Atomistry » Zinc » PDB 5sli-5svb » 5smf
Atomistry »
  Zinc »
    PDB 5sli-5svb »
      5smf »

Zinc in PDB 5smf: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867, PDB code: 5smf was solved by N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.30 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.145, 67.846, 138.596, 90, 90, 90
R / Rfree (%) 27 / 31.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867 (pdb code 5smf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867, PDB code: 5smf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5smf

Go back to Zinc Binding Sites List in 5smf
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:52.7
occ:1.00
 ND1 D:HIS264 2.1 61.5 1.0
NE2 D:HIS257 2.1 59.5 1.0
SG D:CYS279 2.3 49.6 1.0
SG D:CYS261 2.4 58.3 1.0
CE1 D:HIS264 3.0 61.6 1.0
CB D:CYS261 3.0 58.3 1.0
CD2 D:HIS257 3.1 58.0 1.0
CE1 D:HIS257 3.1 59.3 1.0
CG D:HIS264 3.1 60.7 1.0
CB D:CYS279 3.2 47.2 1.0
CB D:HIS264 3.5 62.3 1.0
NE2 D:HIS264 4.1 61.1 1.0
CG D:HIS257 4.1 57.2 1.0
ND1 D:HIS257 4.1 58.9 1.0
CD2 D:HIS264 4.2 60.4 1.0
N D:HIS264 4.3 63.7 1.0
CA D:CYS261 4.5 59.2 1.0
N D:ASP415 4.5 51.5 1.0
CA D:HIS264 4.5 64.1 1.0
CA D:CYS279 4.6 47.3 1.0
O D:HOH756 4.8 59.9 1.0
CA D:CYS414 4.8 49.7 0.4
SG D:CYS414 4.9 52.2 0.6
CA D:CYS414 4.9 50.0 0.6
C D:CYS261 4.9 59.6 1.0

Zinc binding site 2 out of 3 in 5smf

Go back to Zinc Binding Sites List in 5smf
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:59.5
occ:1.00
 SG D:CYS484 2.3 57.9 1.0
ND1 D:HIS487 2.3 55.0 1.0
SG D:CYS477 2.4 58.7 1.0
SG D:CYS452 2.5 65.2 1.0
CB D:CYS477 3.2 55.9 1.0
CB D:CYS484 3.2 56.8 1.0
CG D:HIS487 3.3 53.3 1.0
CB D:CYS452 3.3 70.7 1.0
CE1 D:HIS487 3.4 55.0 1.0
CB D:HIS487 3.4 52.2 1.0
CA D:CYS452 3.9 72.6 1.0
N D:CYS484 4.0 56.7 1.0
CA D:CYS484 4.2 56.5 1.0
N D:HIS487 4.4 54.2 1.0
CA D:CYS477 4.4 55.6 1.0
CD2 D:HIS487 4.4 54.6 1.0
N D:CYS477 4.5 55.8 1.0
NE2 D:HIS487 4.5 55.5 1.0
CA D:HIS487 4.5 53.2 1.0
N D:CYS452 4.7 71.0 1.0
CB D:THR475 4.8 53.1 1.0
OG1 D:THR475 4.8 53.9 1.0
C D:CYS484 4.9 56.9 1.0
O D:CYS484 4.9 57.1 1.0

Zinc binding site 3 out of 3 in 5smf

Go back to Zinc Binding Sites List in 5smf
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:68.2
occ:1.00
 ND1 D:HIS229 1.9 68.2 1.0
SG D:CYS207 2.3 78.3 1.0
SG D:CYS226 2.4 69.2 1.0
SG D:CYS210 2.4 74.7 1.0
CE1 D:HIS229 2.8 68.6 1.0
CB D:CYS207 3.1 77.7 1.0
CG D:HIS229 3.1 66.0 1.0
CB D:CYS210 3.4 72.8 1.0
CB D:CYS226 3.5 61.9 1.0
CB D:HIS229 3.6 63.8 1.0
N D:CYS210 3.8 73.8 1.0
NE2 D:HIS229 3.9 68.2 1.0
N D:CYS226 4.0 60.6 1.0
CA D:CYS210 4.1 73.0 1.0
CD2 D:HIS229 4.1 67.0 1.0
CA D:CYS226 4.4 59.7 1.0
C D:LEU209 4.4 75.0 1.0
N D:HIS229 4.4 61.5 1.0
NH1 D:ARG212 4.5 75.8 1.0
CA D:CYS207 4.5 78.2 1.0
CB D:LEU209 4.6 75.9 1.0
C D:CYS210 4.6 72.4 1.0
CA D:HIS229 4.7 62.4 1.0
CB D:ARG212 4.7 68.8 1.0
N D:LEU209 4.8 76.8 1.0
CD D:ARG212 4.8 73.3 1.0
CA D:LEU209 4.8 75.8 1.0
CB D:HIS228 4.9 60.4 1.0
O D:CYS210 5.0 72.7 1.0
O D:LEU209 5.0 75.3 1.0
C D:CYS226 5.0 57.8 1.0

Reference:

N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman. Pandda Analysis Group Deposition To Be Published.
Page generated: Mon Oct 28 08:02:58 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy