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Manganese in PDB 5j8l: Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity

Enzymatic activity of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity

All present enzymatic activity of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity:
5.1.3.31;

Protein crystallography data

The structure of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity, PDB code: 5j8l was solved by H.Yoshida, A.Yoshihara, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.68 / 1.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.580, 126.535, 98.903, 90.00, 101.45, 90.00
R / Rfree (%) 19.4 / 21.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity (pdb code 5j8l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity, PDB code: 5j8l:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5j8l

Go back to Manganese Binding Sites List in 5j8l
Manganese binding site 1 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:23.6
occ:1.00
 OD2 A:ASP185 1.9 12.8 1.0
OE2 A:GLU152 2.0 17.2 1.0
ND1 A:HIS211 2.1 13.2 1.0
O5 A:TGJ402 2.1 34.5 1.0
OE1 A:GLU246 2.9 19.6 1.0
CE1 A:HIS211 3.0 11.8 1.0
CG A:ASP185 3.0 14.4 1.0
CD A:GLU152 3.1 19.7 1.0
O4 A:TGJ402 3.1 43.7 1.0
CG A:HIS211 3.2 10.8 1.0
C5 A:TGJ402 3.4 39.5 1.0
OE1 A:GLU152 3.5 18.7 1.0
CB A:ASP185 3.5 13.3 1.0
CB A:HIS211 3.6 9.4 1.0
C4 A:TGJ402 3.8 41.5 1.0
CD A:GLU246 3.8 21.2 1.0
OE2 A:GLU246 4.0 22.5 1.0
OD1 A:ASP185 4.1 13.4 1.0
NE2 A:GLN183 4.1 12.7 1.0
NE2 A:HIS211 4.2 13.4 1.0
CD2 A:HIS188 4.2 14.7 1.0
NH2 A:ARG217 4.2 17.8 1.0
CD2 A:HIS211 4.3 12.2 1.0
NE2 A:HIS188 4.3 13.2 1.0
CG A:GLU152 4.3 14.5 1.0
C6 A:TGJ402 4.5 36.1 1.0
O2 A:TGJ402 4.8 45.1 1.0
CA A:ASP185 4.8 12.7 1.0
O A:HOH623 5.0 16.2 1.0
O6 A:TGJ402 5.0 33.6 1.0

Manganese binding site 2 out of 4 in 5j8l

Go back to Manganese Binding Sites List in 5j8l
Manganese binding site 2 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:30.7
occ:1.00
 OD2 B:ASP185 1.9 18.0 1.0
OE2 B:GLU152 2.1 21.4 1.0
O B:HOH642 2.1 26.1 1.0
ND1 B:HIS211 2.1 15.4 1.0
OE1 B:GLU246 2.9 21.6 1.0
CG B:ASP185 3.0 16.3 1.0
CE1 B:HIS211 3.0 17.2 1.0
CD B:GLU152 3.2 19.0 1.0
CG B:HIS211 3.2 14.9 1.0
CB B:ASP185 3.5 12.8 1.0
CB B:HIS211 3.6 12.9 1.0
OE1 B:GLU152 3.7 20.2 1.0
CD B:GLU246 3.9 20.3 1.0
O B:HOH578 4.0 25.9 1.0
CD2 B:HIS188 4.1 14.5 1.0
OD1 B:ASP185 4.1 18.1 1.0
NE2 B:GLN183 4.1 13.6 1.0
OE2 B:GLU246 4.1 23.7 1.0
NE2 B:HIS211 4.2 18.6 1.0
NE2 B:HIS188 4.2 12.9 1.0
NH2 B:ARG217 4.3 23.2 1.0
CD2 B:HIS211 4.3 17.1 1.0
CG B:GLU152 4.4 15.4 1.0
CA B:ASP185 4.8 11.3 1.0
O B:HOH654 4.9 18.7 1.0

Manganese binding site 3 out of 4 in 5j8l

Go back to Manganese Binding Sites List in 5j8l
Manganese binding site 3 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:27.6
occ:1.00
 OD2 C:ASP185 2.0 15.6 1.0
O C:HOH665 2.1 35.9 1.0
ND1 C:HIS211 2.2 19.4 1.0
OE2 C:GLU152 2.2 25.6 1.0
OE1 C:GLU246 2.8 21.4 1.0
CE1 C:HIS211 3.0 20.1 1.0
CG C:ASP185 3.1 17.2 1.0
CG C:HIS211 3.3 17.5 1.0
CD C:GLU152 3.3 22.6 1.0
CB C:ASP185 3.6 14.3 1.0
CB C:HIS211 3.6 15.6 1.0
CD C:GLU246 3.7 21.5 1.0
OE1 C:GLU152 3.8 22.9 1.0
OE2 C:GLU246 3.9 24.2 1.0
CD2 C:HIS188 4.1 12.5 1.0
OD1 C:ASP185 4.2 17.7 1.0
NE2 C:GLN183 4.2 15.1 1.0
NE2 C:HIS211 4.2 20.0 1.0
NE2 C:HIS188 4.2 14.1 1.0
O C:HOH579 4.3 30.5 1.0
NH2 C:ARG217 4.3 19.2 1.0
CD2 C:HIS211 4.3 18.7 1.0
CG C:GLU152 4.5 16.7 1.0
CA C:ASP185 4.8 13.6 1.0
O C:HOH595 4.9 16.6 1.0

Manganese binding site 4 out of 4 in 5j8l

Go back to Manganese Binding Sites List in 5j8l
Manganese binding site 4 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, Using A Crystal Grown in Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:25.3
occ:1.00
 OD2 D:ASP185 2.0 17.0 1.0
ND1 D:HIS211 2.0 18.1 1.0
OE2 D:GLU152 2.1 24.9 1.0
O D:HOH644 2.2 22.0 1.0
CE1 D:HIS211 2.9 16.5 1.0
OE1 D:GLU246 2.9 23.2 1.0
CG D:ASP185 3.1 17.6 1.0
CG D:HIS211 3.1 16.7 1.0
CD D:GLU152 3.2 23.1 1.0
CB D:HIS211 3.6 17.3 1.0
CB D:ASP185 3.6 16.3 1.0
OE1 D:GLU152 3.6 23.4 1.0
CD D:GLU246 3.8 23.0 1.0
OE2 D:GLU246 4.0 23.1 1.0
NE2 D:HIS211 4.1 17.0 1.0
NE2 D:GLN183 4.1 20.7 1.0
OD1 D:ASP185 4.1 20.8 1.0
O D:HOH574 4.1 23.7 1.0
CD2 D:HIS211 4.2 16.4 1.0
CD2 D:HIS188 4.2 14.4 1.0
NH2 D:ARG217 4.3 15.8 1.0
NE2 D:HIS188 4.4 14.7 1.0
O D:HOH569 4.4 32.3 1.0
CG D:GLU152 4.5 21.2 1.0
O D:HOH630 4.8 19.8 1.0
CA D:ASP185 4.8 14.7 1.0

Reference:

H.Yoshida, A.Yoshihara, T.Ishii, K.Izumori, S.Kamitori. X-Ray Structures of the Pseudomonas Cichorii D-Tagatose 3-Epimerase Mutant Form C66S Recognizing Deoxy Sugars As Substrates Appl. Microbiol. Biotechnol. V. 100 10403 2016.
ISSN: ESSN 1432-0614
PubMed: 27368739
DOI: 10.1007/S00253-016-7673-7
Page generated: Sun Oct 6 01:29:47 2024

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