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Nickel in PDB 3iv8: N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate

Enzymatic activity of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate

All present enzymatic activity of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate:
3.5.1.25;

Protein crystallography data

The structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate, PDB code: 3iv8 was solved by J.Osipiuk, N.Maltseva, J.Stam, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.18 / 2.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.181, 123.047, 156.286, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 25.3

Nickel Binding Sites:

The binding sites of Nickel atom in the N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate (pdb code 3iv8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate, PDB code: 3iv8:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3iv8

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Nickel binding site 1 out of 4 in the N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:65.4
occ:1.00
OE2 A:GLU128 2.2 42.2 1.0
NE2 A:HIS192 2.5 28.5 1.0
NE2 A:HIS213 2.5 28.0 1.0
C1 A:F6P500 3.0 71.1 1.0
CE1 A:HIS192 3.1 30.8 1.0
CD A:GLU128 3.2 38.3 1.0
CD2 A:HIS213 3.3 26.1 1.0
CE1 A:HIS213 3.6 23.9 1.0
OE1 A:GLU128 3.6 40.7 1.0
CD2 A:HIS192 3.7 29.9 1.0
NE2 A:HIS140 3.8 30.1 1.0
O1 A:F6P500 3.8 70.2 1.0
O2 A:F6P500 3.9 70.3 1.0
C2 A:F6P500 3.9 71.7 1.0
NE2 A:GLN59 4.1 32.1 1.0
OD2 A:ASP270 4.2 32.5 1.0
ND1 A:HIS192 4.4 29.3 1.0
O5 A:F6P500 4.4 72.0 1.0
CD2 A:HIS140 4.4 31.9 1.0
CG A:GLU128 4.5 33.0 1.0
CG A:HIS213 4.6 27.1 1.0
ND1 A:HIS213 4.6 26.4 1.0
CG A:HIS192 4.7 26.5 1.0
OD1 A:ASP270 4.8 31.9 1.0
CG A:ASP270 4.8 30.5 1.0
CE1 A:HIS140 4.9 32.5 1.0
CG2 A:THR212 4.9 28.1 1.0

Nickel binding site 2 out of 4 in 3iv8

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Nickel binding site 2 out of 4 in the N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:60.8
occ:1.00
OE1 B:GLU128 1.9 44.1 1.0
NE2 B:HIS213 2.2 32.4 1.0
NE2 B:HIS192 2.3 30.4 1.0
O B:HOH455 2.6 40.0 1.0
CE1 B:HIS192 2.9 31.2 1.0
CD B:GLU128 3.1 42.9 1.0
CE1 B:HIS213 3.2 30.9 1.0
CD2 B:HIS213 3.2 27.9 1.0
CD2 B:HIS192 3.5 32.5 1.0
OE2 B:GLU128 3.6 45.6 1.0
NE2 B:HIS140 4.0 55.6 1.0
NE2 B:GLN59 4.1 32.2 1.0
ND1 B:HIS192 4.2 30.7 1.0
ND1 B:HIS213 4.3 28.5 1.0
CG B:GLU128 4.3 37.1 1.0
CG B:HIS213 4.3 27.5 1.0
OD2 B:ASP270 4.4 31.8 1.0
CG B:HIS192 4.4 30.9 1.0
CE1 B:HIS140 4.9 54.1 1.0
OD1 B:ASP270 4.9 36.3 1.0
CD2 B:HIS140 4.9 54.1 1.0
O B:HOH434 5.0 32.9 1.0

Nickel binding site 3 out of 4 in 3iv8

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Nickel binding site 3 out of 4 in the N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni501

b:53.5
occ:1.00
OE1 C:GLU128 1.9 44.4 1.0
NE2 C:HIS192 2.2 30.1 1.0
NE2 C:HIS213 2.3 30.7 1.0
CE1 C:HIS192 2.9 31.0 1.0
O C:HOH448 2.9 29.7 1.0
CD C:GLU128 3.1 42.7 1.0
CD2 C:HIS213 3.3 28.8 1.0
CE1 C:HIS213 3.3 28.9 1.0
CD2 C:HIS192 3.4 27.6 1.0
OE2 C:GLU128 3.5 44.5 1.0
NE2 C:HIS140 3.9 48.6 1.0
ND1 C:HIS192 4.1 29.2 1.0
NE2 C:GLN59 4.2 32.6 1.0
OD2 C:ASP270 4.3 31.5 1.0
CG C:GLU128 4.3 37.0 1.0
CG C:HIS192 4.4 29.5 1.0
ND1 C:HIS213 4.4 30.9 1.0
CG C:HIS213 4.5 28.6 1.0
CD2 C:HIS140 4.7 49.1 1.0
CE1 C:HIS140 4.9 48.2 1.0

Nickel binding site 4 out of 4 in 3iv8

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Nickel binding site 4 out of 4 in the N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni501

b:76.8
occ:1.00
OE2 D:GLU128 2.4 41.7 1.0
NE2 D:HIS192 2.6 30.9 1.0
O D:HOH455 2.6 31.7 1.0
NE2 D:HIS213 2.7 32.4 1.0
CE1 D:HIS192 3.2 30.7 1.0
CD D:GLU128 3.5 37.9 1.0
CD2 D:HIS213 3.5 29.2 1.0
CE1 D:HIS213 3.7 29.1 1.0
O D:HOH428 3.8 35.2 1.0
NE2 D:HIS140 3.8 49.2 1.0
CD2 D:HIS192 3.8 30.5 1.0
OE1 D:GLU128 3.8 40.6 1.0
OD2 D:ASP270 3.9 44.3 1.0
NE2 D:GLN59 4.0 38.0 1.0
ND1 D:HIS192 4.5 30.5 1.0
OD1 D:ASP270 4.5 39.4 1.0
CE1 D:HIS140 4.6 51.3 1.0
CG D:ASP270 4.6 39.0 1.0
CG D:HIS213 4.7 29.1 1.0
CG D:HIS192 4.8 30.6 1.0
ND1 D:HIS213 4.8 30.6 1.0
CG D:GLU128 4.8 32.9 1.0
CD2 D:HIS140 4.8 50.4 1.0

Reference:

J.Osipiuk, N.Maltseva, J.Stam, W.F.Anderson, A.Joachimiak. X-Ray Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae Complexed with Fructose 6-Phosphate. To Be Published.
Page generated: Fri Sep 25 08:25:34 2020
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