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Chlorine in PDB 1yh8: Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate

Protein crystallography data

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate, PDB code: 1yh8 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) 50.00 / 2.70
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 101.610, 101.610, 124.180, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 23.9

Other elements in 1yh8:

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

Zinc (Zn) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate (pdb code 1yh8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate, PDB code: 1yh8:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 1yh8

Go back to Chlorine Binding Sites List in 1yh8
Chlorine binding site 1 out of 3 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:38.2
occ:1.00
O A:SER107 2.6 21.3 1.0
O A:ILE103 2.8 17.0 1.0
ND1 A:HIS79 2.9 19.8 1.0
O A:HOH804 3.1 9.3 1.0
C A:SER107 3.6 21.6 1.0
CB A:HIS79 3.7 17.8 1.0
CG A:HIS79 3.7 18.5 1.0
N A:SER107 3.7 23.0 1.0
C A:GLY106 3.7 22.5 1.0
C A:ILE103 3.8 18.6 1.0
CD1 A:ILE103 3.8 14.8 1.0
CE1 A:HIS79 3.9 18.1 1.0
CA A:GLY106 4.1 22.4 1.0
O A:GLY106 4.1 21.0 1.0
CA A:SER107 4.1 22.8 1.0
N A:GLY106 4.2 23.3 1.0
CA A:ILE103 4.2 17.9 1.0
CE1 A:PHE111 4.4 25.1 1.0
CG1 A:ILE103 4.6 17.0 1.0
O A:PRO102 4.6 18.9 1.0
N A:GLY108 4.6 20.9 1.0
CD1 A:PHE111 4.8 25.5 1.0
CB A:LEU104 4.8 21.0 1.0
CD2 A:HIS79 4.9 18.6 1.0
CA A:GLY108 4.9 22.4 1.0
N A:LEU104 4.9 20.3 1.0
NE2 A:HIS79 5.0 18.5 1.0

Chlorine binding site 2 out of 3 in 1yh8

Go back to Chlorine Binding Sites List in 1yh8
Chlorine binding site 2 out of 3 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:46.5
occ:1.00
N B:LEU104 2.6 18.8 1.0
O B:VAL16 3.0 21.6 1.0
N B:VAL16 3.1 24.0 1.0
CA B:LEU104 3.2 20.4 1.0
CA B:GLY15 3.4 23.8 1.0
N B:ILE103 3.4 16.9 1.0
C B:GLY15 3.5 24.1 1.0
CD2 B:LEU104 3.7 19.5 1.0
C B:ILE103 3.8 17.5 1.0
CG2 B:ILE103 3.8 13.2 1.0
CB B:PRO102 3.8 19.4 1.0
C B:PRO102 3.9 17.8 1.0
C B:VAL16 3.9 21.8 1.0
CA B:PRO102 4.0 18.6 1.0
CG1 B:VAL16 4.0 19.8 1.0
CA B:ILE103 4.0 16.7 1.0
CA B:VAL16 4.1 22.2 1.0
CG B:LEU104 4.2 21.4 1.0
O B:LEU104 4.2 23.6 1.0
C B:LEU104 4.2 22.2 1.0
CB B:LEU104 4.2 20.6 1.0
N B:GLY15 4.4 26.8 1.0
O B:GLU14 4.5 28.1 1.0
O B:GLY15 4.5 23.7 1.0
CB B:ILE103 4.6 15.4 1.0
CB B:VAL16 4.7 22.5 1.0
O B:PRO102 4.7 19.1 1.0
C B:GLU14 4.8 27.6 1.0
O B:ILE103 4.9 17.0 1.0

Chlorine binding site 3 out of 3 in 1yh8

Go back to Chlorine Binding Sites List in 1yh8
Chlorine binding site 3 out of 3 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl603

b:38.3
occ:1.00
ZN B:ZN507 2.0 38.4 1.0
NE2 B:HIS58 2.8 26.8 1.0
NE2 B:HIS200 2.8 33.3 1.0
CE1 B:HIS58 3.3 26.5 1.0
O B:HOH863 3.5 13.5 1.0
CD2 B:HIS200 3.6 31.1 1.0
CE1 B:HIS200 3.8 31.7 1.0
CD2 B:HIS58 3.9 25.1 1.0
ND1 B:HIS58 4.5 24.8 1.0
CB B:ASN57 4.7 31.2 1.0
CG B:HIS200 4.8 30.5 1.0
CG B:HIS58 4.8 25.2 1.0
ND1 B:HIS200 4.8 30.9 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: Sat Dec 12 08:55:26 2020

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