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Zinc in PDB 2go3: Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole.

Protein crystallography data

The structure of Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole., PDB code: 2go3 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) 30.00 / 2.00
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 101.234, 101.234, 122.162, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.5

Other elements in 2go3:

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

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole. (pdb code 2go3). 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 Imidazole., PDB code: 2go3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2go3

Go back to Zinc Binding Sites List in 2go3
Zinc binding site 1 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole.


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 Imidazole. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:15.9
occ:1.00
OD1 A:ASP242 2.0 14.5 1.0
NE2 A:HIS238 2.1 13.5 1.0
N1 A:IMD803 2.1 18.8 0.5
NE2 A:HIS79 2.1 12.9 1.0
O A:HOH1094 2.3 23.1 0.5
O A:HOH1095 2.3 19.9 0.5
CG A:ASP242 2.8 17.1 1.0
OD2 A:ASP242 2.8 17.6 1.0
CE1 A:HIS238 3.0 13.2 1.0
CD2 A:HIS79 3.0 11.0 1.0
C5 A:IMD803 3.0 17.2 0.5
CD2 A:HIS238 3.1 12.9 1.0
CE1 A:HIS79 3.1 15.7 1.0
C2 A:IMD803 3.1 19.9 0.5
OG1 A:THR191 4.0 22.1 1.0
ND1 A:HIS238 4.1 12.8 1.0
CG A:HIS238 4.2 11.5 1.0
CG A:GLU78 4.2 14.6 1.0
C4 A:IMD803 4.2 16.7 0.5
ND1 A:HIS79 4.2 15.7 1.0
CG A:HIS79 4.2 13.5 1.0
CB A:ASP242 4.2 14.6 1.0
N3 A:IMD803 4.2 17.6 0.5
OE2 A:GLU78 4.4 15.3 1.0
CA A:ASP242 4.8 14.3 1.0
CD A:GLU78 4.8 16.6 1.0
NE2 A:HIS265 4.8 21.9 1.0
O A:HOH920 4.8 23.6 1.0
CA A:THR191 4.9 18.1 1.0
CB A:THR191 4.9 19.5 1.0
O A:HIS238 5.0 16.0 1.0

Zinc binding site 2 out of 5 in 2go3

Go back to Zinc Binding Sites List in 2go3
Zinc binding site 2 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole.


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 Imidazole. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:37.6
occ:1.00
N1 A:IMD801 2.2 50.1 1.0
NE2 A:HIS58 2.3 25.2 1.0
CL A:CL607 2.4 36.7 1.0
NE2 A:HIS200 2.4 31.4 1.0
C5 A:IMD801 2.8 51.6 1.0
CD2 A:HIS200 3.1 31.4 1.0
CD2 A:HIS58 3.2 24.2 1.0
CE1 A:HIS58 3.2 25.8 1.0
C2 A:IMD801 3.4 51.3 1.0
CE1 A:HIS200 3.5 31.2 1.0
C4 A:IMD801 4.1 51.3 1.0
ND1 A:HIS58 4.3 25.8 1.0
CG A:HIS200 4.3 30.3 1.0
CG A:HIS58 4.3 23.4 1.0
N3 A:IMD801 4.4 51.0 1.0
ND1 A:HIS200 4.5 31.8 1.0
CG2 A:VAL204 4.5 23.9 1.0
CB A:ASN57 4.8 27.2 1.0
CG1 A:VAL204 4.8 23.4 1.0

Zinc binding site 3 out of 5 in 2go3

Go back to Zinc Binding Sites List in 2go3
Zinc binding site 3 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole.


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 Imidazole. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:15.9
occ:1.00
N1 B:IMD804 2.0 16.5 0.5
OD1 B:ASP242 2.0 13.7 1.0
NE2 B:HIS238 2.0 10.9 1.0
NE2 B:HIS79 2.1 13.3 1.0
O B:HOH1117 2.3 20.6 0.5
O B:HOH1118 2.3 33.9 0.5
CG B:ASP242 2.7 16.7 1.0
OD2 B:ASP242 2.8 16.3 1.0
CE1 B:HIS238 2.9 13.9 1.0
C5 B:IMD804 3.0 15.2 0.5
CD2 B:HIS79 3.0 11.7 1.0
CD2 B:HIS238 3.1 11.3 1.0
C2 B:IMD804 3.1 16.9 0.5
CE1 B:HIS79 3.1 11.3 1.0
OG1 B:THR191 4.0 18.4 1.0
ND1 B:HIS238 4.1 12.1 1.0
C4 B:IMD804 4.1 15.6 0.5
CG B:HIS238 4.1 12.1 1.0
CG B:GLU78 4.2 15.7 1.0
CG B:HIS79 4.2 14.1 1.0
N3 B:IMD804 4.2 15.4 0.5
ND1 B:HIS79 4.2 14.3 1.0
CB B:ASP242 4.2 14.1 1.0
O B:HOH973 4.4 27.8 1.0
OE2 B:GLU78 4.5 17.2 1.0
O B:HOH964 4.7 19.1 1.0
CB B:THR191 4.8 18.2 1.0
CA B:ASP242 4.8 13.4 1.0
NE2 B:HIS265 4.8 22.3 1.0
CD B:GLU78 4.9 16.9 1.0
CA B:THR191 4.9 17.3 1.0
O B:HIS238 4.9 15.2 1.0
CG2 B:THR191 4.9 19.0 1.0

Zinc binding site 4 out of 5 in 2go3

Go back to Zinc Binding Sites List in 2go3
Zinc binding site 4 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole.


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 Imidazole. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:20.5
occ:1.00
OE1 B:GLU126 2.0 19.1 1.0
N B:GLY2 2.2 17.0 1.0
OE2 B:GLU126 2.6 19.8 1.0
CD B:GLU126 2.6 21.1 1.0
CA B:GLY2 2.9 16.8 1.0
C B:GLY2 3.3 16.7 1.0
O B:GLY2 3.3 16.7 1.0
CG B:GLU126 4.1 20.4 1.0
N B:LEU3 4.2 17.7 1.0
O B:HOH984 4.7 27.7 1.0
CD2 B:LEU3 4.7 20.0 1.0
CB B:GLU126 4.8 21.6 1.0

Zinc binding site 5 out of 5 in 2go3

Go back to Zinc Binding Sites List in 2go3
Zinc binding site 5 out of 5 in the Crystal Structure of Aquifex Aeolicus Lpxc Complexed with Imidazole.


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 Imidazole. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn605

b:35.0
occ:1.00
N1 B:IMD802 2.1 40.7 1.0
NE2 B:HIS58 2.2 23.5 1.0
CL B:CL606 2.3 36.1 1.0
NE2 B:HIS200 2.4 28.0 1.0
C5 B:IMD802 2.8 41.0 1.0
CD2 B:HIS58 3.1 22.8 1.0
CD2 B:HIS200 3.2 28.3 1.0
CE1 B:HIS58 3.2 21.8 1.0
C2 B:IMD802 3.3 43.0 1.0
CE1 B:HIS200 3.4 27.0 1.0
C4 B:IMD802 4.1 41.2 1.0
CG B:HIS58 4.3 21.6 1.0
N3 B:IMD802 4.3 42.5 1.0
ND1 B:HIS58 4.3 22.6 1.0
CG B:HIS200 4.4 27.5 1.0
ND1 B:HIS200 4.5 27.7 1.0
CG2 B:VAL204 4.6 24.3 1.0
CB B:ASN57 4.7 25.2 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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