Atomistry » Zinc » PDB 6agb-6av0 » 6atk
Atomistry »
  Zinc »
    PDB 6agb-6av0 »
      6atk »

Zinc in PDB 6atk: Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N

Enzymatic activity of Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N

All present enzymatic activity of Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N, PDB code: 6atk was solved by A.H.Wong, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.80 / 3.51
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 153.820, 153.820, 322.120, 90.00, 90.00, 120.00
R / Rfree (%) 24.4 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N (pdb code 6atk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N, PDB code: 6atk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6atk

Go back to Zinc Binding Sites List in 6atk
Zinc binding site 1 out of 3 in the Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1009

b:62.2
occ:1.00
 OE1 A:GLU411 2.0 62.8 1.0
NE2 A:HIS388 2.2 58.2 1.0
NE2 A:HIS392 2.2 60.3 1.0
CD A:GLU411 2.7 63.5 1.0
OE2 A:GLU411 2.8 64.0 1.0
CD2 A:HIS392 3.1 61.0 1.0
CD2 A:HIS388 3.1 58.8 1.0
CE1 A:HIS388 3.2 57.7 1.0
CE1 A:HIS392 3.2 60.9 1.0
OH A:TYR477 3.7 64.2 1.0
CE2 A:TYR477 3.8 63.5 1.0
OE1 A:GLU355 4.1 68.3 1.0
CZ A:TYR477 4.1 64.0 1.0
CG A:GLU411 4.1 64.0 1.0
CG A:HIS392 4.2 61.6 1.0
ND1 A:HIS392 4.3 61.4 1.0
CG A:HIS388 4.3 58.4 1.0
ND1 A:HIS388 4.3 57.9 1.0
OE2 A:GLU389 4.4 60.5 1.0
CB A:ALA414 4.6 60.3 1.0
CD A:GLU355 4.7 68.2 1.0
CB A:GLU411 4.7 63.8 1.0
OE2 A:GLU355 4.8 67.7 1.0
CD2 A:TYR477 4.8 63.5 1.0
CA A:GLU411 4.8 64.0 1.0

Zinc binding site 2 out of 3 in 6atk

Go back to Zinc Binding Sites List in 6atk
Zinc binding site 2 out of 3 in the Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1008

b:67.3
occ:1.00
 NE2 B:HIS392 2.1 73.0 1.0
OE1 B:GLU411 2.1 71.4 1.0
NE2 B:HIS388 2.2 66.2 1.0
CD B:GLU411 2.8 72.6 1.0
OE2 B:GLU411 2.8 73.1 1.0
CD2 B:HIS392 2.9 72.7 1.0
CD2 B:HIS388 3.0 65.8 1.0
CE1 B:HIS392 3.2 74.0 1.0
CE1 B:HIS388 3.3 66.8 1.0
OH B:TYR477 3.7 75.1 1.0
CE2 B:TYR477 3.9 74.3 1.0
OE1 B:GLU355 3.9 75.6 1.0
CG B:HIS392 4.1 73.3 1.0
ND1 B:HIS392 4.2 74.0 1.0
CZ B:TYR477 4.2 75.1 1.0
CG B:GLU411 4.2 73.8 1.0
CG B:HIS388 4.2 65.8 1.0
OE2 B:GLU389 4.3 68.5 1.0
ND1 B:HIS388 4.3 66.1 1.0
CB B:ALA414 4.5 69.3 1.0
CD B:GLU355 4.6 76.5 1.0
OE2 B:GLU355 4.6 77.7 1.0
CB B:GLU411 4.9 73.8 1.0
OE1 B:GLU389 4.9 71.9 1.0
CA B:GLU411 5.0 73.9 1.0
CD2 B:TYR477 5.0 74.6 1.0
CD B:GLU389 5.0 69.7 1.0

Zinc binding site 3 out of 3 in 6atk

Go back to Zinc Binding Sites List in 6atk
Zinc binding site 3 out of 3 in the Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Human Coronavirus 229E Spike Protein Receptor Binding Domain in Complex with Human Aminopeptidase N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1006

b:87.4
occ:1.00
 OE1 C:GLU411 2.0 91.3 1.0
NE2 C:HIS388 2.1 85.0 1.0
NE2 C:HIS392 2.4 89.4 1.0
CD C:GLU411 2.7 91.9 1.0
OE2 C:GLU411 2.9 92.7 1.0
CD2 C:HIS388 3.0 86.0 1.0
CE1 C:HIS388 3.1 85.0 1.0
CD2 C:HIS392 3.1 90.5 1.0
CE1 C:HIS392 3.5 90.0 1.0
CE2 C:TYR477 3.6 95.8 1.0
OH C:TYR477 3.6 96.5 1.0
CZ C:TYR477 4.0 96.0 1.0
CG C:GLU411 4.1 91.8 1.0
OE2 C:GLU389 4.2 91.0 1.0
CG C:HIS388 4.2 86.2 1.0
ND1 C:HIS388 4.2 85.2 1.0
OE1 C:GLU355 4.2 98.0 1.0
CG C:HIS392 4.4 91.4 1.0
ND1 C:HIS392 4.5 91.0 1.0
CD2 C:TYR477 4.7 95.4 1.0
CB C:GLU411 4.7 91.5 1.0
CA C:GLU411 4.9 92.3 1.0
CD C:GLU355 4.9 99.0 1.0
CB C:ALA414 4.9 87.9 1.0
CD C:GLU389 4.9 93.0 1.0
OE1 C:GLU389 4.9 94.8 1.0

Reference:

A.H.M.Wong, A.C.A.Tomlinson, D.Zhou, M.Satkunarajah, K.Chen, C.Sharon, M.Desforges, P.J.Talbot, J.M.Rini. Receptor-Binding Loops in Alphacoronavirus Adaptation and Evolution. Nat Commun V. 8 1735 2017.
ISSN: ESSN 2041-1723
PubMed: 29170370
DOI: 10.1038/S41467-017-01706-X
Page generated: Mon Oct 28 17:40:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy