Zinc in PDB 6zq9: Racemic Compound of Rna Duplexes.

Protein crystallography data

The structure of Racemic Compound of Rna Duplexes., PDB code: 6zq9 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 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 21, 25.93, 38.53, 105.09, 96.63, 91.95
R / Rfree (%) 19.2 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Racemic Compound of Rna Duplexes. (pdb code 6zq9). 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: 6zq9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6zq9

Go back to Zinc Binding Sites List in 6zq9
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:31.2
occ:0.80
O K:HOH212 2.1 26.6 1.0
N7 K:G82 2.1 16.6 1.0
O K:HOH222 2.2 19.0 1.0
O K:HOH201 2.2 27.5 1.0
O K:HOH237 2.3 27.0 1.0
O K:HOH204 2.3 20.2 1.0
C8 K:G82 3.0 17.4 1.0
C5 K:G82 3.2 16.9 1.0
O6 K:G82 3.7 18.6 1.0
C6 K:G82 3.8 18.0 1.0
O K:HOH218 3.9 26.3 1.0
OP2 K:G82 3.9 19.0 1.0
O K:HOH207 4.0 32.0 1.0
N9 K:G82 4.2 17.1 1.0
C4 K:G82 4.3 16.9 1.0
N7 K:G81 4.5 21.4 1.0
OP2 K:G81 4.5 24.2 1.0
O6 K:G83 4.5 20.1 1.0
O L:HOH202 4.6 24.0 1.0
N7 K:G83 4.7 20.7 1.0
C8 K:G81 4.7 20.3 1.0
O5' K:G82 4.8 20.4 1.0
C5 K:G81 4.9 18.9 1.0

Zinc binding site 2 out of 7 in 6zq9

Go back to Zinc Binding Sites List in 6zq9
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:34.5
occ:0.80
O K:HOH213 2.0 30.4 1.0
O M:HOH236 2.0 29.7 1.0
O K:HOH202 2.1 37.9 1.0
O K:HOH239 2.2 28.3 1.0
O K:HOH220 2.2 21.3 1.0
O K:HOH206 3.3 34.0 1.0
O M:HOH208 3.5 40.5 1.0
N7 K:G85 3.8 24.8 1.0
O6 K:G86 3.9 19.4 1.0
O6 K:G85 4.0 26.2 1.0
O K:HOH215 4.1 31.7 1.0
N7 K:G86 4.3 17.4 1.0
O2 M:0C79 4.4 20.1 1.0
C5 K:G85 4.5 22.8 1.0
C6 K:G85 4.5 23.4 1.0
C6 K:G86 4.8 16.7 1.0
C8 K:G85 4.8 22.7 1.0
C1' M:0C79 4.8 22.0 1.0
O K:HOH229 4.9 31.0 1.0
C5 K:G86 4.9 15.5 1.0
O2' M:0C79 4.9 26.4 1.0

Zinc binding site 3 out of 7 in 6zq9

Go back to Zinc Binding Sites List in 6zq9
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:32.3
occ:0.80
O L:HOH226 2.0 26.7 1.0
O L:HOH210 2.0 32.4 1.0
O L:HOH240 2.1 26.4 1.0
O L:HOH209 2.2 22.2 1.0
O L:HOH225 2.3 31.6 1.0
N7 L:G96 3.8 19.2 1.0
O K:HOH235 3.9 42.9 1.0
O L:HOH218 3.9 27.1 1.0
O6 L:G97 4.1 19.4 1.0
O L:HOH206 4.2 31.8 1.0
N7 L:G97 4.3 17.0 1.0
OP2 L:G96 4.4 21.6 1.0
C8 L:G96 4.4 18.8 1.0
C5 L:G96 4.9 18.8 1.0
C6 L:G97 4.9 18.4 1.0
C5 L:G97 5.0 16.9 1.0

Zinc binding site 4 out of 7 in 6zq9

Go back to Zinc Binding Sites List in 6zq9
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:42.5
occ:0.80
O L:HOH220 2.2 37.9 1.0
O L:HOH238 3.6 41.0 1.0
OP1 L:U95 4.0 20.1 1.0
OP2 L:U95 4.3 19.4 1.0
OP1 L:C94 4.4 16.9 1.0
P L:U95 4.7 18.2 1.0

