Zinc in PDB 6u7f: Hcov-229E Rbd Class IV in Complex with Human Apn

Enzymatic activity of Hcov-229E Rbd Class IV in Complex with Human Apn

All present enzymatic activity of Hcov-229E Rbd Class IV in Complex with Human Apn:
3.4.11.2;

Protein crystallography data

The structure of Hcov-229E Rbd Class IV in Complex with Human Apn, PDB code: 6u7f was solved by A.C.A.Tomlinson, Z.Li, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.38 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.158, 98.572, 147.778, 90.00, 104.42, 90.00
R / Rfree (%) 19 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Hcov-229E Rbd Class IV in Complex with Human Apn (pdb code 6u7f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hcov-229E Rbd Class IV in Complex with Human Apn, PDB code: 6u7f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6u7f

Go back to Zinc Binding Sites List in 6u7f
Zinc binding site 1 out of 2 in the Hcov-229E Rbd Class IV in Complex with Human Apn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hcov-229E Rbd Class IV in Complex with Human Apn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5001

b:43.7
occ:1.00
OE1 A:GLU411 1.8 46.3 1.0
NE2 A:HIS388 2.0 39.2 1.0
NE2 A:HIS392 2.1 43.3 1.0
O A:HOH5220 2.4 35.9 1.0
CD A:GLU411 2.8 45.5 1.0
CE1 A:HIS388 2.9 37.5 1.0
CD2 A:HIS388 3.0 36.5 1.0
CD2 A:HIS392 3.0 43.3 1.0
OE2 A:GLU411 3.2 47.4 1.0
CE1 A:HIS392 3.2 42.3 1.0
OH A:TYR477 3.7 39.5 1.0
CE2 A:TYR477 3.9 32.3 1.0
ND1 A:HIS388 4.0 37.6 1.0
CG A:HIS388 4.1 35.0 1.0
CZ A:TYR477 4.1 35.6 1.0
CG A:GLU411 4.2 43.8 1.0
CG A:HIS392 4.2 47.0 1.0
ND1 A:HIS392 4.3 45.8 1.0
CB A:ALA414 4.4 26.8 1.0
OE1 A:GLU355 4.4 48.8 1.0
CA A:GLU411 4.6 42.0 1.0
CB A:GLU411 4.6 40.7 1.0
OE1 A:GLU389 4.7 53.5 1.0
OE2 A:GLU389 4.8 52.8 1.0
CD2 A:TYR477 4.9 32.6 1.0

Zinc binding site 2 out of 2 in 6u7f

Go back to Zinc Binding Sites List in 6u7f
Zinc binding site 2 out of 2 in the Hcov-229E Rbd Class IV in Complex with Human Apn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hcov-229E Rbd Class IV in Complex with Human Apn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5001

b:41.6
occ:1.00
NE2 B:HIS392 1.8 47.2 1.0
OE2 B:GLU411 1.9 38.3 1.0
NE2 B:HIS388 2.1 39.1 1.0
O B:HOH5176 2.4 33.2 1.0
CD B:GLU411 2.6 38.1 1.0
OE1 B:GLU411 2.7 40.4 1.0
CE1 B:HIS392 2.8 43.9 1.0
CD2 B:HIS392 2.8 45.1 1.0
CE1 B:HIS388 3.0 40.6 1.0
CD2 B:HIS388 3.1 39.0 1.0
ND1 B:HIS392 3.9 45.0 1.0
CG B:HIS392 4.0 45.4 1.0
CG B:GLU411 4.1 36.3 1.0
ND1 B:HIS388 4.1 41.8 1.0
CG B:HIS388 4.2 40.4 1.0
OE1 B:GLU355 4.3 56.0 1.0
CB B:ALA414 4.4 27.5 1.0
CE2 B:TYR477 4.4 30.7 1.0
O B:HOH5148 4.5 54.9 1.0
OH B:TYR477 4.5 37.9 1.0
CA B:GLU411 4.6 37.6 1.0
CB B:GLU411 4.6 38.5 1.0
CD B:GLU355 4.6 53.7 1.0
OE2 B:GLU355 4.6 56.4 1.0
OE2 B:GLU389 4.7 48.8 1.0
OE1 B:GLU389 4.7 56.1 1.0
CZ B:TYR477 4.9 33.8 1.0
O B:HOH5180 4.9 54.6 1.0

Reference:

Z.Li, A.C.A.Tomlinson, A.H.M.Wong, D.Zhou, M.Desforges, P.J.Talbot, S.Benlekbir, J.L.Rubinstein, J.M.Rini. The Human Coronavirus Hcov-229E S-Protein Structure and Receptor Binding. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31650956
DOI: 10.7554/ELIFE.51230
Page generated: Wed Dec 16 12:57:46 2020

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