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Iron in PDB 5nhb: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions

Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions, PDB code: 5nhb 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) 45.30 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.539, 79.510, 92.230, 115.57, 89.96, 116.69
R / Rfree (%) 24.5 / 28.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions (pdb code 5nhb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions, PDB code: 5nhb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5nhb

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Iron binding site 1 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:27.9
occ:1.00
 OD2 A:ASP297 2.0 24.3 1.0
OE2 A:GLU233 2.0 23.5 1.0
OE1 A:GLU269 2.2 23.1 1.0
OD2 A:ASP340 2.2 24.2 1.0
CD A:GLU233 2.8 23.9 1.0
OE1 A:GLU233 2.9 24.5 1.0
CG A:ASP297 3.1 24.1 1.0
CG A:ASP340 3.2 24.4 1.0
CD A:GLU269 3.5 22.5 1.0
CB A:ASP340 3.7 24.3 1.0
CB A:ASP297 3.7 23.4 1.0
FE A:FE2502 4.1 21.9 1.0
OD1 A:ASP297 4.2 24.6 1.0
OD1 A:ASP340 4.3 24.9 1.0
CG A:GLU233 4.3 23.5 1.0
OE2 A:GLU269 4.3 22.4 1.0
CG A:GLU269 4.4 22.1 1.0
CB A:GLU269 4.6 22.0 1.0
CE1 A:HIS272 4.6 22.4 1.0
O A:HOH703 4.6 19.7 1.0
ND2 A:ASN267 4.8 24.6 1.0
NE2 A:HIS272 4.9 22.2 1.0
CZ2 A:TRP50 4.9 26.6 1.0

Iron binding site 2 out of 8 in 5nhb

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Iron binding site 2 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:21.9
occ:1.00
 OE2 A:GLU269 2.2 22.4 1.0
NE2 A:HIS272 2.4 22.2 1.0
OD2 A:ASP308 2.6 22.6 1.0
O A:HOH647 2.7 5.1 1.0
CD A:GLU269 2.9 22.5 1.0
OE1 A:GLU269 2.9 23.1 1.0
CE1 A:HIS272 3.3 22.4 1.0
CD2 A:HIS272 3.5 21.6 1.0
OD2 A:ASP340 3.5 24.2 1.0
CG A:ASP308 3.7 22.2 1.0
OD1 A:ASP310 3.9 22.8 1.0
FE A:FE2501 4.1 27.9 1.0
NZ A:LYS235 4.1 22.8 1.0
OD1 A:ASP308 4.2 21.7 1.0
OD2 A:ASP310 4.3 23.9 1.0
OE2 A:GLU233 4.3 23.5 1.0
CG A:GLU269 4.4 22.1 1.0
ND1 A:HIS272 4.4 22.0 1.0
CG A:ASP340 4.4 24.4 1.0
CG A:ASP310 4.5 23.4 1.0
CG A:HIS272 4.5 21.5 1.0
CE A:LYS235 4.7 22.2 1.0
ND2 A:ASN299 4.9 22.3 1.0
OD1 A:ASP340 5.0 24.9 1.0

Iron binding site 3 out of 8 in 5nhb

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Iron binding site 3 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:22.8
occ:1.00
 OE2 B:GLU233 1.8 21.0 1.0
OD2 B:ASP297 2.0 21.6 1.0
OE1 B:GLU269 2.1 20.6 1.0
OD2 B:ASP340 2.3 21.2 1.0
O B:HOH671 2.7 15.5 1.0
CD B:GLU233 2.7 21.3 1.0
OE1 B:GLU233 2.9 21.7 1.0
CG B:ASP297 3.1 21.6 1.0
CD B:GLU269 3.3 20.2 1.0
CG B:ASP340 3.4 21.3 1.0
CB B:ASP297 3.6 21.2 1.0
FE B:FE2502 3.7 17.3 1.0
CB B:ASP340 3.8 21.4 1.0
CG B:GLU233 4.1 21.2 1.0
OE2 B:GLU269 4.1 20.0 1.0
CG B:GLU269 4.2 20.1 1.0
OD1 B:ASP297 4.2 22.0 1.0
CB B:GLU269 4.3 20.2 1.0
CE1 B:HIS272 4.4 20.1 1.0
OD1 B:ASP340 4.4 21.6 1.0
O B:HOH632 4.5 2.9 1.0
NE2 B:HIS272 4.7 19.9 1.0
ND2 B:ASN267 4.7 22.1 1.0

