Atomistry » Zinc » PDB 6zpf-6zxd » 6zpf
Atomistry »
  Zinc »
    PDB 6zpf-6zxd »
      6zpf »

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

Protein crystallography data

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

Resolution Low / High (Å) 36.78 / 1.44
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 20.85, 26.5, 38.57, 106.11, 96, 92.72
R / Rfree (%) 20.1 / 25

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 6zpf

Go back to Zinc Binding Sites List in 6zpf
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:20.9
occ:0.70
 O K:HOH246 2.1 22.7 1.0
O K:HOH224 2.1 17.9 1.0
O K:HOH223 2.1 19.6 1.0
N7 K:G82 2.2 13.4 1.0
O K:HOH205 2.2 17.1 1.0
O K:HOH202 2.2 22.9 1.0
C8 K:G82 3.0 13.9 1.0
C5 K:G82 3.2 13.2 1.0
O6 K:G82 3.7 15.0 1.0
C6 K:G82 3.8 13.8 1.0
OP2 K:G82 3.9 15.6 1.0
O K:HOH220 4.0 20.1 1.0
O K:HOH232 4.0 38.5 1.0
N9 K:G82 4.2 13.0 1.0
C4 K:G82 4.3 13.7 1.0
O K:HOH249 4.4 30.0 1.0
O6 K:G83 4.5 15.3 1.0
N7 K:G81 4.6 17.0 1.0
O L:HOH201 4.6 26.2 1.0
OP2 K:G81 4.6 20.1 1.0
N7 K:G83 4.7 16.6 1.0
C8 K:G81 4.8 15.5 1.0
O5' K:G82 4.9 15.2 1.0
C5 K:G81 5.0 15.8 1.0

Zinc binding site 2 out of 7 in 6zpf

Go back to Zinc Binding Sites List in 6zpf
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:23.6
occ:0.70
 O K:HOH201 1.9 32.3 1.0
O K:HOH221 2.0 22.1 1.0
O M:HOH245 2.0 29.6 1.0
O K:HOH250 2.0 27.6 1.0
O K:HOH228 2.0 22.4 1.0
N7 K:G85 3.9 19.0 1.0
O6 K:G86 4.0 16.2 1.0
O K:HOH225 4.1 24.2 1.0
O K:HOH215 4.1 30.2 1.0
O6 K:G85 4.2 19.4 1.0
O K:HOH236 4.3 29.4 1.0
O2 M:0C79 4.4 18.5 1.0
N7 K:G86 4.4 15.5 1.0
O M:HOH202 4.4 28.2 1.0
C5 K:G85 4.6 16.9 1.0
C6 K:G85 4.8 18.0 1.0
C1' M:0C79 4.8 18.7 1.0
C8 K:G85 4.8 17.5 1.0
C6 K:G86 4.9 14.9 1.0
O2' M:0C79 4.9 21.4 1.0

Zinc binding site 3 out of 7 in 6zpf

Go back to Zinc Binding Sites List in 6zpf
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:22.6
occ:0.70
 O L:HOH242 1.6 19.9 1.0
O L:HOH215 1.7 29.7 1.0
O L:HOH214 2.0 28.1 1.0
O L:HOH251 2.0 23.1 1.0
O L:HOH216 2.3 21.5 1.0
N7 L:G96 4.0 16.4 1.0
O L:HOH228 4.0 29.7 1.0
O6 L:G97 4.0 15.5 1.0
O K:HOH240 4.1 40.2 1.0
O K:HOH226 4.2 29.9 1.0
O L:HOH219 4.3 28.0 1.0
N7 L:G97 4.3 14.4 1.0
C8 L:G96 4.7 16.6 1.0
O L:HOH206 4.8 26.4 1.0
O4 L:U95 4.9 17.4 1.0
C6 L:G97 4.9 13.8 1.0
C5 L:G96 4.9 17.0 1.0
O6 L:G96 4.9 20.6 1.0
C4 L:U95 5.0 15.6 1.0

