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Iron in PDB 2vhl: The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis

Enzymatic activity of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis

All present enzymatic activity of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis:
3.5.1.25;

Protein crystallography data

The structure of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis, PDB code: 2vhl was solved by F.Vincent, D.Yates, E.Garman, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.84 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 51.680, 107.740, 188.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26

Iron Binding Sites:

The binding sites of Iron atom in the The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis (pdb code 2vhl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis, PDB code: 2vhl:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2vhl

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Iron binding site 1 out of 4 in the The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1397

b:18.2
occ:1.00
 O A:HOH2321 2.0 17.4 1.0
NE2 A:HIS65 2.1 19.1 1.0
NE2 A:HIS63 2.2 19.0 1.0
OD1 A:ASP281 2.2 17.2 1.0
OE1 A:GLU136 2.2 19.2 1.0
CD2 A:HIS65 3.0 18.9 1.0
CD A:GLU136 3.1 17.6 1.0
CE1 A:HIS63 3.1 15.9 1.0
CE1 A:HIS65 3.1 22.6 1.0
CD2 A:HIS63 3.1 17.1 1.0
CG A:ASP281 3.2 18.4 1.0
OE2 A:GLU136 3.4 17.1 1.0
FE A:FE1398 3.6 23.7 1.0
OD2 A:ASP281 3.6 21.5 1.0
O A:HOH2319 3.9 36.7 1.0
N2 A:GLP1395 4.0 29.4 1.0
CG A:HIS65 4.2 18.8 1.0
ND1 A:HIS65 4.2 19.4 1.0
ND1 A:HIS63 4.2 15.1 1.0
CG A:HIS63 4.3 16.3 1.0
CD2 A:HIS223 4.4 13.4 1.0
CG A:GLU136 4.4 17.8 1.0
CB A:ASP281 4.5 16.7 1.0
NE2 A:HIS223 4.5 15.0 1.0
CG2 A:THR98 4.7 17.0 1.0
OE1 A:GLN148 4.7 33.2 1.0
CA A:ASP281 4.9 16.3 1.0
CB A:GLU136 4.9 16.9 1.0

Iron binding site 2 out of 4 in 2vhl

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Iron binding site 2 out of 4 in the The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1398

b:23.7
occ:1.00
 O A:HOH2321 1.9 17.4 1.0
NE2 A:HIS223 2.1 15.0 1.0
OE2 A:GLU136 2.1 17.1 1.0
NE2 A:HIS202 2.2 15.9 1.0
CD2 A:HIS223 3.1 13.4 1.0
CD A:GLU136 3.1 17.6 1.0
CE1 A:HIS223 3.1 18.9 1.0
CE1 A:HIS202 3.1 15.3 1.0
CD2 A:HIS202 3.2 14.4 1.0
O A:HOH2319 3.2 36.7 1.0
OE1 A:GLU136 3.4 19.2 1.0
N2 A:GLP1395 3.5 29.4 1.0
C2 A:GLP1395 3.5 26.0 1.0
FE A:FE1397 3.6 18.2 1.0
OE1 A:GLN148 3.9 33.2 1.0
O3 A:GLP1395 4.0 24.9 1.0
ND1 A:HIS223 4.2 16.7 1.0
CG A:HIS223 4.2 15.7 1.0
ND1 A:HIS202 4.2 11.8 1.0
CG A:HIS202 4.3 15.7 1.0
CE1 A:HIS63 4.3 15.9 1.0
CG A:GLU136 4.4 17.8 1.0
C3 A:GLP1395 4.4 21.4 1.0
OD2 A:ASP281 4.5 21.5 1.0
NE2 A:HIS63 4.5 19.0 1.0
C1 A:GLP1395 4.7 24.0 1.0
CD A:GLN148 4.7 31.0 1.0
CG2 A:THR222 4.8 12.9 1.0
OD1 A:ASP281 4.8 17.2 1.0
CG A:GLN148 4.9 27.8 1.0

