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Zinc in PDB 7ow0: 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad.

Protein crystallography data

The structure of 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad., PDB code: 7ow0 was solved by R.M.Dolot, A.Maciaszek, B.C.Nawrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.09 / 1.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 31.85, 31.85, 91.66, 90, 90, 90
R / Rfree (%) 22.1 / 25.1

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad. (pdb code 7ow0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad., PDB code: 7ow0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7ow0

Go back to Zinc Binding Sites List in 7ow0
Zinc binding site 1 out of 3 in the 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:23.5
occ:1.00
O A:HOH230 2.1 21.5 1.0
O A:HOH233 2.1 28.9 1.0
O A:HOH244 2.1 26.8 1.0
O A:HOH225 2.2 25.8 1.0
N7 A:DG8 2.2 22.8 1.0
O A:HOH203 2.3 21.8 1.0
C8 A:DG8 3.0 22.9 1.0
C5 A:DG8 3.2 21.0 1.0
O6 A:DG8 3.7 18.9 1.0
C6 A:DG8 3.8 19.9 1.0
O A:HOH227 4.0 32.5 1.0
N9 A:DG8 4.2 21.3 1.0
OP2 A:DG8 4.2 29.2 1.0
O A:HOH207 4.2 27.1 1.0
O A:HOH243 4.3 31.3 1.0
C4 A:DG8 4.3 20.4 1.0
O A:HOH246 4.3 37.9 1.0
O A:HOH205 4.4 19.8 1.0
O A:HOH214 4.4 22.8 1.0
N7 A:DG9 4.6 21.6 1.0
N7 A:DA7 4.8 22.0 1.0
C5 A:DA7 4.9 20.0 1.0
O5' A:DG8 4.9 21.5 1.0

Zinc binding site 2 out of 3 in 7ow0

Go back to Zinc Binding Sites List in 7ow0
Zinc binding site 2 out of 3 in the 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:27.0
occ:1.00
O B:HOH203 2.2 29.7 1.0
O B:HOH226 2.2 25.9 1.0
O B:HOH210 2.2 27.9 1.0
O B:HOH234 2.2 35.0 1.0
N7 B:OMG4 2.3 23.3 1.0
O B:HOH243 2.3 34.4 1.0
C8 B:OMG4 3.2 21.7 1.0
C5 B:OMG4 3.3 21.1 1.0
O6 B:OMG4 3.7 20.9 1.0
O B:HOH204 3.9 28.8 1.0
C6 B:OMG4 3.9 19.4 1.0
O B:HOH215 3.9 30.1 1.0
N7 B:A2M3 4.2 23.2 1.0
O B:HOH205 4.2 33.6 1.0
N9 B:OMG4 4.4 21.2 1.0
N6 B:A2M3 4.4 20.3 1.0
O B:HOH207 4.4 28.0 1.0
C4 B:OMG4 4.5 21.6 1.0
C5 B:A2M3 4.7 21.2 1.0
O B:HOH217 4.8 32.1 1.0
C6 B:A2M3 4.9 21.4 1.0

Zinc binding site 3 out of 3 in 7ow0

Go back to Zinc Binding Sites List in 7ow0
Zinc binding site 3 out of 3 in the 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.55 A Crystal Structure of Dna/2'-O-Methyl-Rna Heteroduplex with Overhangs Solved By Zn-Sad. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:32.1
occ:1.00
O B:HOH219 2.1 26.7 1.0
O B:HOH222 2.1 27.8 1.0
O B:HOH214 2.2 27.4 1.0
N7 B:OMG7 2.3 23.5 1.0
O B:HOH240 2.3 31.5 1.0
O B:HOH206 2.8 28.5 1.0
C8 B:OMG7 3.1 21.6 1.0
C5 B:OMG7 3.4 18.2 1.0
O B:HOH232 3.5 29.2 1.0
O6 B:OMG7 3.8 20.0 1.0
O B:HOH238 3.8 37.8 1.0
O B:HOH216 3.8 26.2 1.0
C6 B:OMG7 4.0 20.4 1.0
N7 B:A2M6 4.0 21.2 1.0
O B:HOH218 4.3 36.7 1.0
OP2 B:OMG7 4.3 24.7 1.0
C5 B:A2M6 4.4 19.3 1.0
N9 B:OMG7 4.4 18.8 1.0
C4 B:OMG7 4.5 19.8 1.0
C8 B:A2M6 4.6 21.1 1.0
O B:HOH245 4.6 35.1 1.0
N6 B:A2M6 4.6 22.3 1.0
C6 B:A2M6 4.7 20.7 1.0
OP2 B:A2M6 4.9 30.7 1.0

Reference:

R.M.Dolot, A.Maciaszek, B.Mikolajczyk, B.C.Nawrot. First Crystal Structures of Dna:2'-O-Methyl-Rna Heteroduplexes. To Be Published.
Page generated: Sun Aug 22 09:53:03 2021

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