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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate, PDB code: 1yhc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1yhc

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Zinc binding site 1 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate


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 Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:14.5
occ:1.00
NE2 A:HIS238 2.0 10.4 1.0
NE2 A:HIS79 2.1 12.7 1.0
O2 A:CAC401 2.1 17.4 1.0
OD1 A:ASP242 2.1 16.0 1.0
CG A:ASP242 2.8 17.0 1.0
OD2 A:ASP242 2.8 14.8 1.0
O1 A:CAC401 2.9 16.1 1.0
CE1 A:HIS238 2.9 11.8 1.0
CD2 A:HIS79 3.1 11.3 1.0
CE1 A:HIS79 3.1 13.8 1.0
CD2 A:HIS238 3.1 11.3 1.0
AS A:CAC401 3.1 22.8 1.0
OG1 A:THR191 3.7 15.7 1.0
ND1 A:HIS238 4.1 10.6 1.0
CG A:HIS238 4.2 12.6 1.0
ND1 A:HIS79 4.2 12.0 1.0
CG A:HIS79 4.2 12.4 1.0
CB A:ASP242 4.3 14.0 1.0
CG A:GLU78 4.4 14.1 1.0
C1 A:CAC401 4.4 19.4 1.0
O A:HOH841 4.4 15.3 1.0
C2 A:CAC401 4.5 19.8 1.0
CB A:THR191 4.7 16.7 1.0
CA A:THR191 4.7 14.4 1.0
CA A:ASP242 4.8 13.8 1.0
OE2 A:GLU78 4.8 15.0 1.0
NE2 A:HIS265 4.9 16.4 1.0
O A:HIS238 4.9 13.2 1.0

Zinc binding site 2 out of 5 in 1yhc

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Zinc binding site 2 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate


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 Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:18.4
occ:1.00
OE1 A:GLU126 2.0 15.7 1.0
N A:GLY2 2.3 18.0 1.0
CD A:GLU126 2.7 19.2 1.0
OE2 A:GLU126 2.7 19.5 1.0
CA A:GLY2 3.0 16.2 1.0
C A:GLY2 3.3 16.6 1.0
O A:GLY2 3.4 17.5 1.0
CG A:GLU126 4.2 18.9 1.0
N A:LEU3 4.2 15.6 1.0
O A:HOH870 4.7 26.0 1.0
CB A:GLU126 4.8 20.2 1.0
CD2 A:LEU3 4.8 15.4 1.0

Zinc binding site 3 out of 5 in 1yhc

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Zinc binding site 3 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate


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 Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:26.5
occ:1.00
CL A:CL336 2.0 43.5 1.0
NE2 A:HIS200 2.1 23.1 1.0
NE2 A:HIS58 2.1 22.2 1.0
CL A:CL334 2.1 24.8 1.0
CD2 A:HIS58 3.0 21.7 1.0
CD2 A:HIS200 3.1 21.1 1.0
CE1 A:HIS200 3.1 21.8 1.0
CE1 A:HIS58 3.1 21.7 1.0
CG A:HIS58 4.2 20.5 1.0
ND1 A:HIS58 4.2 20.8 1.0
ND1 A:HIS200 4.2 20.4 1.0
CG A:HIS200 4.2 21.5 1.0
CG2 A:VAL204 4.6 23.2 1.0
CB A:ASN57 4.8 25.9 1.0
CG1 A:VAL204 4.9 21.0 1.0

Zinc binding site 4 out of 5 in 1yhc

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Zinc binding site 4 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:13.8
occ:1.00
NE2 B:HIS79 2.0 9.7 1.0
NE2 B:HIS238 2.0 10.9 1.0
O2 B:CAC402 2.1 19.9 1.0
OD1 B:ASP242 2.1 14.3 1.0
OD2 B:ASP242 2.7 18.5 1.0
CG B:ASP242 2.7 17.6 1.0
O1 B:CAC402 2.9 16.7 1.0
CE1 B:HIS79 3.0 10.7 1.0
CE1 B:HIS238 3.0 10.4 1.0
CD2 B:HIS79 3.0 10.6 1.0
CD2 B:HIS238 3.0 10.3 1.0
AS B:CAC402 3.1 24.3 1.0
OG1 B:THR191 3.7 19.5 1.0
ND1 B:HIS79 4.1 9.4 1.0
ND1 B:HIS238 4.1 11.4 1.0
CG B:HIS79 4.1 10.1 1.0
CG B:HIS238 4.2 11.9 1.0
CB B:ASP242 4.2 14.6 1.0
C2 B:CAC402 4.2 19.1 1.0
CG B:GLU78 4.3 13.6 1.0
C1 B:CAC402 4.5 19.5 1.0
O B:HOH827 4.6 25.3 1.0
CB B:THR191 4.7 16.6 1.0
OE2 B:GLU78 4.8 16.8 1.0
CA B:THR191 4.8 15.3 1.0
CA B:ASP242 4.8 15.1 1.0
NE2 B:HIS265 4.9 17.7 1.0
O B:HIS238 5.0 14.3 1.0

Zinc binding site 5 out of 5 in 1yhc

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Zinc binding site 5 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Aquifex Aeolicus Lpxc Deacetylase Complexed with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn607

b:30.1
occ:1.00
NE2 B:HIS58 2.1 19.4 1.0
NE2 B:HIS200 2.1 25.6 1.0
CL B:CL335 2.4 59.3 1.0
CD2 B:HIS200 3.0 24.4 1.0
CD2 B:HIS58 3.0 14.7 1.0
CE1 B:HIS58 3.1 17.7 1.0
CE1 B:HIS200 3.2 24.3 1.0
CG B:HIS58 4.2 17.9 1.0
ND1 B:HIS58 4.2 18.8 1.0
CG B:HIS200 4.2 24.8 1.0
ND1 B:HIS200 4.3 24.1 1.0
CG2 B:VAL204 4.6 20.4 1.0
CG1 B:VAL204 4.9 19.0 1.0
CB B:ASN57 4.9 22.4 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 Sep 26 00:33:11 2020
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