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Manganese in PDB 5nha: Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol

Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol, PDB code: 5nha was solved by H.J.Rozeboom, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.90 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.961, 79.407, 91.284, 115.67, 89.44, 116.92
R / Rfree (%) 15.5 / 18.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol (pdb code 5nha). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol, PDB code: 5nha:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5nha

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Manganese binding site 1 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


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 Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:17.5
occ:1.00
 OE1 A:GLU269 2.1 13.5 1.0
OD2 A:ASP297 2.1 13.9 1.0
OD2 A:ASP340 2.1 15.2 1.0
OE2 A:GLU233 2.2 14.5 1.0
O3 A:SOR503 2.2 26.6 1.0
O2 A:SOR503 2.4 24.3 1.0
CD A:GLU233 3.1 13.9 1.0
C3 A:SOR503 3.2 27.8 1.0
CG A:ASP340 3.2 14.3 1.0
C2 A:SOR503 3.3 26.8 1.0
CG A:ASP297 3.3 13.4 1.0
CD A:GLU269 3.3 12.6 1.0
OE1 A:GLU233 3.3 14.5 1.0
CB A:ASP340 3.7 13.5 1.0
O4 A:SOR503 3.7 29.1 1.0
CB A:ASP297 3.8 12.7 1.0
O A:HOH794 3.9 19.6 1.0
CE1 A:HIS272 4.0 10.4 1.0
C4 A:SOR503 4.1 31.0 1.0
CG A:GLU269 4.1 12.1 1.0
CB A:GLU269 4.2 11.5 1.0
OE2 A:GLU269 4.2 12.7 1.0
OD1 A:ASP340 4.3 15.1 1.0
OD1 A:ASP297 4.3 14.1 1.0
CG A:GLU233 4.4 13.3 1.0
NE2 A:HIS272 4.5 10.6 1.0
C1 A:SOR503 4.6 25.6 1.0
MN A:MN502 4.6 26.1 1.0
ND1 A:HIS272 4.8 10.2 1.0
C5 A:SOR503 4.8 34.0 1.0
O5 A:SOR503 4.9 36.9 1.0
ND2 A:ASN267 4.9 12.1 1.0

Manganese binding site 2 out of 8 in 5nha

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Manganese binding site 2 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


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 Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:26.1
occ:1.00
 OE2 A:GLU269 2.0 12.7 1.0
OD2 A:ASP308 2.1 19.3 1.0
O A:HOH794 2.1 19.6 1.0
OD1 A:ASP310 2.5 16.4 1.0
OD1 A:ASP308 2.6 18.4 1.0
NE2 A:HIS272 2.7 10.6 1.0
CG A:ASP308 2.7 16.7 1.0
CD A:GLU269 2.9 12.6 1.0
OE1 A:GLU269 3.1 13.5 1.0
CD2 A:HIS272 3.3 10.1 1.0
CG A:ASP310 3.4 15.5 1.0
O A:HOH601 3.4 22.3 1.0
OD2 A:ASP310 3.6 16.4 1.0
CE1 A:HIS272 3.7 10.4 1.0
O A:HOH637 4.0 30.2 1.0
ND2 A:ASN299 4.1 10.5 1.0
CB A:ASP308 4.1 15.5 1.0
CG A:GLU269 4.3 12.1 1.0
O3 A:SOR503 4.3 26.6 1.0
OD2 A:ASP340 4.4 15.2 1.0
CG A:HIS272 4.5 10.0 1.0
CB A:ASN271 4.5 9.6 1.0
O5 A:SOR503 4.6 36.9 1.0
MN A:MN501 4.6 17.5 1.0
ND1 A:HIS272 4.7 10.2 1.0
CB A:ASP310 4.8 14.6 1.0
CG A:ASP340 4.8 14.3 1.0
C5 A:SOR503 4.9 34.0 1.0
CE A:LYS235 5.0 11.9 1.0

Manganese binding site 3 out of 8 in 5nha

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Manganese binding site 3 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


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 Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:14.9
occ:1.00
 OE2 B:GLU233 2.1 10.7 1.0
OE1 B:GLU269 2.1 11.5 1.0
OD2 B:ASP297 2.1 11.4 1.0
OD2 B:ASP340 2.2 13.7 1.0
O2 B:SOR503 2.3 17.5 1.0
O3 B:SOR503 2.4 18.6 1.0
CD B:GLU233 3.0 10.8 1.0
CG B:ASP340 3.3 11.4 1.0
C3 B:SOR503 3.3 20.6 1.0
OE1 B:GLU233 3.3 11.4 1.0
C2 B:SOR503 3.3 19.4 1.0
CG B:ASP297 3.3 10.7 1.0
CD B:GLU269 3.3 10.9 1.0
O4 B:SOR503 3.7 22.9 1.0
CB B:ASP340 3.8 10.6 1.0
CB B:ASP297 3.9 10.0 1.0
O B:HOH829 3.9 18.0 1.0
CE1 B:HIS272 4.0 8.5 1.0
C4 B:SOR503 4.1 23.9 1.0
CG B:GLU269 4.1 10.3 1.0
CB B:GLU269 4.2 9.8 1.0
OE2 B:GLU269 4.3 11.3 1.0
OD1 B:ASP297 4.3 11.5 1.0
OD1 B:ASP340 4.3 12.1 1.0
CG B:GLU233 4.4 10.2 1.0
NE2 B:HIS272 4.5 8.7 1.0
C1 B:SOR503 4.6 18.3 1.0
MN B:MN502 4.7 23.5 1.0
O5 B:SOR503 4.8 31.1 1.0
ND1 B:HIS272 4.8 8.6 1.0
C5 B:SOR503 4.9 26.5 1.0
ND2 B:ASN267 4.9 10.4 1.0

Manganese binding site 4 out of 8 in 5nha

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Manganese binding site 4 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


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 Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:23.5
occ:1.00
 OE2 B:GLU269 2.1 11.3 1.0
OD2 B:ASP308 2.1 13.9 1.0
O B:HOH829 2.1 18.0 1.0
OD1 B:ASP310 2.4 11.9 1.0
OD1 B:ASP308 2.6 12.8 1.0
CG B:ASP308 2.6 12.4 1.0
NE2 B:HIS272 2.7 8.7 1.0
CD B:GLU269 2.9 10.9 1.0
OE1 B:GLU269 3.1 11.5 1.0
CD2 B:HIS272 3.3 8.5 1.0
CG B:ASP310 3.4 11.4 1.0
O B:HOH601 3.4 22.6 1.0
OD2 B:ASP310 3.6 12.7 1.0
CE1 B:HIS272 3.8 8.5 1.0
ND2 B:ASN299 4.1 7.6 1.0
CB B:ASP308 4.1 11.4 1.0
O5 B:SOR503 4.3 31.1 1.0
CG B:GLU269 4.3 10.3 1.0
O3 B:SOR503 4.3 18.6 1.0
OD2 B:ASP340 4.4 13.7 1.0
CB B:ASN271 4.5 8.0 1.0
CG B:HIS272 4.5 8.4 1.0
MN B:MN501 4.7 14.9 1.0
ND1 B:HIS272 4.7 8.6 1.0
CB B:ASP310 4.8 10.6 1.0
CG B:ASP340 4.9 11.4 1.0
C5 B:SOR503 4.9 26.5 1.0
CE B:LYS235 5.0 9.6 1.0

Manganese binding site 5 out of 8 in 5nha

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Manganese binding site 5 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:17.6
occ:1.00
 OD2 C:ASP297 2.1 14.4 1.0
OE2 C:GLU233 2.1 12.2 1.0
OD2 C:ASP340 2.2 16.0 1.0
OE1 C:GLU269 2.2 13.2 1.0
O2 C:SOR503 2.3 20.4 1.0
O3 C:SOR503 2.3 24.2 1.0
CD C:GLU233 3.0 12.1 1.0
OE1 C:GLU233 3.2 13.0 1.0
C3 C:SOR503 3.3 25.2 1.0
CG C:ASP340 3.3 14.8 1.0
CG C:ASP297 3.3 13.0 1.0
C2 C:SOR503 3.3 23.9 1.0
CD C:GLU269 3.4 12.3 1.0
O4 C:SOR503 3.7 27.3 1.0
CB C:ASP340 3.8 13.8 1.0
CB C:ASP297 3.8 12.2 1.0
O C:HOH748 4.0 17.2 1.0
CE1 C:HIS272 4.1 11.2 1.0
C4 C:SOR503 4.1 27.2 1.0
CG C:GLU269 4.1 11.6 1.0
CB C:GLU269 4.2 11.2 1.0
OD1 C:ASP297 4.3 13.5 1.0
OE2 C:GLU269 4.3 12.4 1.0
OD1 C:ASP340 4.3 15.6 1.0
CG C:GLU233 4.4 11.5 1.0
NE2 C:HIS272 4.5 11.4 1.0
C1 C:SOR503 4.6 22.9 1.0
MN C:MN502 4.7 24.6 1.0
O5 C:SOR503 4.8 30.4 1.0
ND1 C:HIS272 4.8 10.8 1.0
C5 C:SOR503 4.9 28.7 1.0
ND2 C:ASN267 4.9 12.2 1.0

