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Manganese in PDB 5nh9: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two MN2+ Ions and Xylose

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

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

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two MN2+ Ions and Xylose, PDB code: 5nh9 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) 46.70 / 2.08
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.690, 79.400, 92.080, 115.37, 90.04, 117.07
R / Rfree (%) 16.8 / 20.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two MN2+ Ions and Xylose (pdb code 5nh9). 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 E2 in Complex with Two MN2+ Ions and Xylose, PDB code: 5nh9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5nh9

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


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

b:16.2
occ:1.00
 OD2 A:ASP340 2.1 11.2 1.0
OD2 A:ASP297 2.1 12.2 1.0
OE1 A:GLU269 2.1 15.9 1.0
OE2 A:GLU233 2.2 12.1 1.0
O2 A:XLS503 2.2 23.4 1.0
O4 A:XLS503 2.2 23.0 1.0
CD A:GLU233 3.0 12.2 1.0
CG A:ASP340 3.2 11.0 1.0
CG A:ASP297 3.2 12.3 1.0
OE1 A:GLU233 3.2 14.0 1.0
C2 A:XLS503 3.2 27.8 1.0
C4 A:XLS503 3.3 25.6 1.0
CD A:GLU269 3.4 14.6 1.0
C3 A:XLS503 3.5 27.0 1.0
O3 A:XLS503 3.5 28.7 1.0
CB A:ASP340 3.7 10.7 1.0
CB A:ASP297 3.8 11.9 1.0
O A:HOH702 3.9 13.9 1.0
MN A:MN502 4.1 30.2 1.0
CE1 A:HIS272 4.1 11.4 1.0
CG A:GLU269 4.2 13.8 1.0
OD1 A:ASP340 4.2 11.1 1.0
OE2 A:GLU269 4.3 16.1 1.0
CB A:GLU269 4.3 12.8 1.0
OD1 A:ASP297 4.3 13.5 1.0
CG A:GLU233 4.4 12.4 1.0
NE2 A:HIS272 4.5 11.5 1.0
C1 A:XLS503 4.5 29.3 1.0
C5 A:XLS503 4.6 25.0 1.0
ND2 A:ASN267 4.8 12.5 1.0
ND1 A:HIS272 5.0 11.4 1.0

Manganese binding site 2 out of 8 in 5nh9

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


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

b:30.2
occ:1.00
 OD2 A:ASP308 2.0 20.6 1.0
O A:HOH702 2.2 13.9 1.0
OE2 A:GLU269 2.3 16.1 1.0
NE2 A:HIS272 2.4 11.5 1.0
O2 A:XLS503 2.7 23.4 1.0
O1 A:XLS503 2.8 31.0 1.0
CD A:GLU269 2.9 14.6 1.0
OE1 A:GLU269 2.9 15.9 1.0
CG A:ASP308 3.2 20.1 1.0
OD1 A:ASP310 3.2 18.6 1.0
CD2 A:HIS272 3.3 11.3 1.0
C1 A:XLS503 3.4 29.3 1.0
CE1 A:HIS272 3.4 11.4 1.0
C2 A:XLS503 3.6 27.8 1.0
OD1 A:ASP308 3.7 22.3 1.0
OD2 A:ASP340 4.0 11.2 1.0
OD2 A:ASP310 4.0 18.5 1.0
CG A:ASP310 4.0 16.9 1.0
MN A:MN501 4.1 16.2 1.0
CG A:GLU269 4.3 13.8 1.0
CG A:HIS272 4.4 11.3 1.0
ND1 A:HIS272 4.4 11.4 1.0
CB A:ASP308 4.5 17.6 1.0
NZ A:LYS235 4.5 13.7 1.0
CG A:ASP340 4.6 11.0 1.0
ND2 A:ASN299 4.6 11.1 1.0
CE A:LYS235 4.7 12.8 1.0
OD1 A:ASP340 4.8 11.1 1.0
OE2 A:GLU233 4.8 12.1 1.0
C3 A:XLS503 4.8 27.0 1.0
O3 A:XLS503 4.8 28.7 1.0
CD A:LYS235 5.0 12.5 1.0

Manganese binding site 3 out of 8 in 5nh9

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


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

b:15.1
occ:1.00
 O2 B:XLS503 2.0 23.6 1.0
OE2 B:GLU233 2.1 15.4 1.0
OD2 B:ASP297 2.1 13.8 1.0
OE1 B:GLU269 2.1 11.5 1.0
OD2 B:ASP340 2.2 12.4 1.0
O4 B:XLS503 2.3 22.4 1.0
CD B:GLU233 3.0 15.4 1.0
C2 B:XLS503 3.1 26.2 1.0
OE1 B:GLU233 3.2 18.9 1.0
CG B:ASP297 3.2 13.4 1.0
CG B:ASP340 3.3 12.2 1.0
C4 B:XLS503 3.3 23.8 1.0
CD B:GLU269 3.4 10.2 1.0
C3 B:XLS503 3.5 25.6 1.0
O3 B:XLS503 3.6 24.1 1.0
CB B:ASP297 3.7 13.2 1.0
CB B:ASP340 3.8 11.9 1.0
O B:HOH719 3.9 16.0 1.0
MN B:MN502 4.1 35.3 1.0
CE1 B:HIS272 4.2 10.2 1.0
CG B:GLU269 4.2 9.7 1.0
CB B:GLU269 4.2 9.1 1.0
OD1 B:ASP297 4.3 14.1 1.0
OE2 B:GLU269 4.3 10.9 1.0
CG B:GLU233 4.3 14.3 1.0
OD1 B:ASP340 4.4 12.4 1.0
C1 B:XLS503 4.4 28.3 1.0
NE2 B:HIS272 4.5 10.5 1.0
C5 B:XLS503 4.6 23.8 1.0
ND2 B:ASN267 4.7 11.4 1.0
ND1 B:HIS272 5.0 10.0 1.0

Manganese binding site 4 out of 8 in 5nh9

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


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

b:35.3
occ:1.00
 OD2 B:ASP308 2.0 19.1 1.0
O B:HOH719 2.2 16.0 1.0
OE2 B:GLU269 2.2 10.9 1.0
NE2 B:HIS272 2.4 10.5 1.0
O2 B:XLS503 2.7 23.6 1.0
CD B:GLU269 2.8 10.2 1.0
OE1 B:GLU269 2.9 11.5 1.0
O1 B:XLS503 2.9 28.8 1.0
CD2 B:HIS272 3.2 10.0 1.0
CG B:ASP308 3.2 19.2 1.0
OD1 B:ASP310 3.2 17.4 1.0
C1 B:XLS503 3.3 28.3 1.0
CE1 B:HIS272 3.3 10.2 1.0
C2 B:XLS503 3.5 26.2 1.0
OD1 B:ASP308 3.7 21.7 1.0
OD2 B:ASP340 4.0 12.4 1.0
CG B:ASP310 4.1 15.3 1.0
OD2 B:ASP310 4.1 16.3 1.0
MN B:MN501 4.1 15.1 1.0
CG B:GLU269 4.3 9.7 1.0
CG B:HIS272 4.3 9.9 1.0
ND1 B:HIS272 4.4 10.0 1.0
CB B:ASP308 4.5 17.2 1.0
NZ B:LYS235 4.5 11.0 1.0
ND2 B:ASN299 4.6 11.6 1.0
CG B:ASP340 4.6 12.2 1.0
CE B:LYS235 4.7 10.6 1.0
OE2 B:GLU233 4.7 15.4 1.0
OD1 B:ASP340 4.9 12.4 1.0
C3 B:XLS503 4.9 25.6 1.0
O3 B:XLS503 4.9 24.1 1.0
CD B:LYS235 5.0 10.3 1.0

Manganese binding site 5 out of 8 in 5nh9

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


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 E2 in Complex with Two MN2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:16.2
occ:1.00
 OE1 C:GLU269 2.1 13.0 1.0
OD2 C:ASP340 2.1 13.7 1.0
OD2 C:ASP297 2.1 12.3 1.0
O2 C:XLS504 2.1 19.8 1.0
OE2 C:GLU233 2.1 12.3 1.0
O4 C:XLS504 2.2 17.8 1.0
CD C:GLU233 3.0 12.4 1.0
C4 C:XLS504 3.2 19.7 1.0
C2 C:XLS504 3.2 22.4 1.0
CG C:ASP340 3.2 12.1 1.0
CG C:ASP297 3.2 11.9 1.0
OE1 C:GLU233 3.3 12.7 1.0
CD C:GLU269 3.3 12.4 1.0
C3 C:XLS504 3.4 20.9 1.0
O3 C:XLS504 3.5 21.8 1.0
CB C:ASP340 3.7 11.2 1.0
CB C:ASP297 3.8 11.3 1.0
MN C:MN503 4.0 24.9 1.0
CE1 C:HIS272 4.2 13.0 1.0
CG C:GLU269 4.2 11.9 1.0
OD1 C:ASP340 4.2 13.1 1.0
OE2 C:GLU269 4.2 13.1 1.0
CB C:GLU269 4.3 11.3 1.0
OD1 C:ASP297 4.3 12.4 1.0
O C:HOH623 4.4 14.6 1.0
CG C:GLU233 4.4 11.8 1.0
NE2 C:HIS272 4.5 13.7 1.0
C1 C:XLS504 4.5 24.9 1.0
C5 C:XLS504 4.6 18.3 1.0
ND2 C:ASN267 4.8 12.1 1.0
ND1 C:HIS272 5.0 12.9 1.0

