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Zinc in PDB 6zrs: Racemic Compound of Rna Duplexes.

Protein crystallography data

The structure of Racemic Compound of Rna Duplexes., PDB code: 6zrs was solved by W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.89 / 1.52
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 20.97, 26.43, 38.68, 105.84, 96.66, 92.03
R / Rfree (%) 18.7 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Racemic Compound of Rna Duplexes. (pdb code 6zrs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Racemic Compound of Rna Duplexes., PDB code: 6zrs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6zrs

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Zinc binding site 1 out of 7 in the Racemic Compound of Rna Duplexes.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Racemic Compound of Rna Duplexes. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn101

b:20.5
occ:0.60
 O K:HOH215 2.1 24.4 1.0
N7 K:G82 2.1 15.1 1.0
O K:HOH209 2.2 16.3 1.0
O K:HOH205 2.2 18.1 1.0
O K:HOH221 2.2 19.7 1.0
O K:HOH239 2.2 19.2 1.0
C8 K:G82 3.0 13.4 1.0
C5 K:G82 3.2 14.5 1.0
O L:HOH248 3.6 38.4 1.0
O6 K:G82 3.7 15.0 1.0
C6 K:G82 3.8 14.9 1.0
O K:HOH208 3.9 19.3 1.0
OP2 K:G82 3.9 14.9 1.0
O K:HOH228 4.0 38.7 1.0
N9 K:G82 4.2 13.6 1.0
C4 K:G82 4.3 14.7 1.0
O6 K:G83 4.5 16.0 1.0
N7 K:G81 4.6 16.8 1.0
OP2 K:G81 4.6 19.8 1.0
N7 K:G83 4.6 17.0 1.0
O L:HOH201 4.7 24.5 1.0
C8 K:G81 4.8 14.9 1.0
O5' K:G82 4.9 15.5 1.0
C5 K:G81 4.9 15.0 1.0

Zinc binding site 2 out of 7 in 6zrs

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Zinc binding site 2 out of 7 in the Racemic Compound of Rna Duplexes.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Racemic Compound of Rna Duplexes. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn102

b:22.8
occ:0.60
 O M:HOH237 1.8 27.5 1.0
O K:HOH203 1.8 26.1 1.0
O K:HOH242 2.1 24.0 1.0
O K:HOH214 2.1 17.6 1.0
O K:HOH201 2.2 32.1 1.0
O K:HOH211 3.6 27.0 1.0
O M:HOH222 3.7 17.9 0.5
N7 K:G85 3.7 21.6 1.0
O K:HOH217 4.0 31.3 1.0
O6 K:G86 4.1 14.1 1.0
O6 K:G85 4.2 19.2 1.0
N7 K:G86 4.4 14.0 1.0
C5 K:G85 4.5 18.0 1.0
O2 M:0C79 4.5 16.4 1.0
O L:HOH243 4.6 38.4 1.0
O M:HOH204 4.6 18.6 0.5
C8 K:G85 4.6 19.1 1.0
O K:HOH231 4.7 29.1 1.0
C6 K:G85 4.7 19.0 1.0
C1' M:0C79 4.9 18.2 1.0
C6 K:G86 4.9 14.7 1.0
OP2 K:G85 5.0 27.9 1.0
O2' M:0C79 5.0 19.6 1.0

Zinc binding site 3 out of 7 in 6zrs

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Zinc binding site 3 out of 7 in the Racemic Compound of Rna Duplexes.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Racemic Compound of Rna Duplexes. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:27.4
occ:0.80
 O L:HOH239 1.7 14.3 1.0
O L:HOH238 1.8 20.8 1.0
O L:HOH251 1.9 21.4 1.0
O L:HOH228 2.0 22.9 1.0
O L:HOH210 2.0 23.2 1.0
O L:HOH231 3.8 24.3 1.0
O K:HOH238 3.9 35.6 1.0
O L:HOH235 4.0 37.5 1.0
N7 L:G96 4.1 16.7 1.0
O6 L:G97 4.1 15.8 1.0
O K:HOH216 4.3 26.9 1.0
N7 L:G97 4.4 13.0 1.0
C8 L:G96 4.7 16.4 1.0
OP2 L:G96 4.9 17.5 1.0
C6 L:G97 4.9 14.6 1.0

