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Nickel in PDB 446d: Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions

Protein crystallography data

The structure of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions, PDB code: 446d was solved by N.G.A.Abrescia, L.Malinina, L.F.Gonzaga, T.Huynh-Dinh, S.Neidle, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 52.460, 52.460, 101.490, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions (pdb code 446d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions, PDB code: 446d:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in 446d

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Nickel binding site 1 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni11

b:16.4
occ:1.00
N7 A:DG10 1.9 4.0 1.0
O A:HOH17 2.0 16.4 1.0
O A:HOH15 2.0 16.4 1.0
O A:HOH16 2.1 16.4 1.0
O A:HOH18 2.1 16.4 1.0
C8 A:DG10 2.8 4.0 1.0
C5 A:DG10 3.1 4.0 1.0
O6 A:DG10 3.5 4.0 1.0
C6 A:DG10 3.7 4.0 1.0
OP2 A:DG10 4.0 2.0 1.0
N9 A:DG10 4.0 4.0 1.0
C4 A:DG10 4.2 4.0 1.0
O A:HOH34 4.7 55.0 1.0
O A:HOH27 4.8 42.6 1.0
O A:HOH31 4.9 55.0 1.0

Nickel binding site 2 out of 9 in 446d

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Nickel binding site 2 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni12

b:22.2
occ:1.00
N7 A:DG2 2.0 2.0 1.0
O A:HOH22 2.0 22.2 1.0
O A:HOH20 2.1 22.2 1.0
O A:HOH19 2.1 22.2 1.0
O A:HOH21 2.1 22.2 1.0
O A:HOH23 2.1 22.2 1.0
C8 A:DG2 2.8 2.0 1.0
C5 A:DG2 3.2 2.0 1.0
O6 A:DG2 3.7 2.0 1.0
C6 A:DG2 3.8 2.0 1.0
N9 A:DG2 4.1 2.0 1.0
C4 A:DG2 4.2 2.0 1.0
O4 A:DT3 4.4 2.0 1.0
C7 A:DT3 4.5 2.0 1.0
OP1 A:DG2 4.6 28.7 1.0
O5' A:DG2 4.9 28.7 1.0
C4 A:DT3 4.9 2.0 1.0

Nickel binding site 3 out of 9 in 446d

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Nickel binding site 3 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni13

b:42.6
occ:1.00
O A:HOH27 2.0 42.6 1.0
O A:HOH24 2.0 42.6 1.0
O A:HOH25 2.1 42.6 1.0
O A:HOH26 2.1 42.6 1.0
O A:HOH28 2.1 42.6 1.0
O A:HOH29 2.2 42.6 1.0
O A:HOH15 4.3 16.4 1.0
OP1 A:DC9 4.3 19.0 1.0
O A:HOH40 4.4 17.4 1.0
OP2 A:DG10 4.9 2.0 1.0
O6 A:DG10 5.0 4.0 1.0
C5' A:DC9 5.0 2.0 1.0

Nickel binding site 4 out of 9 in 446d

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Nickel binding site 4 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni14

b:55.0
occ:1.00
O A:HOH33 1.9 55.0 1.0
O A:HOH30 2.0 55.0 1.0
O A:HOH31 2.0 55.0 1.0
O A:HOH32 2.1 55.0 1.0
O A:HOH35 2.1 55.0 1.0
O A:HOH34 2.1 55.0 1.0
O A:HOH17 4.1 16.4 1.0
OP1 A:DG10 4.4 2.0 1.0
O A:HOH42 4.5 17.4 1.0
C2' A:DG10 4.6 2.0 1.0
O5' A:DG10 5.0 2.0 1.0

Nickel binding site 5 out of 9 in 446d

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Nickel binding site 5 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni7

b:27.2
occ:1.00
O B:HOH21 2.0 27.2 1.0
O B:HOH24 2.0 27.2 1.0
O B:HOH22 2.1 27.2 1.0
O B:HOH23 2.1 27.2 1.0
O B:HOH25 2.1 27.2 1.0
N7 B:DG12 2.2 8.8 1.0
C8 B:DG12 3.1 8.8 1.0
C5 B:DG12 3.3 8.8 1.0
O6 B:DG12 3.6 8.8 1.0
C6 B:DG12 3.8 8.8 1.0
O4 B:DT13 4.2 2.0 1.0
N9 B:DG12 4.3 8.8 1.0
C4 B:DG12 4.4 8.8 1.0
OP2 B:DG12 4.8 46.8 1.0
C7 B:DT13 4.9 2.0 1.0
C4 B:DT13 5.0 2.0 1.0

