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Arsenic in PDB 1yhc: Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate

Protein crystallography data

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate, PDB code: 1yhc was solved by M.Hernick, H.A.Gennadios, D.A.Whittington, K.M.Rusche, D.W.Christianson, C.A.Fierke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 101.279, 101.279, 122.745, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 21

Other elements in 1yhc:

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 5 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate (pdb code 1yhc). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate, PDB code: 1yhc:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 1yhc

Go back to Arsenic Binding Sites List in 1yhc
Arsenic binding site 1 out of 2 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As401

b:22.8
occ:1.00
AS A:CAC401 0.0 22.8 1.0
O1 A:CAC401 1.6 16.1 1.0
O2 A:CAC401 1.6 17.4 1.0
C2 A:CAC401 1.9 19.8 1.0
C1 A:CAC401 1.9 19.4 1.0
ZN A:ZN601 3.1 14.5 1.0
OE2 A:GLU78 3.7 15.0 1.0
O A:HIS58 3.9 16.7 1.0
OG1 A:THR191 4.0 15.7 1.0
O A:HOH841 4.0 15.3 1.0
NE2 A:HIS265 4.1 16.4 1.0
NE2 A:HIS79 4.1 12.7 1.0
CG2 A:THR191 4.1 16.6 1.0
OD2 A:ASP242 4.2 14.8 1.0
OD1 A:ASP242 4.4 16.0 1.0
CE1 A:HIS79 4.6 13.8 1.0
NE2 A:HIS238 4.6 10.4 1.0
CB A:THR191 4.6 16.7 1.0
CD A:GLU78 4.7 14.9 1.0
C4 A:PAM802 4.7 41.0 0.5
CG A:ASP242 4.7 17.0 1.0
C A:HIS58 4.8 17.4 1.0
O4 A:SO4404 4.8 53.0 1.0
CG A:GLU78 4.8 14.1 1.0
CD2 A:HIS265 4.9 14.4 1.0
C6 A:PAM802 5.0 39.2 0.5

Arsenic binding site 2 out of 2 in 1yhc

Go back to Arsenic Binding Sites List in 1yhc
Arsenic binding site 2 out of 2 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As402

b:24.3
occ:1.00
AS B:CAC402 0.0 24.3 1.0
O2 B:CAC402 1.6 19.9 1.0
O1 B:CAC402 1.6 16.7 1.0
C2 B:CAC402 1.9 19.1 1.0
C1 B:CAC402 1.9 19.5 1.0
ZN B:ZN602 3.1 13.8 1.0
OE2 B:GLU78 3.6 16.8 1.0
O B:HIS58 4.0 17.0 1.0
OG1 B:THR191 4.0 19.5 1.0
NE2 B:HIS79 4.0 9.7 1.0
NE2 B:HIS265 4.1 17.7 1.0
O B:HOH827 4.1 25.3 1.0
OD2 B:ASP242 4.2 18.5 1.0
CG2 B:THR191 4.2 16.2 1.0
CE1 B:HIS79 4.4 10.7 1.0
OD1 B:ASP242 4.5 14.3 1.0
NE2 B:HIS238 4.6 10.9 1.0
CD B:GLU78 4.6 14.2 1.0
CG B:ASP242 4.7 17.6 1.0
CB B:THR191 4.7 16.6 1.0
CG B:GLU78 4.8 13.6 1.0
C B:HIS58 4.8 17.1 1.0
CD2 B:HIS265 4.9 16.3 1.0
C4 B:PAM801 4.9 36.9 0.5
O3 B:SO4403 4.9 45.2 1.0

Reference:

M.Hernick, H.A.Gennadios, D.A.Whittington, K.M.Rusche, D.W.Christianson, C.A.Fierke. Udp-3-O-((R)-3-Hydroxymyristoyl)-N-Acetylglucosamine Deacetylase Functions Through A General Acid-Base Catalyst Pair Mechanism J.Biol.Chem. V. 280 16969 2005.
ISSN: ISSN 0021-9258
PubMed: 15705580
DOI: 10.1074/JBC.M413560200
Page generated: Tue Oct 27 16:47:45 2020

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