Zinc binding site 4 out of 7 in 6zrs

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Zinc binding site 4 out of 7 in the Racemic Compound of Rna Duplexes.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Racemic Compound of Rna Duplexes. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn102

b:29.2
occ:0.50
 O L:HOH223 2.1 19.9 1.0
O L:HOH232 2.1 30.3 1.0
O L:HOH227 3.6 41.2 1.0
OP1 L:U95 4.0 15.2 1.0
OP2 L:U95 4.3 15.4 1.0
OP1 L:C94 4.4 16.0 1.0
P L:U95 4.7 14.3 1.0

Zinc binding site 5 out of 7 in 6zrs

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Zinc binding site 5 out of 7 in the Racemic Compound of Rna Duplexes.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Racemic Compound of Rna Duplexes. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn101

b:17.2
occ:0.50
 O M:HOH239 2.0 25.5 1.0
O M:HOH225 2.0 22.8 1.0
O M:HOH226 2.0 20.1 1.0
O M:HOH221 2.1 24.4 1.0
N7 M:0G82 2.1 11.6 1.0
O M:HOH215 2.1 22.1 1.0
C8 M:0G82 3.0 12.3 1.0
C5 M:0G82 3.2 12.8 1.0
O6 M:0G82 3.6 15.1 1.0
O M:HOH244 3.6 44.5 1.0
C6 M:0G82 3.7 14.6 1.0
O M:HOH217 4.0 20.6 1.0
OP1 M:0G82 4.0 13.9 1.0
O M:HOH235 4.0 26.9 1.0
O N:HOH225 4.1 19.7 1.0
N9 M:0G82 4.2 11.6 1.0
C4 M:0G82 4.3 13.0 1.0
N7 M:0G81 4.4 15.8 1.0
O6 M:0G83 4.5 16.4 1.0
O M:HOH242 4.5 33.6 1.0
C8 M:0G81 4.7 15.3 1.0
N7 M:0G83 4.7 13.8 1.0
C5 M:0G81 4.8 16.8 1.0
OP1 M:0G81 4.8 17.6 1.0
O5' M:0G82 5.0 13.4 1.0

Zinc binding site 6 out of 7 in 6zrs

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Zinc binding site 6 out of 7 in the Racemic Compound of Rna Duplexes.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Racemic Compound of Rna Duplexes. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn102

b:27.0
occ:0.60
 O M:HOH211 2.0 28.4 1.0
O M:HOH201 2.1 49.6 1.0
O M:HOH231 2.1 22.8 1.0
N7 M:0G85 3.2 18.4 1.0
O M:HOH203 4.0 34.4 1.0
C8 M:0G85 4.0 17.2 1.0
O6 M:0G85 4.1 16.5 1.0
C5 M:0G85 4.1 15.4 1.0
O6 M:0G86 4.2 13.3 1.0
N7 M:0G86 4.4 13.1 1.0
OP1 M:0G85 4.4 18.7 1.0
C6 M:0G85 4.5 17.4 1.0
O M:HOH234 4.5 32.4 1.0
C5 M:0C84 4.8 14.9 1.0
C4 M:0C84 4.8 13.9 1.0
N4 M:0C84 4.9 16.2 1.0

Zinc binding site 7 out of 7 in 6zrs

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Zinc binding site 7 out of 7 in the Racemic Compound of Rna Duplexes.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Racemic Compound of Rna Duplexes. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:29.6
occ:0.80
 O N:HOH231 2.0 23.1 1.0
O N:HOH242 2.1 20.2 1.0
O L:HOH241 2.1 23.1 1.0
O N:HOH211 2.1 24.2 1.0
O N:HOH232 2.2 29.8 1.0
O L:HOH246 2.2 43.6 1.0
O K:HOH237 4.0 27.7 1.0
N7 N:0G96 4.1 16.6 1.0
O N:HOH206 4.2 31.8 1.0
N7 N:0G97 4.3 13.4 1.0
O6 N:0G97 4.4 18.1 1.0
O L:HOH244 4.5 40.4 1.0
C8 N:0G96 4.8 17.1 1.0
C5 N:0U95 4.8 17.2 1.0
OP1 N:0G96 4.8 22.1 1.0
C4 N:0U95 4.9 15.0 1.0
O4 N:0U95 4.9 17.0 1.0
O2 L:C90 4.9 16.2 1.0

Reference:

W.Rypniewski, A.Kiliszek, L.Blaszczyk, M.Bejger. Racemic Compound of Rna Duplexes. To Be Published.
Page generated: Mon Jul 12 16:48:06 2021

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