Manganese binding site 6 out of 8 in 5nha

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Manganese binding site 6 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:24.6
occ:1.00
 OE2 C:GLU269 2.0 12.4 1.0
O C:HOH748 2.1 17.2 1.0
OD2 C:ASP308 2.1 19.6 1.0
OD1 C:ASP310 2.4 15.0 1.0
OD1 C:ASP308 2.6 18.8 1.0
CG C:ASP308 2.7 17.1 1.0
NE2 C:HIS272 2.7 11.4 1.0
CD C:GLU269 2.9 12.3 1.0
OE1 C:GLU269 3.1 13.2 1.0
CD2 C:HIS272 3.3 10.8 1.0
O C:HOH602 3.3 29.7 1.0
CG C:ASP310 3.4 14.7 1.0
OD2 C:ASP310 3.5 15.9 1.0
CE1 C:HIS272 3.8 11.2 1.0
ND2 C:ASN299 4.0 10.6 1.0
CB C:ASP308 4.1 16.1 1.0
O5 C:SOR503 4.2 30.4 1.0
CG C:GLU269 4.3 11.6 1.0
O3 C:SOR503 4.4 24.2 1.0
OD2 C:ASP340 4.4 16.0 1.0
CB C:ASN271 4.5 9.7 1.0
CG C:HIS272 4.5 10.4 1.0
MN C:MN501 4.7 17.6 1.0
ND1 C:HIS272 4.7 10.8 1.0
CB C:ASP310 4.8 14.1 1.0
CG C:ASP340 4.8 14.8 1.0
C5 C:SOR503 4.9 28.7 1.0
CE C:LYS235 5.0 11.3 1.0
OD1 C:ASN271 5.0 9.9 1.0
CG C:ASN271 5.0 9.7 1.0

Manganese binding site 7 out of 8 in 5nha

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Manganese binding site 7 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:15.4
occ:1.00
 OE2 D:GLU233 2.1 10.0 1.0
OE1 D:GLU269 2.1 11.0 1.0
OD2 D:ASP297 2.1 11.6 1.0
OD2 D:ASP340 2.2 15.0 1.0
O2 D:SOR503 2.3 19.9 1.0
O3 D:SOR503 2.4 21.8 1.0
CD D:GLU233 3.0 9.9 1.0
OE1 D:GLU233 3.3 10.8 1.0
CG D:ASP340 3.3 12.6 1.0
CG D:ASP297 3.3 10.6 1.0
C2 D:SOR503 3.3 22.2 1.0
C3 D:SOR503 3.3 23.4 1.0
CD D:GLU269 3.3 9.9 1.0
O4 D:SOR503 3.6 27.3 1.0
CB D:ASP340 3.8 11.3 1.0
O D:HOH872 3.8 17.9 1.0
CB D:ASP297 3.8 10.1 1.0
CE1 D:HIS272 4.0 10.2 1.0
C4 D:SOR503 4.1 27.4 1.0
CG D:GLU269 4.1 9.5 1.0
CB D:GLU269 4.2 9.1 1.0
OE2 D:GLU269 4.2 10.4 1.0
OD1 D:ASP297 4.3 11.0 1.0
CG D:GLU233 4.3 9.6 1.0
OD1 D:ASP340 4.4 13.8 1.0
NE2 D:HIS272 4.5 10.6 1.0
C1 D:SOR503 4.6 20.9 1.0
MN D:MN502 4.6 23.4 1.0
ND1 D:HIS272 4.8 9.9 1.0
O5 D:SOR503 4.8 33.7 1.0
C5 D:SOR503 4.9 30.5 1.0
ND2 D:ASN267 4.9 10.4 1.0

Manganese binding site 8 out of 8 in 5nha

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Manganese binding site 8 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Xylose Isomerase From Piromyces Sp. E2 in Complex with Two MN2+ Ions and Sorbitol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:23.4
occ:1.00
 OE2 D:GLU269 2.0 10.4 1.0
O D:HOH872 2.1 17.9 1.0
OD2 D:ASP308 2.1 16.5 1.0
OD1 D:ASP310 2.5 13.3 1.0
OD1 D:ASP308 2.6 15.5 1.0
NE2 D:HIS272 2.7 10.6 1.0
CG D:ASP308 2.7 14.5 1.0
CD D:GLU269 2.9 9.9 1.0
OE1 D:GLU269 3.1 11.0 1.0
CD2 D:HIS272 3.3 10.1 1.0
CG D:ASP310 3.4 12.1 1.0
OD2 D:ASP310 3.6 13.5 1.0
O D:HOH601 3.6 23.6 1.0
CE1 D:HIS272 3.7 10.2 1.0
ND2 D:ASN299 4.1 8.0 1.0
CB D:ASP308 4.1 13.0 1.0
O D:HOH843 4.2 29.7 1.0
O5 D:SOR503 4.3 33.7 1.0
CG D:GLU269 4.3 9.5 1.0
O3 D:SOR503 4.4 21.8 1.0
OD2 D:ASP340 4.4 15.0 1.0
CG D:HIS272 4.5 9.7 1.0
CB D:ASN271 4.5 8.6 1.0
MN D:MN501 4.6 15.4 1.0
ND1 D:HIS272 4.7 9.9 1.0
CB D:ASP310 4.8 11.0 1.0
CG D:ASP340 4.8 12.6 1.0
C5 D:SOR503 4.9 30.5 1.0
CE D:LYS235 4.9 8.8 1.0

Reference:

M.Lee, H.J.Rozeboom, P.P.De Waal, R.M.De Jong, H.M.Dudek, D.B.Janssen. Metal Dependence of the Xylose Isomerase From Piromyces Sp. E2 Explored By Activity Profiling and Protein Crystallography. Biochemistry V. 56 5991 2017.
ISSN: ISSN 1520-4995
PubMed: 29045784
DOI: 10.1021/ACS.BIOCHEM.7B00777
Page generated: Sun Oct 6 02:03:58 2024

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