Nickel binding site 6 out of 9 in 446d

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Nickel binding site 6 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni5

b:28.3
occ:1.00
N7 B:DG20 1.8 23.9 1.0
O B:HOH27 2.1 28.3 1.0
O B:HOH26 2.1 28.3 1.0
O B:HOH28 2.1 28.3 1.0
O B:HOH29 2.1 28.3 1.0
O B:HOH30 2.1 28.3 1.0
C8 B:DG20 2.5 23.9 1.0
C5 B:DG20 3.1 23.9 1.0
N9 B:DG20 3.8 23.9 1.0
O6 B:DG20 3.9 23.9 1.0
C6 B:DG20 3.9 23.9 1.0
OP2 B:DG20 4.0 12.8 1.0
C4 B:DG20 4.1 23.9 1.0
C5' D:DA34 4.4 12.8 1.0
C4' D:DA34 4.7 12.8 1.0
O5' B:DG20 4.8 12.8 1.0
P B:DG20 4.8 12.8 1.0
C2' B:DG20 4.9 2.0 1.0
C1' B:DG20 5.0 2.0 1.0

Nickel binding site 7 out of 9 in 446d

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Nickel binding site 7 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni1

b:18.1
occ:1.00
N7 C:DG22 1.9 2.0 1.0
O C:HOH34 2.0 18.1 1.0
O C:HOH38 2.1 18.1 1.0
O C:HOH36 2.1 18.1 1.0
O C:HOH37 2.1 18.1 1.0
O C:HOH35 2.1 18.1 1.0
C8 C:DG22 2.8 2.0 1.0
C5 C:DG22 3.0 2.0 1.0
O6 C:DG22 3.5 2.0 1.0
C6 C:DG22 3.6 2.0 1.0
N9 C:DG22 4.0 2.0 1.0
OP1 C:DG22 4.1 40.0 1.0
C4 C:DG22 4.1 2.0 1.0
O4 C:DT23 4.3 2.0 1.0
C7 C:DT23 4.4 2.0 1.0
C4 C:DT23 4.9 2.0 1.0
N1 C:DG22 5.0 2.0 1.0
O5' C:DG22 5.0 40.0 1.0
C5 C:DT23 5.0 2.0 1.0

Nickel binding site 8 out of 9 in 446d

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Nickel binding site 8 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni9

b:20.0
occ:1.00
O D:HOH45 2.0 20.0 1.0
O D:HOH41 2.0 20.0 1.0
O D:HOH43 2.1 20.0 1.0
O D:HOH44 2.1 20.0 1.0
O D:HOH42 2.1 20.0 1.0
N7 D:DG32 2.2 2.0 1.0
C8 D:DG32 3.0 2.0 1.0
C5 D:DG32 3.4 2.0 1.0
O6 D:DG32 3.9 2.0 1.0
C6 D:DG32 4.0 2.0 1.0
N9 D:DG32 4.3 2.0 1.0
C4 D:DG32 4.5 2.0 1.0
O4 D:DT33 4.5 13.0 1.0
OP1 D:DG32 4.6 26.0 1.0

Nickel binding site 9 out of 9 in 446d

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Nickel binding site 9 out of 9 in the Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex with Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni2

b:24.8
occ:1.00
N7 D:DG40 2.0 15.4 1.0
O D:HOH46 2.0 24.8 1.0
O D:HOH48 2.0 24.8 1.0
O D:HOH49 2.1 24.8 1.0
O D:HOH47 2.1 24.8 1.0
O D:HOH50 2.1 24.8 1.0
C8 D:DG40 2.5 15.4 1.0
C5 D:DG40 3.3 15.4 1.0
N9 D:DG40 3.9 15.4 1.0
C6 D:DG40 4.1 15.4 1.0
O6 D:DG40 4.1 15.4 1.0
C4 D:DG40 4.2 15.4 1.0
OP2 D:DG40 4.3 16.1 1.0

Reference:

N.G.Abrescia, L.Malinina, L.G.Fernandez, T.Huynh-Dinh, S.Neidle, J.A.Subirana. Structure of the Oligonucleotide D(Cgtatatacg) As A Site-Specific Complex with Nickel Ions. Nucleic Acids Res. V. 27 1593 1999.
ISSN: ISSN 0305-1048
PubMed: 10075989
DOI: 10.1093/NAR/27.7.1593
Page generated: Fri Sep 25 08:38:01 2020
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