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

Protein crystallography data

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

Resolution Low / High (Å) 36.97 / 1.53
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 21.01, 26.47, 38.75, 105.8, 96.71, 91.89
R / Rfree (%) 21.3 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Racemic Compound of Rna Duplexes. (pdb code 6zrl). 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: 6zrl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6zrl

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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:22.1
occ:0.60
 O K:HOH220 2.0 23.1 1.0
O K:HOH223 2.0 19.4 1.0
N7 K:0G82 2.1 14.8 1.0
O K:HOH203 2.2 20.7 1.0
O K:HOH236 2.2 17.2 1.0
O K:HOH208 2.2 21.9 1.0
C8 K:0G82 3.0 14.2 1.0
C5 K:0G82 3.3 14.0 1.0
O6 K:0G82 3.7 17.0 1.0
OP1 K:0G82 3.8 18.1 1.0
C6 K:0G82 3.8 16.1 1.0
O K:HOH218 4.1 21.9 1.0
O L:HOH235 4.2 25.7 1.0
N9 K:0G82 4.2 14.8 1.0
C4 K:0G82 4.4 13.9 1.0
O K:HOH228 4.4 30.5 1.0
O6 K:0G83 4.5 17.9 1.0
N7 K:0G81 4.5 17.7 1.0
N7 K:0G83 4.6 17.5 1.0
OP1 K:0G81 4.7 21.1 1.0
C8 K:0G81 4.7 16.2 1.0
O5' K:0G82 4.9 16.9 1.0
C5 K:0G81 4.9 16.8 1.0

Zinc binding site 2 out of 7 in 6zrl

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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:28.8
occ:0.80
 O M:HOH242 1.9 32.2 1.0
O K:HOH215 2.0 27.4 1.0
O K:HOH221 2.0 18.4 1.0
O K:HOH240 2.1 34.6 1.0
O K:HOH201 2.4 30.2 1.0
O K:HOH205 3.5 27.2 1.0
N7 K:0G85 3.7 24.2 1.0
O K:HOH224 3.8 37.6 1.0
O6 K:0G86 4.0 17.3 1.0
O L:HOH243 4.0 39.8 1.0
O6 K:0G85 4.1 23.5 1.0
O M:HOH219 4.1 31.8 1.0
N7 K:0G86 4.3 15.8 1.0
O K:HOH217 4.3 32.9 1.0
C5 K:0G85 4.5 21.1 1.0
O2 M:C79 4.6 18.8 1.0
C6 K:0G85 4.6 22.9 1.0
C8 K:0G85 4.7 20.9 1.0
C1' M:C79 4.8 20.8 1.0
C6 K:0G86 4.8 16.1 1.0
OP1 K:0G85 4.9 30.2 1.0
C5 K:0G86 4.9 14.1 1.0
N4 K:0C84 5.0 20.8 1.0

Zinc binding site 3 out of 7 in 6zrl

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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:30.7
occ:1.00
 O L:HOH217 1.8 30.6 1.0
O L:HOH249 2.0 19.1 1.0
O L:HOH240 2.0 22.0 1.0
O L:HOH237 2.0 26.9 1.0
O L:HOH208 2.0 28.9 1.0
O L:HOH209 4.0 41.6 1.0
N7 L:0G96 4.1 17.9 1.0
O K:HOH227 4.1 30.4 1.0
O L:HOH220 4.1 36.3 1.0
O6 L:0G97 4.1 16.1 1.0
N7 L:0G97 4.3 14.7 1.0
O K:HOH235 4.5 38.6 1.0
C8 L:0G96 4.7 18.4 1.0
OP1 L:0G96 4.8 18.6 1.0
C6 L:0G97 4.9 14.7 1.0

