Zinc in PDB 6jku: Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida

The structure of Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida, PDB code: 6jku was solved by L.Manjunath, S.Bose, R.Subramanian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.13 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.162, 139.549, 166.556, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20

The structure of Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida (pdb code 6jku). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida, PDB code: 6jku:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.9 occ:1.00 OE2 A:GLU128 1.9 20.5 1.0 O3 A:PO4402 2.0 30.9 1.0 NE2 A:HIS192 2.1 19.5 1.0 NE2 A:HIS213 2.2 25.1 1.0 CD A:GLU128 2.8 27.4 1.0 CD2 A:HIS192 3.0 20.7 1.0 P A:PO4402 3.1 33.5 1.0 OE1 A:GLU128 3.1 27.7 1.0 CE1 A:HIS213 3.1 22.9 1.0 O2 A:PO4402 3.2 31.4 1.0 CE1 A:HIS192 3.2 24.9 1.0 CD2 A:HIS213 3.2 22.6 1.0 NE2 A:HIS140 3.9 24.3 1.0 O1 A:PO4402 3.9 35.7 1.0 NE2 A:GLN59 4.0 26.4 1.0 CG A:GLU128 4.1 21.2 1.0 CG A:HIS192 4.2 20.9 1.0 O A:HOH512 4.3 25.5 1.0 O4 A:PO4402 4.3 40.3 1.0 ND1 A:HIS213 4.3 24.1 1.0 ND1 A:HIS192 4.3 20.8 1.0 CG A:HIS213 4.4 22.3 1.0 CG2 A:THR212 4.6 22.8 1.0 CE1 A:HIS140 4.6 24.0 1.0 O A:HOH763 4.7 38.0 1.0 CD2 A:HIS140 4.7 22.8 1.0 O A:HOH542 4.8 38.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:26.8 occ:1.00 O3 B:PO4402 1.9 24.4 1.0 OE2 B:GLU128 2.0 23.9 1.0 NE2 B:HIS192 2.1 22.9 1.0 NE2 B:HIS213 2.2 22.8 1.0 CD B:GLU128 2.8 28.9 1.0 OE1 B:GLU128 3.0 24.9 1.0 CD2 B:HIS192 3.0 24.5 1.0 CE1 B:HIS213 3.0 21.2 1.0 CE1 B:HIS192 3.1 25.8 1.0 P B:PO4402 3.1 30.1 1.0 CD2 B:HIS213 3.2 19.9 1.0 O2 B:PO4402 3.4 29.7 1.0 NE2 B:HIS140 3.9 26.8 1.0 NE2 B:GLN59 3.9 22.0 1.0 O1 B:PO4402 4.0 31.0 1.0 O B:HOH520 4.1 26.9 1.0 O4 B:PO4402 4.2 37.0 1.0 CG B:HIS192 4.2 21.4 1.0 CG B:GLU128 4.2 24.0 1.0 ND1 B:HIS192 4.2 23.4 1.0 ND1 B:HIS213 4.2 24.5 1.0 CG B:HIS213 4.3 20.2 1.0 CE1 B:HIS140 4.6 24.7 1.0 CG2 B:THR212 4.7 24.3 1.0 CD2 B:HIS140 4.7 25.0 1.0 O B:HOH519 4.9 36.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:27.2 occ:1.00 O3 C:PO4402 2.0 27.0 0.8 OE2 C:GLU128 2.0 26.0 1.0 NE2 C:HIS192 2.1 21.5 1.0 NE2 C:HIS213 2.1 24.6 1.0 CD C:GLU128 2.8 26.3 1.0 CE1 C:HIS213 3.0 22.1 1.0 CD2 C:HIS192 3.0 21.3 1.0 CE1 C:HIS192 3.1 24.1 1.0 OE1 C:GLU128 3.1 24.1 1.0 P C:PO4402 3.1 26.1 0.8 CD2 C:HIS213 3.2 23.0 1.0 O2 C:PO4402 3.3 30.0 0.8 NE2 C:GLN59 3.8 23.4 1.0 NE2 C:HIS140 3.8 25.1 1.0 O1 C:PO4402 3.9 29.4 0.8 O C:HOH506 4.1 28.3 1.0 ND1 C:HIS213 4.2 21.0 1.0 ND1 C:HIS192 4.2 23.2 1.0 CG C:HIS192 4.2 23.6 1.0 CG C:GLU128 4.2 23.1 1.0 O4 C:PO4402 4.3 32.0 0.8 CG C:HIS213 4.3 21.5 1.0 CE1 C:HIS140 4.5 29.1 1.0 CG2 C:THR212 4.6 19.4 1.0 CD2 C:HIS140 4.7 26.1 1.0 CD C:GLN59 5.0 26.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:26.4 occ:1.00 OE2 D:GLU128 1.9 23.3 1.0 O3 D:PO4402 2.0 30.4 1.0 NE2 D:HIS192 2.1 22.6 1.0 NE2 D:HIS213 2.2 23.1 1.0 CD D:GLU128 2.8 26.8 1.0 CD2 D:HIS192 3.1 21.6 1.0 CE1 D:HIS213 3.1 21.8 1.0 OE1 D:GLU128 3.1 26.7 1.0 P D:PO4402 3.1 35.1 1.0 CE1 D:HIS192 3.1 23.9 1.0 CD2 D:HIS213 3.2 21.6 1.0 O2 D:PO4402 3.4 37.9 1.0 O1 D:PO4402 3.8 37.5 1.0 NE2 D:GLN59 3.9 23.2 1.0 NE2 D:HIS140 3.9 27.2 1.0 O D:HOH506 4.2 25.5 1.0 CG D:GLU128 4.2 22.2 1.0 CG D:HIS192 4.2 24.9 1.0 ND1 D:HIS213 4.2 23.5 1.0 ND1 D:HIS192 4.2 21.4 1.0 CG D:HIS213 4.3 19.5 1.0 O4 D:PO4402 4.3 41.7 1.0 CG2 D:THR212 4.6 17.7 1.0 CE1 D:HIS140 4.7 23.7 1.0 CD2 D:HIS140 4.7 28.1 1.0 O D:HOH623 4.8 44.6 1.0

L.Manjunath, S.Bose, R.Subramanian. Crystal Structure of Pasteurella Multocida N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase To Be Published.