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Mercury in PDB 3fw0: Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate)

Enzymatic activity of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate)

All present enzymatic activity of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate):
4.3.2.5;

Protein crystallography data

The structure of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate), PDB code: 3fw0 was solved by E.E.Chufan, M.De, B.A.Eipper, R.E.Mains, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.34 / 2.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.930, 75.080, 97.026, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26

Other elements in 3fw0:

The structure of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate) (pdb code 3fw0). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate), PDB code: 3fw0:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 3fw0

Go back to Mercury Binding Sites List in 3fw0
Mercury binding site 1 out of 2 in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg821

b:69.0
occ:1.00
 NE2 A:HIS786 2.3 52.6 1.0
NE2 A:HIS585 2.3 52.8 1.0
NE2 A:HIS690 2.4 51.7 1.0
O2 A:HH31 2.4 61.2 1.0
O4 A:HH31 3.0 55.5 1.0
CD2 A:HIS585 3.1 48.3 1.0
CD2 A:HIS786 3.2 48.5 1.0
CE1 A:HIS690 3.3 47.9 1.0
CE1 A:HIS786 3.3 49.3 1.0
OH A:TYR654 3.3 39.6 1.0
CE1 A:HIS585 3.3 49.2 1.0
CD2 A:HIS690 3.4 46.5 1.0
CE1 A:TYR654 3.4 38.6 1.0
C9 A:HH31 3.5 58.5 1.0
C10 A:HH31 3.6 57.3 1.0
CZ A:TYR654 3.8 39.6 1.0
CG A:HIS585 4.3 47.4 1.0
ND1 A:HIS585 4.3 48.3 1.0
CG A:HIS786 4.4 48.4 1.0
ND1 A:HIS786 4.4 49.8 1.0
ND1 A:HIS690 4.4 46.9 1.0
CG A:HIS690 4.5 45.6 1.0
N1 A:HH31 4.5 59.2 1.0
CD1 A:TYR654 4.6 39.5 1.0
NH2 A:ARG533 4.7 37.1 1.0
O3 A:HH31 4.7 57.0 1.0
CZ3 A:TRP538 4.8 40.9 1.0
CE A:MET784 4.9 47.1 1.0

Mercury binding site 2 out of 2 in 3fw0

Go back to Mercury Binding Sites List in 3fw0
Mercury binding site 2 out of 2 in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) Bound to Alpha-Hydroxyhippuric Acid (Non- Peptidic Substrate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg822

b:62.4
occ:0.35
 OD2 A:ASP498 2.4 56.0 1.0
NE2 A:HIS492 2.5 65.8 1.0
OD1 A:ASP498 3.0 53.5 1.0
CG A:ASP498 3.0 53.3 1.0
CE1 A:HIS492 3.2 65.8 1.0
CD2 A:HIS492 3.6 65.8 1.0
NE2 A:HIS495 3.6 65.1 1.0
CE1 A:HIS495 3.9 64.9 1.0
CD2 A:HIS495 4.0 64.8 1.0
O A:HIS493 4.1 65.2 1.0
ND1 A:HIS492 4.3 66.1 1.0
ND1 A:HIS495 4.4 64.7 1.0
CG A:HIS495 4.4 64.3 1.0
O A:HIS496 4.4 59.6 1.0
CB A:ASP498 4.5 53.1 1.0
CG A:HIS492 4.6 65.8 1.0
O A:HIS494 4.9 64.3 1.0

Reference:

E.E.Chufan, M.De, B.A.Eipper, R.E.Mains, L.M.Amzel. Amidation of Bioactive Peptides: the Structure of the Lyase Domain of the Amidating Enzyme. Structure V. 17 965 2009.
ISSN: ISSN 0969-2126
PubMed: 19604476
DOI: 10.1016/J.STR.2009.05.008
Page generated: Sun Dec 13 19:09:23 2020

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