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Manganese in PDB 5yn3: Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2

Enzymatic activity of Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2

All present enzymatic activity of Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2:
5.3.1.5;

Protein crystallography data

The structure of Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2, PDB code: 5yn3 was solved by H.-F.Son, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.38 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.472, 126.417, 171.181, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 27.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2 (pdb code 5yn3). 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 Strcuture of Xylose Isomerase From Piromyces Sp. E2, PDB code: 5yn3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5yn3

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Manganese binding site 1 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:47.1
occ:1.00
 OE2 A:GLU269 2.2 15.5 1.0
O1 A:GOL503 2.2 31.0 1.0
OD2 A:ASP340 2.2 14.3 1.0
OE2 A:GLU233 2.3 21.2 1.0
OD2 A:ASP297 2.6 17.6 1.0
O2 A:GOL503 2.8 31.0 1.0
C1 A:GOL503 3.3 30.5 1.0
CG A:ASP340 3.3 14.2 1.0
CD A:GLU269 3.3 15.1 1.0
C2 A:GOL503 3.3 31.0 1.0
CD A:GLU233 3.4 20.4 1.0
OE1 A:GLU233 3.8 21.0 1.0
CG A:ASP297 3.8 17.0 1.0
CE1 A:HIS272 3.9 15.8 1.0
OE1 A:GLU269 3.9 15.3 1.0
O A:HOH649 3.9 25.2 1.0
OD1 A:ASP340 3.9 15.3 1.0
NE2 A:HIS272 4.2 15.5 1.0
CB A:ASP340 4.2 14.0 1.0
MN A:MN502 4.4 37.0 1.0
CB A:ASP297 4.4 16.4 1.0
CG A:GLU269 4.5 14.7 1.0
CB A:GLU269 4.6 14.2 1.0
CG A:GLU233 4.6 20.0 1.0
ND1 A:HIS272 4.8 15.4 1.0
C3 A:GOL503 4.8 30.7 1.0
OD1 A:ASP297 4.8 17.3 1.0
CZ2 A:TRP50 5.0 11.9 1.0

Manganese binding site 2 out of 8 in 5yn3

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Manganese binding site 2 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:37.0
occ:1.00
 OD2 A:ASP308 1.9 25.7 1.0
OE1 A:GLU269 2.3 15.3 1.0
OD1 A:ASP310 2.6 20.5 1.0
O A:HOH649 2.9 25.2 1.0
CG A:ASP308 3.0 27.4 1.0
NE2 A:HIS272 3.1 15.5 1.0
CD A:GLU269 3.3 15.1 1.0
OD2 A:ASP310 3.4 21.0 1.0
CG A:ASP310 3.4 20.1 1.0
OD1 A:ASP308 3.6 26.9 1.0
OE2 A:GLU269 3.8 15.5 1.0
CD2 A:HIS272 3.8 15.2 1.0
OD1 A:ASP340 4.1 15.3 1.0
CE1 A:HIS272 4.2 15.8 1.0
CB A:ASP308 4.2 28.2 1.0
NZ A:LYS235 4.3 17.7 1.0
ND2 A:ASN299 4.3 13.8 1.0
MN A:MN501 4.4 47.1 1.0
CG A:GLU269 4.6 14.7 1.0
CG A:ASP340 4.6 14.2 1.0
OD2 A:ASP340 4.7 14.3 1.0
CB A:ASP310 4.9 19.4 1.0
CB A:ASN271 4.9 15.5 1.0
CE A:LYS235 4.9 18.0 1.0

