B:G256 4.9 29.4 1.0

Cobalt binding site 8 out of 11 in 3ds7

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Cobalt binding site 8 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co303

b:19.0
occ:1.00
 CO B:NCO303 0.0 19.0 1.0
N3 B:NCO303 1.9 27.9 1.0
N4 B:NCO303 1.9 30.0 1.0
N6 B:NCO303 2.0 28.8 1.0
N2 B:NCO303 2.0 29.3 1.0
N5 B:NCO303 2.0 28.9 1.0
N1 B:NCO303 2.1 29.9 1.0
O B:HOH1461 3.3 65.3 1.0
O B:HOH1155 3.5 40.4 1.0
O B:HOH1525 3.9 41.5 1.0
O4 B:U269 4.0 16.7 1.0
O6 B:G256 4.2 21.4 1.0
O B:HOH1414 4.4 28.1 1.0
O B:HOH1138 4.4 25.1 1.0
OP1 B:C239 4.4 18.4 1.0
N7 B:G256 4.5 23.0 1.0
OP2 B:C239 4.6 18.5 1.0
O6 B:G268 4.7 14.9 1.0
C6 B:G256 5.0 24.2 1.0

Cobalt binding site 9 out of 11 in 3ds7

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Cobalt binding site 9 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co304

b:1.4
occ:1.00
 CO B:NCO304 0.0 1.4 1.0
N5 B:NCO304 1.9 17.4 1.0
N6 B:NCO304 2.0 17.3 1.0
N2 B:NCO304 2.1 16.6 1.0
N1 B:NCO304 2.1 16.4 1.0
N4 B:NCO304 2.1 16.3 1.0
N3 B:NCO304 2.1 13.3 1.0
OP2 B:A266 3.8 28.0 1.0
O B:HOH1000 3.9 20.2 1.0
O B:HOH1042 3.9 21.4 1.0
O6 B:G232 3.9 20.8 1.0
O B:HOH1087 4.1 21.3 1.0
O6 B:G231 4.1 13.6 1.0
O B:HOH1003 4.2 17.9 1.0
N7 B:G231 4.3 16.9 1.0
O B:HOH1129 4.3 29.7 1.0
O B:HOH1039 4.3 16.8 1.0
O B:HOH1179 4.3 21.5 1.0
C6 B:G231 4.8 17.4 1.0
C5 B:G231 4.9 16.1 1.0
C6 B:G232 5.0 19.8 1.0
O4 B:U230 5.0 18.1 1.0

Cobalt binding site 10 out of 11 in 3ds7

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Cobalt binding site 10 out of 11 in the Structure of An Rna-2'-Deoxyguanosine Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Structure of An Rna-2'-Deoxyguanosine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co305

b:34.9
occ:1.00
 CO B:NCO305 0.0 34.9 1.0
N5 B:NCO305 1.9 37.2 1.0
N4 B:NCO305 2.0 37.8 1.0
N1 B:NCO305 2.0 36.5 1.0
N6 B:NCO305 2.0 37.1 1.0
N2 B:NCO305 2.1 35.3 1.0
N3 B:NCO305 2.1 38.3 1.0
O B:HOH1374 3.6 36.1 1.0
OP2 B:G237 4.0 17.2 1.0
O6 B:G238 4.1 17.7 1.0
N7 B:G238 4.1 19.1 1.0
O B:HOH1144 4.1 47.1 1.0
O B:HOH1035 4.2 16.4 1.0
O B:HOH1522 4.2 36.9 1.0
N7 B:G237 4.3 19.5 1.0
O B:HOH1269 4.4 26.9 1.0
O B:HOH1301 4.5 27.9 1.0
C8 B:G237 4.8 22.1 1.0
C6 B:G238 4.8 18.8 1.0
C5 B:G238 4.8 18.1 1.0
O B:HOH1222 4.9 41.0 1.0
O B:HOH1424 5.0 35.3 1.0

Reference:

A.L.Edwards, R.T.Batey. A Structural Basis For the Recognition of 2'-Deoxyguanosine By the Purine Riboswitch. J.Mol.Biol. V. 385 938 2009.
ISSN: ISSN 0022-2836
PubMed: 19007790
DOI: 10.1016/J.JMB.2008.10.074
Page generated: Tue Jul 30 15:53:01 2024

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