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Zinc in PDB 2go4: Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514

Protein crystallography data

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514, PDB code: 2go4 was solved by H.A.Gennadios, D.A.Whittington, X.Li, C.A.Fierke, D.W.Christianson, 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 (°) 100.729, 100.729, 121.299, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 24.1

Other elements in 2go4:

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514 (pdb code 2go4). 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 Complexed with Tu-514, PDB code: 2go4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2go4

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Zinc binding site 1 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:41.6
occ:1.00
OXH A:TUX901 2.0 54.3 1.0
NE2 A:HIS238 2.0 38.7 1.0
NE2 A:HIS79 2.1 43.3 1.0
OD1 A:ASP242 2.2 45.7 1.0
OYH A:TUX901 2.2 55.5 1.0
NXH A:TUX901 2.8 54.0 1.0
OD2 A:ASP242 2.8 45.5 1.0
CG A:ASP242 2.8 46.1 1.0
CYH A:TUX901 2.8 56.9 1.0
CE1 A:HIS238 2.9 38.5 1.0
CE1 A:HIS79 3.0 41.9 1.0
CD2 A:HIS238 3.1 38.8 1.0
CD2 A:HIS79 3.1 44.7 1.0
OG1 A:THR191 3.8 55.8 1.0
ND1 A:HIS238 4.0 39.0 1.0
ND1 A:HIS79 4.1 45.0 1.0
CG A:HIS238 4.1 40.0 1.0
CG A:HIS79 4.2 43.4 1.0
CB A:ASP242 4.3 46.1 1.0
CZH A:TUX901 4.3 60.5 1.0
OE2 A:GLU78 4.4 52.0 1.0
CG A:GLU78 4.5 51.7 1.0
CB A:THR191 4.7 52.2 1.0
CG2 A:THR191 4.8 54.0 1.0
CA A:THR191 4.8 51.3 1.0
NE2 A:HIS265 4.9 51.1 1.0
O A:HIS238 4.9 39.5 1.0
CA A:ASP242 5.0 43.3 1.0
CD A:GLU78 5.0 53.9 1.0

Zinc binding site 2 out of 5 in 2go4

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Zinc binding site 2 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:51.7
occ:0.80
CL A:CL401 2.0 55.1 1.0
NE2 A:HIS58 2.2 56.2 1.0
O A:HOH925 2.3 36.8 1.0
NE2 A:HIS200 2.3 63.0 1.0
CD2 A:HIS58 3.0 55.0 1.0
CE1 A:HIS200 3.0 62.8 1.0
CE1 A:HIS58 3.3 56.9 1.0
CD2 A:HIS200 3.5 62.3 1.0
CG A:HIS58 4.2 55.2 1.0
ND1 A:HIS200 4.2 63.1 1.0
ND1 A:HIS58 4.3 56.1 1.0
CG2 A:VAL204 4.4 59.0 1.0
CG A:HIS200 4.5 62.2 1.0
CB A:ASN57 4.6 60.9 1.0
CG1 A:VAL204 4.7 58.7 1.0
OD1 A:ASN57 5.0 66.7 1.0

Zinc binding site 3 out of 5 in 2go4

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Zinc binding site 3 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:52.5
occ:1.00
N A:GLY2 2.1 61.5 1.0
OE1 A:GLU126 2.1 73.4 1.0
OE2 A:GLU126 2.4 72.3 1.0
CD A:GLU126 2.5 73.4 1.0
CA A:GLY2 3.2 59.4 1.0
C A:GLY2 3.5 59.9 1.0
O A:GLY2 3.5 58.0 1.0
CG A:GLU126 4.0 73.5 1.0
N A:LEU3 4.4 61.5 1.0
CB A:GLU126 4.8 72.5 1.0
CD2 A:LEU3 5.0 64.5 1.0

Zinc binding site 4 out of 5 in 2go4

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Zinc binding site 4 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:48.2
occ:1.00
OXH B:TUX902 1.9 56.0 1.0
OD1 B:ASP242 2.0 46.5 1.0
OYH B:TUX902 2.1 56.8 1.0
NE2 B:HIS79 2.1 41.7 1.0
NE2 B:HIS238 2.1 41.3 1.0
NXH B:TUX902 2.7 57.1 1.0
CG B:ASP242 2.7 46.7 1.0
OD2 B:ASP242 2.7 49.5 1.0
CYH B:TUX902 2.7 60.2 1.0
CE1 B:HIS238 3.0 43.3 1.0
CE1 B:HIS79 3.1 44.0 1.0
CD2 B:HIS79 3.1 43.5 1.0
CD2 B:HIS238 3.1 43.1 1.0
OG1 B:THR191 4.0 54.0 1.0
ND1 B:HIS238 4.1 43.5 1.0
CB B:ASP242 4.1 44.8 1.0
ND1 B:HIS79 4.2 45.0 1.0
CZH B:TUX902 4.2 63.0 1.0
CG B:HIS79 4.2 44.7 1.0
CG B:HIS238 4.2 43.6 1.0
OE2 B:GLU78 4.3 55.8 1.0
CG B:GLU78 4.3 51.8 1.0
NE2 B:HIS265 4.7 52.2 1.0
CA B:ASP242 4.8 44.9 1.0
CE1 B:HIS265 4.8 53.7 1.0
CD B:GLU78 4.9 54.2 1.0
O B:HIS238 4.9 43.0 1.0
CB B:THR191 4.9 51.9 1.0
C2G B:TUX902 4.9 66.5 1.0

Zinc binding site 5 out of 5 in 2go4

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Zinc binding site 5 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Tu-514


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 Complexed with Tu-514 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:64.0
occ:0.80
NE2 B:HIS58 2.2 58.9 1.0
NE2 B:HIS200 2.2 63.9 1.0
CE1 B:HIS200 3.0 63.0 1.0
CE1 B:HIS58 3.1 58.0 1.0
CD2 B:HIS58 3.2 57.6 1.0
CD2 B:HIS200 3.4 62.9 1.0
ND1 B:HIS58 4.2 56.5 1.0
ND1 B:HIS200 4.2 62.4 1.0
CG B:HIS58 4.3 56.0 1.0
CG B:HIS200 4.4 61.7 1.0
CB B:ASN57 4.8 61.9 1.0
CG2 B:VAL204 4.9 57.8 1.0

Reference:

H.A.Gennadios, D.A.Whittington, X.Li, C.A.Fierke, D.W.Christianson. Mechanistic Inferences From the Binding of Ligands to Lpxc, A Metal-Dependent Deacetylase Biochemistry V. 45 7940 2006.
ISSN: ISSN 0006-2960
PubMed: 16800620
DOI: 10.1021/BI060823M
Page generated: Wed Dec 16 03:29:34 2020

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