Zinc binding site 4 out of 7 in 6zpf

Go back to Zinc Binding Sites List in 6zpf
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:31.1
occ:0.60
 O L:HOH225 2.1 20.6 1.0
O L:HOH244 2.1 41.1 1.0
OP1 L:U95 4.0 15.8 1.0
OP2 L:U95 4.3 15.3 1.0
OP1 L:C94 4.4 16.4 1.0
P L:U95 4.6 14.4 1.0

Zinc binding site 5 out of 7 in 6zpf

Go back to Zinc Binding Sites List in 6zpf
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:19.5
occ:0.60
 O M:HOH217 2.0 19.7 1.0
O M:HOH226 2.0 20.4 1.0
O M:HOH246 2.1 22.1 1.0
O M:HOH223 2.1 26.2 1.0
O M:HOH222 2.1 17.8 1.0
N7 M:0G82 2.1 12.1 1.0
C8 M:0G82 3.0 12.3 1.0
C5 M:0G82 3.2 13.4 1.0
O6 M:0G82 3.6 17.1 1.0
C6 M:0G82 3.8 15.2 1.0
O M:HOH225 3.9 20.2 1.0
OP1 M:0G82 3.9 13.7 1.0
O M:HOH236 4.0 27.7 1.0
O N:HOH231 4.1 19.2 1.0
N9 M:0G82 4.3 12.5 1.0
C4 M:0G82 4.3 13.9 1.0
N7 M:0G81 4.4 18.5 1.0
O M:HOH249 4.4 29.6 1.0
O M:HOH244 4.5 27.6 1.0
O6 M:0G83 4.5 14.8 1.0
O M:HOH248 4.6 39.6 1.0
C8 M:0G81 4.7 16.9 1.0
N7 M:0G83 4.7 12.5 1.0
OP1 M:0G81 4.7 21.1 1.0
C5 M:0G81 4.8 16.7 1.0
O5' M:0G82 4.9 13.0 1.0

Zinc binding site 6 out of 7 in 6zpf

Go back to Zinc Binding Sites List in 6zpf
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:28.1
occ:0.70
 O M:HOH247 1.5 20.3 1.0
O M:HOH213 2.0 20.0 1.0
O M:HOH233 2.0 28.7 1.0
O M:HOH203 2.3 30.5 1.0
N7 M:0G85 3.7 15.7 1.0
O M:HOH228 3.8 36.6 1.0
O M:HOH230 3.8 21.7 1.0
O6 M:0G86 4.0 13.3 1.0
O6 M:0G85 4.2 16.9 1.0
O M:HOH240 4.3 31.0 1.0
N7 M:0G86 4.4 13.8 1.0
C5 M:0G85 4.5 13.8 1.0
C8 M:0G85 4.6 13.1 1.0
C6 M:0G85 4.7 15.6 1.0
C6 M:0G86 4.8 12.9 1.0
OP1 M:0G85 5.0 17.9 1.0

Zinc binding site 7 out of 7 in 6zpf

Go back to Zinc Binding Sites List in 6zpf
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:23.8
occ:0.70
 O L:HOH245 2.0 26.8 1.0
O N:HOH235 2.0 27.1 1.0
O N:HOH242 2.0 23.1 1.0
O L:HOH247 2.0 25.1 1.0
O N:HOH216 2.1 19.7 1.0
O N:HOH236 2.3 30.0 1.0
O L:HOH232 3.5 36.1 1.0
O N:HOH218 4.1 30.7 1.0
N7 N:0G96 4.1 16.9 1.0
O6 N:0G97 4.3 16.8 1.0
N7 N:0G97 4.3 14.9 1.0
O L:HOH246 4.3 36.4 1.0
O K:HOH241 4.3 30.7 1.0
O2 L:C90 4.8 18.0 1.0
C5 N:0U95 4.8 16.5 1.0
O4 N:0U95 4.8 19.5 1.0
C8 N:0G96 4.8 16.4 1.0
C4 N:0U95 4.8 16.0 1.0
O N:HOH205 4.9 31.7 1.0
OP1 N:0G96 4.9 22.5 1.0

Reference:

W.Rypniewski, A.Kiliszek, L.Blaszczyk, M.Bejger. Racemic Compound of Rna Duplexes. To Be Published.
Page generated: Tue Oct 29 15:52:49 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy