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Zinc in PDB 1p26: Crystal Structure of Zinc(II)-D(Ggcgcc)2

Protein crystallography data

The structure of Crystal Structure of Zinc(II)-D(Ggcgcc)2, PDB code: 1p26 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 / 2.92
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.800, 68.800, 55.280, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Zinc(II)-D(Ggcgcc)2 (pdb code 1p26). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Zinc(II)-D(Ggcgcc)2, PDB code: 1p26:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1p26

Go back to Zinc Binding Sites List in 1p26
Zinc binding site 1 out of 5 in the Crystal Structure of Zinc(II)-D(Ggcgcc)2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Zinc(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:28.9
occ:1.00
O A:HOH204 2.1 38.9 1.0
O A:HOH205 2.1 38.9 1.0
O A:HOH203 2.1 38.9 1.0
O A:HOH202 2.1 38.9 1.0
N7 A:DG1 2.1 10.0 1.0
O A:HOH201 2.1 38.9 1.0
C8 A:DG1 3.0 10.0 1.0
C5 A:DG1 3.2 10.0 1.0
O6 A:DG1 3.6 10.0 1.0
C6 A:DG1 3.8 10.0 1.0
N9 A:DG1 4.3 10.0 1.0
C4 A:DG1 4.3 10.0 1.0
O5' A:DG1 4.7 24.6 1.0
O6 A:DG2 4.7 10.0 1.0

Zinc binding site 2 out of 5 in 1p26

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Zinc(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:18.6
occ:1.00
N7 B:DG7 2.1 10.0 1.0
O B:HOH207 2.1 28.6 1.0
O B:HOH208 2.1 28.6 1.0
O B:HOH210 2.1 28.6 1.0
O B:HOH209 2.1 28.6 1.0
O B:HOH206 2.1 28.6 1.0
C8 B:DG7 3.0 10.0 1.0
C5 B:DG7 3.1 10.0 1.0
O6 B:DG7 3.4 10.0 1.0
C6 B:DG7 3.7 10.0 1.0
N9 B:DG7 4.3 10.0 1.0
C4 B:DG7 4.3 10.0 1.0
O6 B:DG8 4.5 10.0 1.0
N4 A:DC6 4.8 10.0 1.0

Zinc binding site 3 out of 5 in 1p26

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Zinc(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn103

b:47.0
occ:1.00
O C:HOH211 2.1 43.3 1.0
N7 C:DG13 2.1 22.3 1.0
O C:HOH214 2.1 43.3 1.0
O C:HOH212 2.1 43.3 1.0
O C:HOH215 2.1 43.3 1.0
O C:HOH213 2.1 43.3 1.0
C8 C:DG13 3.0 22.3 1.0
C5 C:DG13 3.2 22.3 1.0
O6 C:DG13 3.5 22.3 1.0
C6 C:DG13 3.7 22.3 1.0
N9 C:DG13 4.2 22.3 1.0
C4 C:DG13 4.3 22.3 1.0
O6 C:DG14 4.4 10.2 1.0
O5' C:DG13 4.9 53.4 1.0

Zinc binding site 4 out of 5 in 1p26

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Zinc(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn104

b:27.7
occ:1.00
O D:HOH216 2.1 37.7 1.0
O D:HOH219 2.1 37.7 1.0
O D:HOH220 2.1 37.7 1.0
O D:HOH217 2.1 37.7 1.0
N7 D:DG19 2.1 10.7 1.0
O D:HOH218 2.1 37.7 1.0
C8 D:DG19 3.0 10.7 1.0
C5 D:DG19 3.1 10.7 1.0
O6 D:DG19 3.6 10.7 1.0
C6 D:DG19 3.7 10.7 1.0
N9 D:DG19 4.1 10.7 1.0
C4 D:DG19 4.2 10.7 1.0
O6 D:DG20 4.5 10.0 1.0
N4 B:DC12 4.6 10.2 1.0
N7 D:DG20 4.9 10.0 1.0

Zinc binding site 5 out of 5 in 1p26

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Zinc(II)-D(Ggcgcc)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn105

b:40.3
occ:1.00
O E:HOH225 2.1 44.8 1.0
O E:HOH222 2.1 44.8 1.0
O E:HOH223 2.1 44.8 1.0
O E:HOH221 2.1 44.8 1.0
N7 E:DG25 2.1 10.6 1.0
O E:HOH224 2.1 44.8 1.0
C8 E:DG25 3.0 10.6 1.0
C5 E:DG25 3.3 10.6 1.0
O6 E:DG25 3.8 10.6 1.0
C6 E:DG25 3.9 10.6 1.0
N9 E:DG25 4.2 10.6 1.0
C4 E:DG25 4.4 10.6 1.0
O6 E:DG26 4.7 15.5 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: Wed Dec 16 03:00:26 2020

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