Zinc binding site 4 out of 7 in 6zrl

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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:41.5
occ:0.80
 O L:HOH229 2.1 27.2 1.0
OP2 L:0U95 4.0 16.8 1.0
OP1 L:0U95 4.1 16.0 1.0
OP2 L:0C94 4.3 16.9 1.0
P L:0U95 4.6 15.6 1.0

Zinc binding site 5 out of 7 in 6zrl

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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:18.5
occ:0.50
 O M:HOH215 1.9 21.7 1.0
O M:HOH245 2.0 24.3 1.0
O M:HOH216 2.0 22.0 1.0
O M:HOH225 2.1 18.0 1.0
N7 M:G82 2.1 13.9 1.0
O M:HOH213 2.2 24.6 1.0
C8 M:G82 3.0 14.7 1.0
C5 M:G82 3.2 14.7 1.0
O6 M:G82 3.7 18.1 1.0
C6 M:G82 3.8 16.9 1.0
OP2 M:G82 3.9 16.2 1.0
O M:HOH235 4.0 17.2 0.5
O M:HOH226 4.1 19.5 1.0
O N:HOH221 4.2 21.2 1.0
N9 M:G82 4.2 13.6 1.0
C4 M:G82 4.3 14.2 1.0
O M:HOH246 4.4 36.6 1.0
N7 M:G81 4.5 16.6 1.0
O6 M:G83 4.6 15.0 1.0
OP2 M:G81 4.7 20.6 1.0
C8 M:G81 4.8 15.5 1.0
N7 M:G83 4.8 14.2 1.0
C5 M:G81 4.8 17.0 1.0
O5' M:G82 4.9 16.1 1.0
O M:HOH218 4.9 14.8 0.5

Zinc binding site 6 out of 7 in 6zrl

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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:45.5
occ:1.00
 O M:HOH202 2.0 27.4 1.0
O M:HOH206 2.1 19.9 1.0
O M:HOH227 2.2 29.0 1.0
O M:HOH217 2.2 23.6 1.0
N7 M:G85 2.7 20.9 1.0
C8 M:G85 3.5 19.2 1.0
O M:HOH221 3.7 26.4 1.0
C5 M:G85 3.7 17.9 1.0
O6 M:G85 4.0 19.2 1.0
OP2 M:G85 4.0 19.9 1.0
C6 M:G85 4.2 18.5 1.0
N7 M:G86 4.3 15.2 1.0
O6 M:G86 4.4 15.8 1.0
C5 M:C84 4.5 16.7 1.0
C4 M:C84 4.6 16.4 1.0
O M:HOH239 4.6 32.7 1.0
N9 M:G85 4.7 18.6 1.0
N4 M:C84 4.8 17.9 1.0
C4 M:G85 4.8 17.3 1.0
C6 M:C84 4.9 16.5 1.0

Zinc binding site 7 out of 7 in 6zrl

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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:28.3
occ:0.80
 O N:HOH227 1.9 25.9 1.0
O N:HOH235 2.0 27.0 1.0
O N:HOH209 2.0 22.5 1.0
O N:HOH234 2.0 32.3 1.0
O N:HOH246 2.1 19.9 1.0
O L:HOH245 2.2 27.9 1.0
O L:HOH231 3.4 37.8 1.0
N7 N:G96 4.1 19.8 1.0
O N:HOH206 4.2 29.3 1.0
O L:HOH242 4.2 29.9 1.0
O6 N:G97 4.3 18.0 1.0
N7 N:G97 4.3 14.6 1.0
C8 N:G96 4.7 18.5 1.0
OP2 N:G96 4.8 24.9 1.0
O2 L:0C90 4.9 21.0 1.0
O4 N:U95 4.9 19.9 1.0
C4 N:U95 4.9 17.7 1.0
C5 N:U95 4.9 20.0 1.0

Reference:

W.Rypniewski, A.Kiliszek, L.Blaszczyk, M.Bejger. Racemic Compound of Rna Duplexes. To Be Published.
Page generated: Tue Oct 29 15:56:34 2024

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