Iron binding site 4 out of 8 in 5nhb

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Iron binding site 4 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:17.3
occ:1.00
 O B:HOH632 1.8 2.9 1.0
OE2 B:GLU269 2.3 20.0 1.0
NE2 B:HIS272 2.3 19.9 1.0
O B:HOH623 2.4 13.6 1.0
OE1 B:GLU269 2.8 20.6 1.0
CD B:GLU269 2.8 20.2 1.0
OD2 B:ASP308 2.9 19.9 1.0
CE1 B:HIS272 3.1 20.1 1.0
OD2 B:ASP340 3.4 21.2 1.0
CD2 B:HIS272 3.4 19.6 1.0
FE B:FE2501 3.7 22.8 1.0
CG B:ASP308 4.0 19.6 1.0
OE2 B:GLU233 4.0 21.0 1.0
OD1 B:ASP310 4.2 20.1 1.0
NZ B:LYS235 4.2 19.9 1.0
ND1 B:HIS272 4.2 20.0 1.0
CG B:GLU269 4.3 20.1 1.0
CG B:ASP340 4.4 21.3 1.0
OD1 B:ASP308 4.4 19.4 1.0
CG B:HIS272 4.4 19.6 1.0
OD2 B:ASP310 4.6 20.7 1.0
CE B:LYS235 4.7 19.6 1.0
CG B:ASP310 4.8 20.4 1.0
OD1 B:ASP340 5.0 21.6 1.0
CB B:GLU269 5.0 20.2 1.0
CD B:LYS235 5.0 19.8 1.0

Iron binding site 5 out of 8 in 5nhb

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Iron binding site 5 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:25.7
occ:1.00
 OE1 C:GLU269 2.1 23.9 1.0
OD2 C:ASP297 2.1 25.3 1.0
OE2 C:GLU233 2.1 24.4 1.0
OD2 C:ASP340 2.1 25.1 1.0
CD C:GLU233 2.9 24.7 1.0
O C:HOH646 3.0 10.7 1.0
OE1 C:GLU233 3.1 25.4 1.0
CG C:ASP340 3.1 25.4 1.0
CG C:ASP297 3.2 25.2 1.0
CD C:GLU269 3.3 23.3 1.0
CB C:ASP340 3.6 25.2 1.0
CB C:ASP297 3.7 24.4 1.0
FE C:FE2502 3.9 24.0 1.0
OE2 C:GLU269 4.1 23.0 1.0
O C:HOH632 4.2 10.7 1.0
OD1 C:ASP340 4.2 25.8 1.0
OD1 C:ASP297 4.2 25.7 1.0
CG C:GLU269 4.3 22.8 1.0
CG C:GLU233 4.4 24.3 1.0
CB C:GLU269 4.5 22.8 1.0
CE1 C:HIS272 4.5 23.0 1.0
NE2 C:HIS272 4.8 22.8 1.0
ND2 C:ASN267 4.9 25.6 1.0
CZ2 C:TRP50 4.9 27.7 1.0

