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Cobalt in PDB 4pco: Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs

Protein crystallography data

The structure of Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs, PDB code: 4pco was solved by B.H.M.Mooers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.52 / 1.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 36.616, 43.224, 83.256, 90.00, 102.48, 90.00
R / Rfree (%) 15.5 / 18.4

Other elements in 4pco:

The structure of Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Cobalt Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs (pdb code 4pco). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 13 binding sites of Cobalt where determined in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs, PDB code: 4pco:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 13 in 4pco

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Cobalt binding site 1 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


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 Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co101

b:19.9
occ:1.00
 CO A:NCO101 0.0 19.9 1.0
N1 A:NCO101 2.0 23.2 1.0
N4 A:NCO101 2.0 22.8 1.0
N5 A:NCO101 2.0 21.3 1.0
N2 A:NCO101 2.0 17.6 1.0
N6 A:NCO101 2.0 21.1 1.0
N3 A:NCO101 2.0 20.2 1.0
O4 B:U7 3.8 13.2 1.0
O4 B:U9 4.1 12.4 1.0
CL B:CL104 4.1 30.2 0.7
O B:HOH230 4.1 17.5 1.0
O4 A:U3 4.2 13.3 1.0
O6 A:G2 4.2 14.6 1.0
O6 A:G1 4.2 19.5 1.0
N7 A:G1 4.4 20.3 1.0
O B:HOH236 4.5 36.5 1.0
C4 B:U7 4.6 12.3 1.0
O A:HOH214 4.7 37.5 1.0
C6 A:G1 4.9 18.4 1.0

Cobalt binding site 2 out of 13 in 4pco

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Cobalt binding site 2 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


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 Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:17.8
occ:0.56
 CO A:NCO102 0.0 17.8 0.6
N6 A:NCO102 2.0 17.7 0.6
N2 A:NCO102 2.0 17.0 0.6
N3 A:NCO102 2.0 19.5 0.6
N5 A:NCO102 2.0 18.3 0.6
N4 A:NCO102 2.0 17.4 0.6
N1 A:NCO102 2.0 16.4 0.6
O A:HOH210 3.5 50.8 1.0
O4 A:U10 3.8 12.8 1.0
O A:HOH212 4.0 15.0 1.0
HO5' C:G1 4.1 23.3 1.0
O A:HOH237 4.2 50.4 1.0
O A:HOH209 4.3 30.9 1.0
CL A:CL105 4.5 20.6 0.6
H5 A:U10 4.6 13.7 1.0
O5' C:G1 4.7 19.4 1.0
C4 A:U10 4.8 11.6 1.0
O A:HOH226 4.8 16.3 1.0
O A:HOH203 4.9 29.9 1.0
H5' C:G1 5.0 17.7 1.0

Cobalt binding site 3 out of 13 in 4pco

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Cobalt binding site 3 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


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 Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:18.1
occ:0.34
 CO A:NCO103 0.0 18.1 0.3
N1 A:NCO103 2.0 17.7 0.3
N6 A:NCO103 2.0 18.0 0.3
N3 A:NCO103 2.0 15.6 0.3
N2 A:NCO103 2.0 19.5 0.3
N4 A:NCO103 2.0 16.6 0.3
N5 A:NCO103 2.0 17.9 0.3
O A:HOH215 3.7 24.7 1.0
OP1 A:G5 4.0 15.5 1.0
O3' A:G4 4.7 12.2 1.0
O A:HOH241 4.9 36.4 1.0

Cobalt binding site 4 out of 13 in 4pco

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Cobalt binding site 4 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


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 Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co101

b:12.7
occ:0.99
 CO B:NCO101 0.0 12.7 1.0
N2 B:NCO101 2.0 15.3 1.0
N1 B:NCO101 2.0 17.4 1.0
N4 B:NCO101 2.0 15.5 1.0
N3 B:NCO101 2.0 16.9 1.0
N6 B:NCO101 2.0 14.7 1.0
N5 B:NCO101 2.0 14.4 1.0
O4 A:U7 3.9 11.9 1.0
O4 A:U9 4.2 10.9 1.0
O4 B:U3 4.2 12.3 1.0
O6 B:G1 4.2 11.2 1.0
CL A:CL105 4.3 20.6 0.6
O6 B:G2 4.3 11.2 1.0
N7 B:G1 4.4 11.1 1.0
O B:HOH204 4.7 28.0 1.0
C4 A:U7 4.8 11.1 1.0
O6 A:G8 4.9 12.1 1.0
O B:HOH209 4.9 38.6 1.0
C6 B:G1 4.9 10.5 1.0
C5 B:G1 5.0 9.7 1.0
N7 B:G2 5.0 10.5 1.0

