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Cobalt in PDB 5fhj: Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)

Protein crystallography data

The structure of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc), PDB code: 5fhj was solved by A.Thirugnanasambandam, S.Karthik, N.Gautham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.44 / 1.68
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.500, 48.500, 111.120, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 22.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) (pdb code 5fhj). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 10 binding sites of Cobalt where determined in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc), PDB code: 5fhj:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 5fhj

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Cobalt binding site 1 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co101

b:24.4
occ:1.00
 O A:HOH207 2.0 22.2 1.0
O A:HOH223 2.1 24.8 1.0
O A:HOH208 2.1 22.3 1.0
N7 A:DG9 2.2 21.4 1.0
N7 A:DG1 2.2 18.6 1.0
C8 A:DG1 3.0 21.5 1.0
C8 A:DG9 3.0 23.7 1.0
C5 A:DG9 3.3 26.4 1.0
C5 A:DG1 3.3 22.9 1.0
O6 A:DG9 3.7 24.1 1.0
O6 A:DG1 3.8 22.6 1.0
C6 A:DG9 3.9 24.5 1.0
C6 A:DG1 3.9 20.1 1.0
N4 A:DC2 4.0 25.2 1.0
OP1 A:DT8 4.1 24.8 1.0
O A:HOH231 4.2 31.9 1.0
O A:HOH213 4.3 23.9 1.0
N9 A:DG1 4.3 24.6 1.0
N9 A:DG9 4.3 23.9 1.0
O3' A:DA7 4.4 24.1 1.0
C4 A:DG9 4.4 25.6 1.0
C4 A:DG1 4.5 24.1 1.0
O C:HOH207 4.7 28.9 1.0
C4 A:DC2 4.7 27.2 1.0
P A:DT8 4.8 25.9 1.0
C1' A:DA7 4.8 25.3 1.0
C2' A:DT8 4.9 25.3 1.0
O4' A:DA7 4.9 24.1 1.0
C5 A:DC2 4.9 27.1 1.0
O5' A:DG1 5.0 29.6 1.0

Cobalt binding site 2 out of 10 in 5fhj

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Cobalt binding site 2 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:23.9
occ:0.57
 CO A:CO102 0.0 23.9 0.6
CO A:CO102 1.0 27.3 0.4
O A:HOH229 1.9 26.9 1.0
O A:HOH222 2.1 27.0 0.3
O A:HOH222 2.1 26.4 0.7
O B:HOH226 2.1 26.2 1.0
O A:HOH203 2.2 26.2 1.0
N7 A:DG5 2.2 24.2 1.0
O A:HOH220 2.7 28.1 1.0
C8 A:DG5 3.1 31.0 1.0
C5 A:DG5 3.4 24.9 1.0
O A:HOH227 3.7 35.4 1.0
O6 A:DG5 3.8 25.4 1.0
N4 A:DC6 3.9 21.8 1.0
O A:HOH234 3.9 24.5 1.0
C6 A:DG5 3.9 25.8 1.0
O B:HOH229 4.0 33.0 1.0
O A:HOH236 4.1 42.1 1.0
N9 A:DG5 4.3 27.9 1.0
C4 A:DG5 4.5 26.6 1.0
OP2 A:DG5 4.5 38.7 1.0
O A:HOH226 4.6 33.8 1.0
C4 A:DC6 4.7 25.1 1.0
O3' A:DA3 4.8 41.4 1.0
C5 A:DC6 4.9 27.2 1.0
O4' A:DA3 4.9 33.3 1.0

Cobalt binding site 3 out of 10 in 5fhj

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Cobalt binding site 3 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:27.3
occ:0.43
 CO A:CO102 0.0 27.3 0.4
CO A:CO102 1.0 23.9 0.6
O A:HOH220 1.8 28.1 1.0
O A:HOH203 2.0 26.2 1.0
O B:HOH226 2.3 26.2 1.0
O A:HOH222 2.3 26.4 0.7
N7 A:DG5 2.3 24.2 1.0
O A:HOH222 2.7 27.0 0.3
O A:HOH229 2.8 26.9 1.0
C5 A:DG5 3.3 24.9 1.0
C8 A:DG5 3.3 31.0 1.0
O6 A:DG5 3.4 25.4 1.0
C6 A:DG5 3.7 25.8 1.0
O A:HOH226 3.7 33.8 1.0
O3' A:DA3 4.1 41.4 1.0
O A:HOH234 4.2 24.5 1.0
O A:HOH236 4.3 42.1 1.0
C1' A:DA3 4.3 31.4 1.0
O4' A:DA3 4.4 33.3 1.0
N4 A:DC6 4.4 21.8 1.0
C4 A:DG5 4.5 26.6 1.0
N9 A:DG5 4.5 27.9 1.0
O A:HOH227 4.6 35.4 1.0
OP2 A:DT4 4.7 58.5 1.0
O B:HOH229 4.8 33.0 1.0
C4' A:DA3 4.8 36.7 1.0
OP2 A:DG5 4.9 38.7 1.0
C3' A:DA3 4.9 37.6 1.0