Iron binding site 6 out of 8 in 5nhb

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Iron binding site 6 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:24.0
occ:1.00
 O C:HOH632 2.1 10.7 1.0
OE2 C:GLU269 2.3 23.0 1.0
NE2 C:HIS272 2.5 22.8 1.0
OD2 C:ASP308 2.6 23.0 1.0
OE1 C:GLU269 3.0 23.9 1.0
CD C:GLU269 3.0 23.3 1.0
CE1 C:HIS272 3.3 23.0 1.0
OD2 C:ASP340 3.5 25.1 1.0
CD2 C:HIS272 3.5 22.2 1.0
CG C:ASP308 3.7 22.5 1.0
FE C:FE2501 3.9 25.7 1.0
OD1 C:ASP310 4.0 23.3 1.0
NZ C:LYS235 4.1 23.1 1.0
OD1 C:ASP308 4.2 22.0 1.0
OD2 C:ASP310 4.3 24.5 1.0
OE2 C:GLU233 4.3 24.4 1.0
CG C:ASP340 4.4 25.4 1.0
CG C:GLU269 4.5 22.8 1.0
ND1 C:HIS272 4.5 22.6 1.0
CG C:ASP310 4.6 23.9 1.0
CG C:HIS272 4.6 22.0 1.0
CE C:LYS235 4.7 22.5 1.0
OD1 C:ASP340 4.9 25.8 1.0
CZ A:PHE61 5.0 28.1 1.0
ND2 C:ASN299 5.0 23.1 1.0

Iron binding site 7 out of 8 in 5nhb

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Iron binding site 7 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:19.3
occ:1.00
 O D:HOH624 1.9 7.8 1.0
OE2 D:GLU233 2.0 19.3 1.0
OE1 D:GLU269 2.1 18.9 1.0
OD2 D:ASP297 2.1 19.8 1.0
OD2 D:ASP340 2.2 19.5 1.0
CD D:GLU233 2.8 19.6 1.0
OE1 D:GLU233 3.0 20.0 1.0
CG D:ASP297 3.2 19.9 1.0
CG D:ASP340 3.3 19.6 1.0
CD D:GLU269 3.3 18.6 1.0
CB D:ASP297 3.7 19.4 1.0
CB D:ASP340 3.8 19.6 1.0
OE2 D:GLU269 4.1 18.4 1.0
FE D:FE2502 4.2 18.8 1.0
CG D:GLU233 4.2 19.5 1.0
CG D:GLU269 4.3 18.4 1.0
OD1 D:ASP297 4.3 20.3 1.0
OD1 D:ASP340 4.3 19.9 1.0
CB D:GLU269 4.4 18.5 1.0
CE1 D:HIS272 4.5 18.5 1.0
O D:HOH676 4.5 13.1 1.0
NE2 D:HIS272 4.7 18.4 1.0
ND2 D:ASN267 4.8 20.4 1.0
CZ2 D:TRP50 5.0 21.0 1.0

Iron binding site 8 out of 8 in 5nhb

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Iron binding site 8 out of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:18.8
occ:1.00
 OE2 D:GLU269 2.3 18.4 1.0
OD2 D:ASP308 2.4 18.4 1.0
NE2 D:HIS272 2.4 18.4 1.0
O D:HOH676 2.5 13.1 1.0
CD D:GLU269 3.1 18.6 1.0
OE1 D:GLU269 3.2 18.9 1.0
CE1 D:HIS272 3.3 18.5 1.0
CD2 D:HIS272 3.4 18.1 1.0
CG D:ASP308 3.5 18.2 1.0
OD2 D:ASP340 3.7 19.5 1.0
OD1 D:ASP310 3.9 18.6 1.0
NZ D:LYS235 3.9 18.6 1.0
OD1 D:ASP308 4.0 18.0 1.0
FE D:FE2501 4.2 19.3 1.0
OD2 D:ASP310 4.3 19.2 1.0
ND1 D:HIS272 4.4 18.4 1.0
CE D:LYS235 4.5 18.3 1.0
CG D:GLU269 4.5 18.4 1.0
CG D:ASP310 4.5 18.9 1.0
OE2 D:GLU233 4.5 19.3 1.0
CG D:HIS272 4.5 18.1 1.0
CG D:ASP340 4.7 19.6 1.0
CZ B:PHE61 4.8 22.6 1.0
CD D:LYS235 4.9 18.5 1.0
CB D:ASP308 4.9 18.4 1.0
ND2 D:ASN299 5.0 18.4 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: Tue Aug 6 06:11:26 2024

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