Cobalt binding site 5 out of 13 in 4pco

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Cobalt binding site 5 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


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 Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:16.8
occ:0.50
 CO B:NCO102 0.0 16.8 0.5
N6 B:NCO102 1.5 29.2 0.5
N1 B:NCO102 2.0 18.9 0.5
N3 B:NCO102 2.0 14.8 0.5
N4 B:NCO102 2.0 17.2 0.5
N2 B:NCO102 2.0 13.2 0.5
N5 B:NCO102 2.0 14.5 0.5
N6 B:NCO102 2.0 15.0 0.5
N1 B:NCO102 2.1 30.1 0.5
CO B:NCO102 2.5 29.5 0.5
N5 B:NCO102 3.1 29.1 0.5
N3 B:NCO102 3.3 31.2 0.5
N2 B:NCO102 4.0 28.3 0.5
O B:HOH244 4.0 22.1 1.0
O B:HOH236 4.2 36.5 1.0
O6 A:G5 4.2 10.6 1.0
O A:HOH208 4.2 22.2 1.0
H42 B:C6 4.2 14.5 1.0
H41 B:C6 4.2 14.5 1.0
N4 B:NCO102 4.3 25.3 0.5
O A:HOH222 4.4 25.9 1.0
N7 A:G4 4.4 9.3 1.0
O6 B:G5 4.5 10.6 1.0
O6 A:G4 4.6 10.8 1.0
N4 B:C6 4.6 12.1 1.0
O4 A:U3 4.6 13.3 1.0
O B:HOH240 4.7 29.1 1.0
O A:HOH221 4.8 22.6 1.0
C4 A:U3 4.9 11.4 1.0
H42 A:C6 5.0 12.8 1.0

Cobalt binding site 6 out of 13 in 4pco

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Cobalt binding site 6 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


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 Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:29.5
occ:0.50
 CO B:NCO102 0.0 29.5 0.5
N5 B:NCO102 1.8 14.5 0.5
N4 B:NCO102 1.8 17.2 0.5
N5 B:NCO102 2.0 29.1 0.5
N1 B:NCO102 2.0 30.1 0.5
N2 B:NCO102 2.0 28.3 0.5
N3 B:NCO102 2.0 31.2 0.5
N6 B:NCO102 2.0 29.2 0.5
N4 B:NCO102 2.0 25.3 0.5
CO B:NCO102 2.5 16.8 0.5
N2 B:NCO102 3.1 13.2 0.5
N1 B:NCO102 3.3 18.9 0.5
O B:HOH240 3.8 29.1 1.0
O6 B:G5 3.8 10.6 1.0
O B:HOH209 3.9 38.6 1.0
N3 B:NCO102 4.2 14.8 0.5
N6 B:NCO102 4.2 15.0 0.5
H42 A:C6 4.3 12.8 1.0
O A:HOH236 4.3 22.5 1.0
N7 B:G4 4.4 12.1 1.0
H41 A:C6 4.5 12.8 1.0
O6 B:G4 4.5 11.3 1.0
O B:HOH215 4.6 26.1 1.0
N4 A:C6 4.7 10.6 1.0
O A:HOH208 4.8 22.2 1.0
O4 B:U3 4.9 12.3 1.0
C6 B:G5 4.9 10.2 1.0
O B:HOH244 4.9 22.1 1.0

Cobalt binding site 7 out of 13 in 4pco

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Cobalt binding site 7 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co103

b:22.7
occ:0.51
 CO B:NCO103 0.0 22.7 0.5
N5 B:NCO103 2.0 24.1 0.5
N1 B:NCO103 2.0 23.6 0.5
N2 B:NCO103 2.0 21.2 0.5
N3 B:NCO103 2.0 22.6 0.5
N6 B:NCO103 2.0 23.0 0.5
N4 B:NCO103 2.0 22.6 0.5
O B:HOH213 3.9 14.6 1.0
O4 B:U10 4.0 15.1 1.0
CL B:CL104 4.2 30.2 0.7
O B:HOH246 4.4 52.8 1.0
O B:HOH216 4.6 22.1 1.0
H5 B:U10 4.7 15.1 1.0
O B:HOH229 5.0 16.8 1.0

Cobalt binding site 8 out of 13 in 4pco

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Cobalt binding site 8 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co101

b:16.9
occ:0.96
 CO C:NCO101 0.0 16.9 1.0
N2 C:NCO101 2.0 18.5 1.0
N6 C:NCO101 2.0 19.3 1.0
N1 C:NCO101 2.0 18.4 1.0
N5 C:NCO101 2.0 18.1 1.0
N4 C:NCO101 2.0 14.6 1.0
N3 C:NCO101 2.0 17.9 1.0
O4 D:U9 4.0 13.7 1.0
O D:HOH223 4.0 24.3 1.0
O6 C:G1 4.1 13.1 1.0
O D:HOH210 4.1 31.9 1.0
O D:HOH214 4.2 34.0 1.0
O D:HOH225 4.2 16.7 1.0
O C:HOH227 4.2 31.8 1.0
N7 C:G1 4.3 13.2 1.0
CL A:CL105 4.3 20.6 0.6
O C:HOH220 4.3 17.7 1.0
O4 D:U10 4.4 16.6 1.0
O D:HOH204 4.8 26.2 0.8
C6 C:G1 4.8 11.5 1.0
H3 D:U10 4.9 15.9 1.0
C5 C:G1 5.0 11.2 1.0

Cobalt binding site 9 out of 13 in 4pco

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Cobalt binding site 9 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co102

b:24.8
occ:0.74
 CO C:NCO102 0.0 24.8 0.7
N5 C:NCO102 2.0 25.5 0.7
N6 C:NCO102 2.0 25.1 0.7
N2 C:NCO102 2.0 26.9 0.7
N1 C:NCO102 2.0 24.1 0.7
N4 C:NCO102 2.0 25.9 0.7
N3 C:NCO102 2.0 22.1 0.7
O C:HOH214 4.0 30.0 1.0
O6 C:G5 4.0 27.5 1.0
O C:HOH217 4.3 23.5 1.0
N7 C:G4 4.3 14.3 1.0
O6 C:G4 4.3 17.2 1.0
O C:HOH224 4.4 16.0 0.5
O4 C:U3 4.5 13.3 1.0
H42 D:C6 4.6 36.4 1.0
O C:HOH205 4.8 31.0 1.0
H41 D:C6 4.8 36.4 1.0
H5 C:U3 4.9 13.2 1.0
H42 C:C6 4.9 39.4 1.0
C4 C:U3 4.9 11.1 1.0
C5 C:G4 5.0 15.2 1.0
C6 C:G4 5.0 15.5 1.0
N7 C:G5 5.0 25.5 1.0

Cobalt binding site 10 out of 13 in 4pco

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Cobalt binding site 10 out of 13 in the Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Double-Stranded Rna with Four Terminal Gu Wobble Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co103

b:32.9
occ:0.44
 CO C:NCO103 0.0 32.9 0.4
N1 C:NCO103 2.0 33.2 0.4
N6 C:NCO103 2.0 32.1 0.4
N4 C:NCO103 2.0 32.6 0.4
N3 C:NCO103 2.0 32.9 0.4
N5 C:NCO103 2.0 32.5 0.4
N2 C:NCO103 2.0 32.7 0.4
O4 C:U10 3.8 29.9 1.0
O C:HOH226 4.1 33.1 1.0
C4 C:U10 4.8 31.4 1.0
H5 C:U9 4.9 37.3 1.0

Reference:

X.Gu, B.H.Mooers, L.M.Thomas, J.Malone, S.Harris, S.J.Schroeder. Structures and Energetics of Four Adjacent Gu Pairs That Stabilize An Rna Helix. J.Phys.Chem.B V. 119 13252 2015.
ISSN: ISSN 1089-5647
PubMed: 26425937
DOI: 10.1021/ACS.JPCB.5B06970
Page generated: Tue Jul 30 17:24:01 2024

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