Iron binding site 3 out of 4 in 2vhl

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Iron binding site 3 out of 4 in the The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1397

b:24.3
occ:1.00
 OE2 B:GLU136 2.0 22.3 1.0
O B:HOH2224 2.1 30.1 1.0
NE2 B:HIS202 2.1 14.8 1.0
NE2 B:HIS223 2.2 17.7 1.0
O B:HOH2301 2.7 33.5 1.0
CD B:GLU136 3.0 21.6 1.0
CE1 B:HIS202 3.0 16.3 1.0
CE1 B:HIS223 3.1 17.3 1.0
CD2 B:HIS223 3.2 14.4 1.0
CD2 B:HIS202 3.2 14.5 1.0
OE1 B:GLU136 3.3 20.4 1.0
FE B:FE1398 3.5 20.4 1.0
C2 B:GLP1395 3.6 28.3 1.0
N2 B:GLP1395 3.7 32.5 1.0
OE1 B:GLN148 3.7 30.7 1.0
O3 B:GLP1395 3.9 27.4 1.0
ND1 B:HIS202 4.2 17.6 1.0
CE1 B:HIS63 4.2 10.7 1.0
ND1 B:HIS223 4.2 15.4 1.0
CG B:GLU136 4.3 20.5 1.0
CG B:HIS223 4.3 14.5 1.0
CG B:HIS202 4.3 15.1 1.0
C3 B:GLP1395 4.4 26.0 1.0
NE2 B:HIS63 4.4 14.3 1.0
OD2 B:ASP281 4.5 23.3 1.0
C1 B:GLP1395 4.7 25.9 1.0
CD B:GLN148 4.8 31.2 1.0
CG2 B:THR222 4.8 14.3 1.0
OD1 B:ASP281 4.9 15.8 1.0

Iron binding site 4 out of 4 in 2vhl

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Iron binding site 4 out of 4 in the The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Three-Dimensional Structure of the N-Acetylglucosamine- 6-Phosphate Deacetylase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1398

b:20.4
occ:1.00
 O B:HOH2224 2.0 30.1 1.0
NE2 B:HIS63 2.1 14.3 1.0
NE2 B:HIS65 2.1 18.7 1.0
OD1 B:ASP281 2.2 15.8 1.0
OE1 B:GLU136 2.2 20.4 1.0
CD2 B:HIS65 3.0 22.6 1.0
CE1 B:HIS63 3.0 10.7 1.0
CD2 B:HIS63 3.1 16.3 1.0
CG B:ASP281 3.1 19.6 1.0
CD B:GLU136 3.1 21.6 1.0
CE1 B:HIS65 3.2 23.2 1.0
OD2 B:ASP281 3.5 23.3 1.0
OE2 B:GLU136 3.5 22.3 1.0
FE B:FE1397 3.5 24.3 1.0
O B:HOH2301 3.8 33.5 1.0
ND1 B:HIS63 4.1 12.6 1.0
CG B:HIS63 4.2 13.8 1.0
CG B:HIS65 4.2 21.6 1.0
N2 B:GLP1395 4.2 32.5 1.0
ND1 B:HIS65 4.2 21.7 1.0
CB B:ASP281 4.4 19.1 1.0
CD2 B:HIS223 4.4 14.4 1.0
CG B:GLU136 4.5 20.5 1.0
NE2 B:HIS223 4.5 17.7 1.0
CG2 B:THR98 4.8 19.6 1.0
CB B:GLU136 4.8 20.7 1.0
CA B:ASP281 4.9 18.4 1.0

Reference:

F.Vincent, D.Yates, E.Garman, G.J.Davies. The Three-Dimensional Structure of the N- Acetylglucosamine-6-Phosphate Deacetylase From Bacillus Subtilis J.Biol.Chem. V. 279 2809 2004.
ISSN: ISSN 0021-9258
PubMed: 14557261
DOI: 10.1074/JBC.M310165200
Page generated: Sun Aug 4 02:38:47 2024

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