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Nickel in PDB 1p25: Crystal Structure of Nickel(II)-D(Ggcgcc)2

Protein crystallography data

The structure of Crystal Structure of Nickel(II)-D(Ggcgcc)2, PDB code: 1p25 was solved by S.L.Labiuk, L.T.Delbaere, J.S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.990, 68.990, 56.180, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 27.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Nickel(II)-D(Ggcgcc)2 (pdb code 1p25). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Crystal Structure of Nickel(II)-D(Ggcgcc)2, PDB code: 1p25:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 1p25

Go back to Nickel Binding Sites List in 1p25
Nickel binding site 1 out of 5 in the Crystal Structure of Nickel(II)-D(Ggcgcc)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Nickel(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni101

b:33.3
occ:1.00
O A:HOH201 2.1 36.6 1.0
O A:HOH205 2.1 36.6 1.0
O A:HOH204 2.1 36.6 1.0
O A:HOH202 2.1 36.6 1.0
O A:HOH203 2.1 36.6 1.0
N7 A:DG1 2.1 18.5 1.0
C8 A:DG1 3.0 18.5 1.0
C5 A:DG1 3.3 18.5 1.0
O6 A:DG1 3.8 18.5 1.0
C6 A:DG1 3.9 18.5 1.0
N9 A:DG1 4.3 18.5 1.0
C4 A:DG1 4.4 18.5 1.0
O6 A:DG2 4.5 10.5 1.0
O5' A:DG1 4.9 20.5 1.0

Nickel binding site 2 out of 5 in 1p25

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Nickel binding site 2 out of 5 in the Crystal Structure of Nickel(II)-D(Ggcgcc)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Nickel(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni102

b:29.7
occ:1.00
N7 B:DG7 2.1 12.3 1.0
O B:HOH208 2.1 32.7 1.0
O B:HOH209 2.1 32.7 1.0
O B:HOH207 2.1 32.7 1.0
O B:HOH210 2.1 32.7 1.0
O B:HOH206 2.1 32.7 1.0
C8 B:DG7 3.0 12.3 1.0
C5 B:DG7 3.1 12.3 1.0
O6 B:DG7 3.3 12.3 1.0
C6 B:DG7 3.6 12.3 1.0
N9 B:DG7 4.2 12.3 1.0
C4 B:DG7 4.3 12.3 1.0
N4 A:DC6 4.9 10.0 1.0
O5' B:DG7 5.0 26.6 1.0

Nickel binding site 3 out of 5 in 1p25

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Nickel binding site 3 out of 5 in the Crystal Structure of Nickel(II)-D(Ggcgcc)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Nickel(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni103

b:41.6
occ:1.00
O C:HOH211 2.1 34.3 1.0
O C:HOH214 2.1 34.3 1.0
O C:HOH215 2.1 34.3 1.0
O C:HOH213 2.1 34.3 1.0
O C:HOH212 2.1 34.3 1.0
N7 C:DG13 2.1 19.4 1.0
C8 C:DG13 3.0 19.4 1.0
C5 C:DG13 3.2 19.4 1.0
O6 C:DG13 3.7 19.4 1.0
C6 C:DG13 3.9 19.4 1.0
O6 C:DG14 4.2 10.5 1.0
N9 C:DG13 4.2 19.4 1.0
C4 C:DG13 4.3 19.4 1.0
N7 C:DG14 4.8 10.5 1.0

Nickel binding site 4 out of 5 in 1p25

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Nickel binding site 4 out of 5 in the Crystal Structure of Nickel(II)-D(Ggcgcc)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Nickel(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni104

b:35.4
occ:1.00
O D:HOH216 2.1 33.5 1.0
N7 D:DG19 2.1 22.1 1.0
O D:HOH217 2.1 33.5 1.0
O D:HOH220 2.1 33.5 1.0
O D:HOH219 2.1 33.5 1.0
O D:HOH218 2.1 33.5 1.0
C8 D:DG19 3.0 22.1 1.0
C5 D:DG19 3.1 22.1 1.0
O6 D:DG19 3.3 22.1 1.0
C6 D:DG19 3.6 22.1 1.0
N9 D:DG19 4.3 22.1 1.0
O6 D:DG20 4.3 10.2 1.0
C4 D:DG19 4.3 22.1 1.0
N4 B:DC12 4.8 10.0 1.0

Nickel binding site 5 out of 5 in 1p25

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Nickel binding site 5 out of 5 in the Crystal Structure of Nickel(II)-D(Ggcgcc)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Nickel(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni105

b:42.1
occ:1.00
O E:HOH225 2.1 35.6 1.0
O E:HOH222 2.1 35.6 1.0
O E:HOH223 2.1 35.6 1.0
O E:HOH224 2.1 35.6 1.0
O E:HOH221 2.1 35.6 1.0
N7 E:DG25 2.1 10.0 1.0
C8 E:DG25 3.0 10.0 1.0
C5 E:DG25 3.3 10.0 1.0
O6 E:DG25 3.8 10.0 1.0
C6 E:DG25 3.9 10.0 1.0
N9 E:DG25 4.2 10.0 1.0
C4 E:DG25 4.3 10.0 1.0
O6 E:DG26 4.8 10.0 1.0

Reference:

S.L.Labiuk, L.T.Delbaere, J.S.Lee. Cobalt(II), Nickel(II) and Zinc(II) Do Not Bind to Intra-Helical N(7) Guanine Positions in the B-Form Crystal Structure of D(Ggcgcc) J.Biol.Inorg.Chem. V. 8 715 2003.
ISSN: ISSN 0949-8257
PubMed: 14505075
DOI: 10.1007/S00775-003-0473-4
Page generated: Fri Sep 25 07:58:02 2020
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