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Zinc in PDB 2p53: Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate

Enzymatic activity of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate

All present enzymatic activity of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate:
3.5.1.25;

Protein crystallography data

The structure of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate, PDB code: 2p53 was solved by A.A.Fedorov, E.V.Fedorov, R.S.Hall, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.399, 81.399, 206.452, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate (pdb code 2p53). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate, PDB code: 2p53:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2p53

Go back to Zinc Binding Sites List in 2p53
Zinc binding site 1 out of 2 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate


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-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:24.4
occ:1.00
 O71 A:NNG411 1.8 20.3 1.0
OE1 A:GLU131 1.9 20.7 1.0
NE2 A:HIS195 2.0 22.8 1.0
NE2 A:HIS216 2.2 23.0 1.0
CD A:GLU131 2.7 21.3 1.0
OE2 A:GLU131 2.9 19.6 1.0
CD2 A:HIS195 3.0 22.1 1.0
P7 A:NNG411 3.0 27.9 1.0
CE1 A:HIS195 3.1 22.8 1.0
CD2 A:HIS216 3.1 22.4 1.0
O72 A:NNG411 3.2 19.6 1.0
CE1 A:HIS216 3.3 25.5 1.0
NE2 A:GLN59 3.8 24.3 1.0
N2 A:NNG411 4.0 22.5 1.0
CG A:GLU131 4.1 24.1 1.0
NE2 A:HIS143 4.1 29.9 1.0
CG A:HIS195 4.2 22.4 1.0
ND1 A:HIS195 4.2 21.2 1.0
C2 A:NNG411 4.2 24.7 1.0
O A:HOH459 4.2 21.0 1.0
C8 A:NNG411 4.3 22.1 1.0
CG A:HIS216 4.3 23.2 1.0
ND1 A:HIS216 4.3 24.2 1.0
CG2 A:THR215 4.4 19.0 1.0
ND2 A:ASN273 4.8 25.6 1.0
OD1 A:ASN273 4.8 26.0 1.0
CE1 A:HIS143 4.9 29.6 1.0
O3 A:NNG411 4.9 24.9 1.0
CD A:GLN59 4.9 24.9 1.0

Zinc binding site 2 out of 2 in 2p53

Go back to Zinc Binding Sites List in 2p53
Zinc binding site 2 out of 2 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate


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-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D273N Mutant Complexed with N-Acetyl Phosphonamidate-D-Glucosamine-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:25.6
occ:1.00
 OE1 B:GLU131 1.8 22.7 1.0
O71 B:NNG411 1.9 26.4 1.0
NE2 B:HIS195 2.0 24.0 1.0
NE2 B:HIS216 2.2 22.4 1.0
CD B:GLU131 2.7 24.4 1.0
OE2 B:GLU131 2.9 23.2 1.0
CE1 B:HIS195 2.9 22.1 1.0
O72 B:NNG411 3.0 24.3 1.0
P7 B:NNG411 3.0 26.7 1.0
CD2 B:HIS195 3.1 23.1 1.0
CD2 B:HIS216 3.1 21.2 1.0
CE1 B:HIS216 3.3 25.2 1.0
NE2 B:GLN59 3.8 29.2 1.0
N2 B:NNG411 4.0 26.0 1.0
CG B:GLU131 4.1 23.2 1.0
ND1 B:HIS195 4.1 22.9 1.0
O B:HOH430 4.1 23.7 1.0
CG B:HIS195 4.2 24.2 1.0
C2 B:NNG411 4.2 24.8 1.0
NE2 B:HIS143 4.2 30.8 1.0
C8 B:NNG411 4.2 22.7 1.0
CG B:HIS216 4.3 23.5 1.0
ND1 B:HIS216 4.3 25.8 1.0
CG2 B:THR215 4.4 21.8 1.0
O3 B:NNG411 4.8 26.0 1.0
OD1 B:ASN273 4.8 26.3 1.0
CD B:GLN59 4.9 30.8 1.0
CE1 B:HIS143 5.0 28.8 1.0
ND2 B:ASN273 5.0 25.5 1.0
CD2 B:HIS143 5.0 30.0 1.0

Reference:

R.S.Hall, S.Brown, A.A.Fedorov, E.V.Fedorov, C.Xu, P.C.Babbitt, S.C.Almo, F.M.Raushel. Structural Diversity Within the Mononuclear and Binuclear Active Sites of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase. Biochemistry V. 46 7953 2007.
ISSN: ISSN 0006-2960
PubMed: 17567048
DOI: 10.1021/BI700544C
Page generated: Thu Oct 17 02:57:42 2024

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