Manganese binding site 6 out of 8 in 5nh9

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


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 E2 in Complex with Two MN2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn503

b:24.9
occ:1.00
 OD2 C:ASP308 2.1 18.8 1.0
O C:HOH623 2.2 14.6 1.0
OE2 C:GLU269 2.4 13.1 1.0
NE2 C:HIS272 2.4 13.7 1.0
O2 C:XLS504 2.5 19.8 1.0
OE1 C:GLU269 2.9 13.0 1.0
CD C:GLU269 2.9 12.4 1.0
O1 C:XLS504 3.0 28.7 1.0
CG C:ASP308 3.3 20.9 1.0
CD2 C:HIS272 3.3 12.9 1.0
CE1 C:HIS272 3.3 13.0 1.0
OD1 C:ASP310 3.4 19.6 1.0
C1 C:XLS504 3.4 24.9 1.0
C2 C:XLS504 3.4 22.4 1.0
OD1 C:ASP308 3.8 26.8 1.0
MN C:MN502 4.0 16.2 1.0
OD2 C:ASP340 4.0 13.7 1.0
OD2 C:ASP310 4.1 21.7 1.0
CG C:ASP310 4.2 18.5 1.0
CG C:GLU269 4.4 11.9 1.0
ND1 C:HIS272 4.4 12.9 1.0
CG C:HIS272 4.4 12.7 1.0
NZ C:LYS235 4.5 14.9 1.0
CB C:ASP308 4.6 19.4 1.0
CG C:ASP340 4.6 12.1 1.0
O3 C:XLS504 4.6 21.8 1.0
CE C:LYS235 4.6 13.8 1.0
OE2 C:GLU233 4.7 12.3 1.0
C3 C:XLS504 4.7 20.9 1.0
ND2 C:ASN299 4.8 10.8 1.0
OD1 C:ASP340 4.8 13.1 1.0
CD C:LYS235 4.9 13.3 1.0

Manganese binding site 7 out of 8 in 5nh9

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


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 E2 in Complex with Two MN2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:19.0
occ:1.00
 OD2 D:ASP297 2.1 13.5 1.0
OE2 D:GLU233 2.1 15.8 1.0
OE1 D:GLU269 2.2 15.6 1.0
OD2 D:ASP340 2.2 16.3 1.0
O2 D:XLS504 2.2 25.8 1.0
O4 D:XLS504 2.4 26.3 1.0
CD D:GLU233 3.0 15.7 1.0
CG D:ASP297 3.2 12.8 1.0
OE1 D:GLU233 3.2 16.3 1.0
C2 D:XLS504 3.3 28.7 1.0
CG D:ASP340 3.3 15.2 1.0
C4 D:XLS504 3.3 27.4 1.0
CD D:GLU269 3.4 14.1 1.0
C3 D:XLS504 3.6 28.4 1.0
O3 D:XLS504 3.7 30.1 1.0
CB D:ASP297 3.8 12.1 1.0
CB D:ASP340 3.8 14.0 1.0
O D:HOH711 4.0 21.3 1.0
MN D:MN503 4.1 32.7 1.0
CE1 D:HIS272 4.1 12.7 1.0
CG D:GLU269 4.2 12.7 1.0
OD1 D:ASP297 4.3 12.5 1.0
CB D:GLU269 4.3 11.6 1.0
OE2 D:GLU269 4.3 15.9 1.0
OD1 D:ASP340 4.3 16.7 1.0
CG D:GLU233 4.4 15.5 1.0
NE2 D:HIS272 4.5 12.8 1.0
C1 D:XLS504 4.6 29.8 1.0
C5 D:XLS504 4.7 25.7 1.0
ND2 D:ASN267 4.7 13.9 1.0
ND1 D:HIS272 5.0 12.3 1.0

Manganese binding site 8 out of 8 in 5nh9

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


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 E2 in Complex with Two MN2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn503

b:32.7
occ:1.00
 OD2 D:ASP308 2.0 22.0 1.0
O D:HOH711 2.1 21.3 1.0
OE2 D:GLU269 2.4 15.9 1.0
NE2 D:HIS272 2.4 12.8 1.0
O1 D:XLS504 2.6 29.3 1.0
O2 D:XLS504 2.6 25.8 1.0
OE1 D:GLU269 2.9 15.6 1.0
CD D:GLU269 2.9 14.1 1.0
CG D:ASP308 3.2 22.6 1.0
C1 D:XLS504 3.2 29.8 1.0
OD1 D:ASP310 3.3 21.2 1.0
CD2 D:HIS272 3.3 11.6 1.0
CE1 D:HIS272 3.4 12.7 1.0
C2 D:XLS504 3.5 28.7 1.0
OD1 D:ASP308 3.8 26.8 1.0
OD2 D:ASP340 4.0 16.3 1.0
OD2 D:ASP310 4.1 22.2 1.0
CG D:ASP310 4.1 18.9 1.0
MN D:MN502 4.1 19.0 1.0
CG D:GLU269 4.4 12.7 1.0
ND1 D:HIS272 4.4 12.3 1.0
CG D:HIS272 4.4 11.6 1.0
NZ D:LYS235 4.5 15.4 1.0
CB D:ASP308 4.5 20.1 1.0
CG D:ASP340 4.6 15.2 1.0
CE D:LYS235 4.6 14.3 1.0
ND2 D:ASN299 4.7 9.8 1.0
C3 D:XLS504 4.8 28.4 1.0
OE2 D:GLU233 4.8 15.8 1.0
OD1 D:ASP340 4.8 16.7 1.0
O3 D:XLS504 4.8 30.1 1.0
CD D:LYS235 5.0 13.7 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 02:01:56 2024

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