Manganese binding site 3 out of 8 in 5yn3

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Manganese binding site 3 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:34.4
occ:1.00
 OD2 B:ASP308 2.1 43.8 1.0
OE1 B:GLU269 2.5 15.4 1.0
OD1 B:ASP310 2.6 18.6 1.0
OD1 B:ASP308 2.6 39.1 1.0
CG B:ASP308 2.7 41.6 1.0
O B:HOH639 3.2 16.4 1.0
NE2 B:HIS272 3.3 18.0 1.0
CD B:GLU269 3.3 15.6 1.0
CG B:ASP310 3.6 19.8 1.0
OE2 B:GLU269 3.6 16.1 1.0
OD2 B:ASP310 3.8 19.8 1.0
CD2 B:HIS272 3.9 17.6 1.0
OD1 B:ASP340 3.9 12.8 1.0
CB B:ASP308 4.1 40.7 1.0
CE1 B:HIS272 4.3 17.9 1.0
ND2 B:ASN299 4.4 12.6 1.0
MN B:MN502 4.5 53.5 1.0
CG B:ASP340 4.5 12.3 1.0
OD2 B:ASP340 4.5 12.7 1.0
CG B:GLU269 4.7 15.6 1.0
NZ B:LYS235 4.7 22.2 1.0
CB B:ASP310 5.0 20.3 1.0

Manganese binding site 4 out of 8 in 5yn3

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Manganese binding site 4 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:53.5
occ:1.00
 OE2 B:GLU233 2.1 23.1 1.0
O1 B:GOL503 2.2 35.5 1.0
OD2 B:ASP340 2.4 12.7 1.0
OE2 B:GLU269 2.5 16.1 1.0
OD2 B:ASP297 2.8 14.8 1.0
C1 B:GOL503 2.9 36.6 1.0
O2 B:GOL503 3.0 41.2 1.0
CD B:GLU233 3.0 22.1 1.0
OE1 B:GLU233 3.4 22.6 1.0
C2 B:GOL503 3.5 37.2 1.0
O B:HOH639 3.6 16.4 1.0
CG B:ASP340 3.6 12.3 1.0
CD B:GLU269 3.7 15.6 1.0
CE1 B:HIS272 3.9 17.9 1.0
CG B:ASP297 4.0 15.1 1.0
C3 B:GOL503 4.1 37.5 1.0
OD1 B:ASP340 4.2 12.8 1.0
NE2 B:HIS272 4.3 18.0 1.0
OE1 B:GLU269 4.3 15.4 1.0
CG B:GLU233 4.3 21.5 1.0
MN B:MN501 4.5 34.4 1.0
CB B:ASP340 4.5 12.1 1.0
CB B:ASP297 4.7 15.4 1.0
CB B:GLU269 4.8 15.3 1.0
CG B:GLU269 4.8 15.6 1.0
ND1 B:HIS272 4.8 17.7 1.0
OD1 B:ASP297 4.9 14.9 1.0

Manganese binding site 5 out of 8 in 5yn3

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Manganese binding site 5 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

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

b:27.3
occ:1.00
 OE1 C:GLU233 1.9 19.9 1.0
OD2 C:ASP297 2.3 19.2 1.0
OE2 C:GLU269 2.4 17.5 1.0
O3 C:GOL503 2.4 32.8 1.0
C3 C:GOL503 2.8 33.8 1.0
CD C:GLU233 2.8 19.8 1.0
OD2 C:ASP340 2.9 13.6 1.0
OE2 C:GLU233 3.1 21.0 1.0
CG C:ASP297 3.5 17.9 1.0
CG C:ASP340 3.6 13.6 1.0
CD C:GLU269 3.6 17.3 1.0
CB C:ASP340 4.0 13.3 1.0
CB C:ASP297 4.0 16.5 1.0
C2 C:GOL503 4.1 35.3 1.0
CG C:GLU233 4.2 18.9 1.0
CE1 C:HIS272 4.4 19.5 1.0
OE1 C:GLU269 4.4 17.6 1.0
CB C:GLU269 4.4 17.6 1.0
CG C:GLU269 4.5 17.5 1.0
OD1 C:ASP297 4.5 19.0 1.0
OD1 C:ASP340 4.5 13.6 1.0
ND2 C:ASN267 4.7 18.9 1.0
NE2 C:HIS272 4.9 19.6 1.0
C1 C:GOL503 4.9 35.2 1.0

Manganese binding site 6 out of 8 in 5yn3

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Manganese binding site 6 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