Zinc binding site 5 out of 7 in 6zq9

Go back to Zinc Binding Sites List in 6zq9
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:27.6
occ:0.60
O M:HOH224 2.1 20.9 1.0
O M:HOH228 2.1 22.8 1.0
N7 M:0G82 2.1 14.5 1.0
O M:HOH218 2.2 20.8 1.0
O M:HOH239 2.2 32.1 1.0
O M:HOH217 2.2 28.0 1.0
C8 M:0G82 3.0 15.1 1.0
C5 M:0G82 3.2 15.9 1.0
O6 M:0G82 3.6 20.3 1.0
C6 M:0G82 3.8 17.3 1.0
OP1 M:0G82 3.9 18.6 1.0
O M:HOH226 3.9 24.6 1.0
O M:HOH231 4.0 35.0 1.0
O N:HOH218 4.1 29.1 1.0
N9 M:0G82 4.2 15.0 1.0
C4 M:0G82 4.3 16.2 1.0
N7 M:0G81 4.4 19.1 1.0
C8 M:0G81 4.6 19.3 1.0
O6 M:0G83 4.6 19.6 1.0
OP1 M:0G81 4.7 23.2 1.0
N7 M:0G83 4.7 16.6 1.0
C5 M:0G81 4.7 19.0 1.0
O5' M:0G82 4.8 18.1 1.0

Zinc binding site 6 out of 7 in 6zq9

Go back to Zinc Binding Sites List in 6zq9
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:33.0
occ:0.80
O M:HOH237 1.5 18.5 1.0
O M:HOH222 1.9 32.0 1.0
O M:HOH209 1.9 23.6 1.0
O M:HOH206 2.2 28.1 1.0
O M:HOH202 2.3 30.5 1.0
N7 M:0G85 2.5 21.5 1.0
C8 M:0G85 3.3 19.9 1.0
C5 M:0G85 3.6 19.9 1.0
O6 M:0G85 3.9 25.3 1.0
OP1 M:0G85 3.9 23.2 1.0
O M:HOH203 4.1 34.1 1.0
C6 M:0G85 4.1 21.7 1.0
N7 M:0G86 4.2 17.3 1.0
C5 M:0C84 4.3 17.4 1.0
C4 M:0C84 4.4 17.1 1.0
O6 M:0G86 4.4 16.6 1.0
O M:HOH234 4.4 34.3 1.0
N4 M:0C84 4.5 16.9 1.0
N9 M:0G85 4.5 19.3 1.0
C4 M:0G85 4.7 18.6 1.0
C6 M:0C84 4.8 17.2 1.0
N3 M:0C84 4.8 16.3 1.0
O5' M:0G85 4.9 19.7 1.0
C5 M:0G86 4.9 16.9 1.0
C6 M:0G86 5.0 17.9 1.0

Zinc binding site 7 out of 7 in 6zq9

Go back to Zinc Binding Sites List in 6zq9
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:37.7
occ:0.80
O N:HOH226 1.9 34.6 1.0
O N:HOH206 2.0 22.4 1.0
O N:HOH212 2.1 32.0 1.0
O L:HOH233 2.1 32.4 1.0
O N:HOH232 2.3 35.1 1.0
N7 N:0G96 4.0 21.5 1.0
N7 N:0G97 4.3 16.4 1.0
O6 N:0G97 4.3 20.3 1.0
O K:HOH233 4.4 41.5 1.0
O L:HOH234 4.6 35.8 1.0
C8 N:0G96 4.7 20.9 1.0
OP1 N:0G96 4.7 26.6 1.0
C5 N:0U95 4.7 21.4 1.0
C4 N:0U95 4.8 20.6 1.0
O2 L:C90 4.9 21.6 1.0
O4 N:0U95 4.9 21.8 1.0
O L:HOH235 5.0 43.4 1.0
O6 N:0G96 5.0 22.7 1.0

Reference:

W.Rypniewski, A.Kiliszek, L.Blaszczyk, M.Bejger. Racemic Compound of Rna Duplexes. To Be Published.
Page generated: Mon Jul 12 16:47:22 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy