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Zinc in PDB 2pdo: Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri

Protein crystallography data

The structure of Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri, PDB code: 2pdo was solved by Y.Kim, H.Li, D.Holzle, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.62 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.053, 134.388, 70.467, 90.00, 105.93, 90.00
R / Rfree (%) 19.3 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri (pdb code 2pdo). 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 the Putative Acetyltransferase of Gnat Family From Shigella Flexneri, PDB code: 2pdo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2pdo

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Zinc binding site 1 out of 5 in the Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri


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 the Putative Acetyltransferase of Gnat Family From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:34.9
occ:0.70
O H:HOH618 2.3 20.3 1.0
O B:HOH625 2.3 31.2 1.0
O B:HOH628 2.4 30.8 1.0
OE1 H:GLU124 2.4 32.9 1.0
O H:HIS125 2.4 25.5 1.0
O B:HIS125 2.5 31.9 1.0
OE2 B:GLU124 2.7 39.4 1.0
CD H:GLU124 3.6 35.2 1.0
C H:HIS125 3.6 27.4 1.0
C B:HIS125 3.7 32.2 1.0
CD B:GLU124 3.9 40.4 1.0
CG H:GLU124 4.1 33.3 1.0
OD1 H:ASP127 4.3 36.6 1.0
CA H:HIS125 4.3 26.6 1.0
OD2 B:ASP127 4.4 34.4 1.0
N H:HIS125 4.4 27.7 1.0
CB H:HIS125 4.4 27.1 1.0
N B:HIS125 4.5 31.7 1.0
O H:HOH688 4.5 25.9 1.0
CA B:HIS125 4.5 31.7 1.0
O B:HOH623 4.5 31.1 1.0
OE1 B:GLU124 4.6 47.8 1.0
N H:ALA126 4.6 28.2 1.0
OE2 H:GLU124 4.6 36.8 1.0
OD1 B:ASP127 4.6 34.8 1.0
N B:ALA126 4.7 32.3 1.0
CG B:ASP127 4.7 34.3 1.0
CA H:ALA126 4.7 29.1 1.0
CA B:ALA126 4.7 32.4 1.0
CB B:HIS125 4.8 32.9 1.0
CG H:ASP127 4.9 33.6 1.0
OD2 H:ASP127 4.9 35.4 1.0
CG H:HIS125 5.0 27.1 1.0

Zinc binding site 2 out of 5 in 2pdo

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Zinc binding site 2 out of 5 in the Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri


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 the Putative Acetyltransferase of Gnat Family From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:48.7
occ:0.40
O B:HOH661 2.1 40.7 1.0
OE1 B:GLU13 2.3 27.8 1.0
O B:GLU9 2.3 27.4 0.5
OE2 B:GLU13 2.7 32.3 1.0
CD B:GLU13 2.9 33.6 1.0
OE2 B:GLU9 3.0 23.9 0.5
O B:GLU9 3.2 27.7 0.5
OE2 B:GLU12 3.2 31.2 1.0
CD B:GLU9 3.3 29.0 0.5
O B:HOH662 3.3 80.8 1.0
OE1 B:GLU12 3.4 36.1 1.0
C B:GLU9 3.5 27.3 0.5
CD B:GLU12 3.6 36.0 1.0
CG B:GLU9 3.6 28.0 0.5
C B:GLU9 3.8 27.2 0.5
OE1 B:GLU9 4.1 30.9 0.5
CA B:GLU9 4.2 27.4 0.5
CA B:GLU9 4.3 27.1 0.5
CG B:GLU13 4.4 33.8 1.0
CB B:GLU9 4.4 27.6 0.5
N B:ASP10 4.6 27.0 1.0
N B:GLU12 4.7 30.1 1.0
N B:GLU13 4.7 32.8 1.0
N B:PHE11 4.7 27.7 1.0
CA B:ASP10 4.8 26.9 1.0
CB B:GLU9 4.8 26.9 0.5
CG B:GLU12 4.8 33.1 1.0
C B:ASP10 4.9 27.1 1.0
CB B:GLU12 4.9 31.9 1.0

Zinc binding site 3 out of 5 in 2pdo

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Zinc binding site 3 out of 5 in the Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri


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 the Putative Acetyltransferase of Gnat Family From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn602

b:30.7
occ:0.70
O E:HOH661 2.2 21.9 1.0
OE2 E:GLU124 2.3 28.7 1.0
O D:HIS125 2.4 25.6 1.0
O E:HOH638 2.4 23.5 1.0
O E:HIS125 2.5 27.9 1.0
O E:HOH619 2.6 28.0 1.0
OE1 D:GLU124 2.8 37.3 1.0
CD E:GLU124 3.4 33.0 1.0
C D:HIS125 3.6 27.5 1.0
C E:HIS125 3.6 28.4 1.0
CG E:GLU124 3.9 32.3 1.0
CD D:GLU124 4.0 36.9 1.0
O D:HOH678 4.2 31.9 1.0
N E:HIS125 4.3 28.4 1.0
CA E:HIS125 4.4 27.9 1.0
CA D:HIS125 4.5 26.8 1.0
CB E:HIS125 4.5 28.4 1.0
OE1 E:GLU124 4.5 39.4 1.0
OD2 E:ASP127 4.5 35.2 1.0
N D:HIS125 4.6 27.7 1.0
CB D:HIS125 4.6 27.8 1.0
N D:ALA126 4.6 27.8 1.0
O D:HOH630 4.6 19.3 1.0
OE2 D:GLU124 4.6 43.4 1.0
N E:ALA126 4.7 27.7 1.0
OD1 D:ASP127 4.7 30.5 1.0
OD2 D:ASP127 4.7 32.3 1.0
CA D:ALA126 4.8 29.0 1.0
CA E:ALA126 4.8 28.6 1.0
OD1 E:ASP127 4.8 34.0 1.0
CG D:ASP127 4.9 31.4 1.0
CG E:ASP127 5.0 31.9 1.0
CG E:HIS125 5.0 28.6 1.0
O D:HOH623 5.0 25.7 1.0

Zinc binding site 4 out of 5 in 2pdo

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Zinc binding site 4 out of 5 in the Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri


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 the Putative Acetyltransferase of Gnat Family From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn603

b:30.4
occ:0.70
O G:HOH610 2.3 23.4 1.0
OD2 G:ASP127 2.3 27.1 1.0
OD1 G:ASP127 2.6 29.0 1.0
CG G:ASP127 2.8 29.2 1.0
O G:HOH627 3.7 29.1 1.0
ZN H:ZN605 3.9 35.5 0.7
CB G:ASP127 4.3 28.2 1.0
OE1 H:GLU109 4.7 23.8 1.0
O G:HIS125 4.9 27.9 1.0

Zinc binding site 5 out of 5 in 2pdo

Go back to Zinc Binding Sites List in 2pdo
Zinc binding site 5 out of 5 in the Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri


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 the Putative Acetyltransferase of Gnat Family From Shigella Flexneri within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn605

b:35.5
occ:0.70
OD1 G:ASP127 2.3 29.0 1.0
OE2 H:GLU109 2.4 27.5 1.0
OE1 H:GLU109 2.5 23.8 1.0
O G:HOH627 2.5 29.1 1.0
O G:HOH654 2.5 31.0 1.0
CD H:GLU109 2.8 30.1 1.0
CG G:ASP127 3.4 29.2 1.0
ZN G:ZN603 3.9 30.4 0.7
O G:HOH610 4.0 23.4 1.0
CA G:ASP127 4.0 28.5 1.0
CB G:ASP127 4.1 28.2 1.0
OD2 G:ASP127 4.3 27.1 1.0
CG H:GLU109 4.3 29.7 1.0
O H:HOH702 4.5 38.7 1.0
O G:ALA126 4.6 29.1 1.0
N G:ASP127 4.8 27.6 1.0
O G:HOH669 5.0 29.5 1.0
C G:ASP127 5.0 28.6 1.0

Reference:

Y.Kim, H.Li, D.Holzle, A.Joachimiak. Crystal Structure of the Putative Acetyltransferase of Gnat Family From Shigella Flexneri To Be Published.
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