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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

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