Cobalt binding site 4 out of 10 in 5fhj

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Cobalt binding site 4 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:44.8
occ:0.33
 O A:HOH216 2.3 43.7 1.0
O A:HOH238 2.5 36.6 0.5
O A:HOH204 4.0 50.9 1.0
O A:HOH238 4.0 38.0 0.5
OP1 A:DG9 4.1 28.2 1.0
C5' A:DG9 4.9 24.7 1.0

Cobalt binding site 5 out of 10 in 5fhj

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Cobalt binding site 5 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co101

b:23.3
occ:1.00
 O B:HOH218 2.0 21.4 1.0
O B:HOH210 2.1 20.4 1.0
O B:HOH208 2.1 22.5 1.0
N7 B:DG9 2.2 19.1 1.0
N7 B:DG1 2.2 18.5 1.0
C8 B:DG9 3.0 23.7 1.0
C8 B:DG1 3.1 24.9 1.0
C5 B:DG9 3.3 26.2 1.0
C5 B:DG1 3.4 23.2 1.0
O6 B:DG9 3.7 23.7 1.0
O6 B:DG1 3.8 21.2 1.0
C6 B:DG9 3.9 25.6 1.0
C6 B:DG1 4.0 19.7 1.0
N4 B:DC2 4.0 23.6 1.0
OP1 B:DT8 4.2 23.8 1.0
N9 B:DG9 4.3 23.6 1.0
O B:HOH207 4.3 22.9 1.0
N9 B:DG1 4.3 22.1 1.0
O3' B:DA7 4.4 27.4 1.0
C4 B:DG9 4.4 25.8 1.0
C4 B:DG1 4.5 22.8 1.0
C4 B:DC2 4.7 24.6 1.0
O A:HOH234 4.8 24.5 1.0
C5 B:DC2 4.9 23.6 1.0
C1' B:DA7 4.9 24.4 1.0
P B:DT8 4.9 25.5 1.0
O4' B:DA7 4.9 24.9 1.0

Cobalt binding site 6 out of 10 in 5fhj

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Cobalt binding site 6 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:25.7
occ:0.56
 CO B:CO102 0.0 25.7 0.6
CO B:CO102 1.1 28.7 0.4
O B:HOH202 1.8 30.7 0.5
O B:HOH223 1.9 32.0 1.0
O B:HOH213 1.9 28.1 1.0
O B:HOH227 2.2 25.1 0.6
N7 B:DG5 2.3 25.7 1.0
O B:HOH227 2.3 25.2 0.4
O B:HOH202 2.5 29.7 0.5
O B:HOH225 2.7 33.1 1.0
C8 B:DG5 3.2 30.2 1.0
C5 B:DG5 3.3 26.0 1.0
O6 B:DG5 3.5 28.1 1.0
C6 B:DG5 3.8 27.2 1.0
O B:HOH220 3.9 31.5 1.0
N4 B:DC6 4.2 25.0 1.0
O C:HOH207 4.2 28.9 1.0
O3' B:DA3 4.3 36.6 1.0
O B:HOH222 4.4 39.4 1.0
N9 B:DG5 4.4 26.4 1.0
C4 B:DG5 4.5 24.6 1.0
OP2 B:DT4 4.6 45.8 1.0
C1' B:DA3 4.6 31.9 1.0
O4' B:DA3 4.7 30.7 1.0
OP2 B:DG5 4.7 45.6 1.0
C4 B:DC6 5.0 26.7 1.0

Cobalt binding site 7 out of 10 in 5fhj

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Cobalt binding site 7 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:28.7
occ:0.44
 CO B:CO102 0.0 28.7 0.4
CO B:CO102 1.1 25.7 0.6
O B:HOH225 1.7 33.1 1.0
O B:HOH202 1.9 30.7 0.5
O B:HOH202 2.1 29.7 0.5
O B:HOH227 2.1 25.1 0.6
N7 B:DG5 2.3 25.7 1.0
O B:HOH213 2.4 28.1 1.0
O B:HOH227 2.7 25.2 0.4
C8 B:DG5 2.9 30.2 1.0
O B:HOH223 2.9 32.0 1.0
C5 B:DG5 3.5 26.0 1.0
O B:HOH222 3.8 39.4 1.0
N4 B:DC6 4.0 25.0 1.0
OP2 B:DG5 4.0 45.6 1.0
O6 B:DG5 4.2 28.1 1.0
N9 B:DG5 4.2 26.4 1.0
C6 B:DG5 4.3 27.2 1.0
O C:HOH207 4.4 28.9 1.0
C4 B:DG5 4.5 24.6 1.0
C5 B:DC6 4.6 25.7 1.0
C4 B:DC6 4.7 26.7 1.0
O3' B:DA3 4.8 36.6 1.0

Cobalt binding site 8 out of 10 in 5fhj

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Cobalt binding site 8 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co101

b:44.3
occ:0.52
 CO C:CO101 0.0 44.3 0.5
CO C:CO101 1.2 41.5 0.5
N7 C:DG9 1.8 43.4 1.0
O C:HOH201 2.2 52.9 1.0
O C:HOH206 2.3 50.4 1.0
O D:HOH201 2.3 45.4 1.0
C8 C:DG9 2.7 43.8 1.0
C5 C:DG9 2.9 45.5 1.0
O C:HOH208 3.0 57.1 1.0
O6 C:DG9 3.4 47.0 1.0
C6 C:DG9 3.5 48.2 1.0
N9 C:DG9 3.9 45.6 1.0
C2' C:DT8 4.0 59.0 1.0
O6 D:DG1 4.0 46.7 1.0
C4 C:DG9 4.0 44.0 1.0
N4 C:DC10 4.3 37.1 1.0
OP2 C:DG9 4.3 59.7 1.0
O3' C:DT8 4.7 59.1 1.0
C3' C:DT8 4.8 57.3 1.0
N1 C:DG9 4.9 45.1 1.0
C1' C:DT8 4.9 58.0 1.0

Cobalt binding site 9 out of 10 in 5fhj

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Cobalt binding site 9 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co101

b:41.5
occ:0.48
 CO C:CO101 0.0 41.5 0.5
CO C:CO101 1.2 44.3 0.5
O C:HOH208 1.8 57.1 1.0
O C:HOH206 2.2 50.4 1.0
O D:HOH201 2.3 45.4 1.0
O C:HOH201 2.4 52.9 1.0
N7 C:DG9 3.0 43.4 1.0
C8 C:DG9 3.9 43.8 1.0
C5 C:DG9 4.1 45.5 1.0
O6 C:DG9 4.1 47.0 1.0
C6 C:DG9 4.5 48.2 1.0
O6 D:DG1 4.6 46.7 1.0
C2' C:DT8 4.6 59.0 1.0
OP2 C:DG9 4.7 59.7 1.0

Cobalt binding site 10 out of 10 in 5fhj

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Cobalt binding site 10 out of 10 in the Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Extensive Amphimorphism in Dna: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co101

b:43.4
occ:1.00
 O D:HOH204 2.0 38.5 1.0
O D:HOH209 2.0 40.3 1.0
O D:HOH206 2.0 41.2 1.0
O A:HOH212 2.1 40.4 1.0
O C:HOH203 2.1 33.4 1.0
N7 D:DG9 2.2 35.4 1.0
C8 D:DG9 3.1 36.6 1.0
C5 D:DG9 3.3 34.3 1.0
O6 D:DG9 3.6 40.3 1.0
C6 D:DG9 3.8 38.2 1.0
O A:HOH235 4.0 39.6 1.0
C2' D:DT8 4.1 49.0 1.0
O D:HOH208 4.2 50.3 1.0
OP2 A:DA7 4.3 26.2 1.0
O6 C:DG1 4.3 34.0 1.0
N9 D:DG9 4.4 38.3 1.0
C4 D:DG9 4.4 34.2 1.0
N4 D:DC10 4.5 31.6 1.0
OP2 D:DG9 4.5 51.7 1.0
O3' D:DT8 4.9 50.1 1.0
C3' D:DT8 5.0 49.6 1.0

Reference:

A.Thirugnanasambandam, S.Karthik, G.Artheswari, N.Gautham. Dna Polymorphism in Crystals: Three Stable Conformations For the Decadeoxynucleotide D(Gcatgcatgc). Acta Crystallogr D Struct V. 72 780 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27303798
DOI: 10.1107/S2059798316006306
Page generated: Tue Jul 30 17:53:03 2024

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