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

b:41.9
occ:1.00
 OD2 C:ASP308 2.5 42.9 1.0
OE1 C:GLU269 2.6 17.6 1.0
O C:HOH632 2.7 8.2 1.0
OD1 C:ASP310 2.7 22.2 1.0
CG C:ASP308 3.2 39.6 1.0
NE2 C:HIS272 3.3 19.6 1.0
OD2 C:ASP340 3.4 13.6 1.0
OD1 C:ASP308 3.5 39.4 1.0
CD C:GLU269 3.5 17.3 1.0
CG C:ASP310 3.6 21.0 1.0
OE2 C:GLU269 3.6 17.5 1.0
OD2 C:ASP310 3.7 21.0 1.0
CD2 C:HIS272 4.1 19.3 1.0
NZ C:LYS235 4.1 19.0 1.0
CE1 C:HIS272 4.3 19.5 1.0
CB C:ASP308 4.4 38.3 1.0
CG C:ASP340 4.5 13.6 1.0
ND2 C:ASN299 4.6 14.2 1.0
CG C:GLU269 4.9 17.5 1.0
CE C:LYS235 4.9 18.9 1.0

Manganese binding site 7 out of 8 in 5yn3

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Manganese binding site 7 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

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

b:31.1
occ:1.00
 O3 D:GOL503 1.9 38.1 1.0
OE2 D:GLU269 1.9 13.3 1.0
OE2 D:GLU233 2.1 18.7 1.0
OD2 D:ASP340 2.4 10.4 1.0
OD2 D:ASP297 2.5 16.2 1.0
C3 D:GOL503 2.9 38.4 1.0
CD D:GLU233 3.1 18.8 1.0
CD D:GLU269 3.2 13.5 1.0
OE1 D:GLU233 3.5 19.4 1.0
CG D:ASP340 3.5 10.3 1.0
O2 D:GOL503 3.5 42.2 1.0
CG D:ASP297 3.6 16.1 1.0
C2 D:GOL503 3.7 39.7 1.0
OE1 D:GLU269 4.0 14.0 1.0
CB D:ASP340 4.1 10.4 1.0
CG D:GLU269 4.1 13.6 1.0
CB D:ASP297 4.1 15.5 1.0
CE1 D:HIS272 4.2 16.0 1.0
CB D:GLU269 4.3 13.7 1.0
CG D:GLU233 4.4 18.5 1.0
NE2 D:HIS272 4.4 16.2 1.0
OD1 D:ASP340 4.5 10.4 1.0
MN D:MN502 4.7 37.5 1.0
OD1 D:ASP297 4.7 17.9 1.0
ND2 D:ASN267 4.8 16.7 1.0

Manganese binding site 8 out of 8 in 5yn3

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Manganese binding site 8 out of 8 in the Crystal Strcuture of Xylose Isomerase From Piromyces Sp. E2


Mono view


Stereo pair view

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

b:37.5
occ:1.00
 OD2 D:ASP308 1.9 28.1 1.0
OE1 D:GLU269 2.4 14.0 1.0
OD1 D:ASP310 2.9 22.8 1.0
CG D:ASP308 2.9 31.2 1.0
CD D:GLU269 3.4 13.5 1.0
OD1 D:ASP308 3.5 30.7 1.0
OD2 D:ASP310 3.5 20.9 1.0
OE2 D:GLU269 3.6 13.3 1.0
CG D:ASP310 3.6 20.6 1.0
NE2 D:HIS272 3.7 16.2 1.0
CB D:ASP308 4.0 32.5 1.0
OD2 D:ASP340 4.0 10.4 1.0
CD2 D:HIS272 4.3 16.1 1.0
NZ D:LYS235 4.4 25.9 1.0
ND2 D:ASN299 4.5 15.4 1.0
MN D:MN501 4.7 31.1 1.0
CE1 D:HIS272 4.7 16.0 1.0
CG D:GLU269 4.7 13.6 1.0
CG D:ASP340 4.8 10.3 1.0

Reference:

H.Son, S.M.Lee, K.J.Kim. Crystal Structure and Biochemical Characterization of Xylose Isomerase Frompiromycessp. E2. J. Microbiol. Biotechnol. V. 28 571 2018.
ISSN: ESSN 1738-8872
PubMed: 29385668
DOI: 10.4014/JMB.1711.11026
Page generated: Sun Oct 6 03:32:52 2024

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