Iron in PDB 9evv: HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate

Enzymatic activity of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate

All present enzymatic activity of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate:
4.2.1.25; 4.2.1.6; 4.2.1.67;

Protein crystallography data

The structure of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate, PDB code: 9evv was solved by Y.Ren, J.Rouvinen, N.Hakulinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.48 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.947, 148.211, 165.025, 90, 90, 90
R / Rfree (%) 18.5 / 23.7

Other elements in 9evv:

The structure of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate (pdb code 9evv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate, PDB code: 9evv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 9evv

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Iron binding site 1 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:40.6
occ:0.73
 FE1 A:FES602 0.0 40.6 0.7
S1 A:FES602 2.2 42.4 0.7
S2 A:FES602 2.2 36.9 0.7
SG A:CYS59 2.3 43.1 1.0
SG A:CYS127 2.3 42.5 1.0
FE2 A:FES602 2.7 37.8 0.7
CB A:CYS59 3.3 38.2 1.0
CB A:CYS127 3.7 36.4 1.0
CA A:CYS127 3.9 34.2 1.0
O A:HOH767 3.9 30.2 1.0
ND2 A:ASN92 3.9 43.8 1.0
CB A:GLU91 4.4 38.8 1.0
OD1 A:ASP128 4.4 45.5 1.0
N A:ASP128 4.4 38.6 1.0
SG A:CYS200 4.5 49.0 1.0
O A:HOH763 4.6 37.4 1.0
C A:CYS127 4.7 35.8 1.0
CD1 B:TRP30 4.7 43.3 1.0
CA A:CYS59 4.8 38.4 1.0
NE1 B:TRP30 4.8 45.8 1.0
CG2 A:THR199 4.9 33.2 1.0
CG A:ASP128 4.9 39.0 1.0
N A:CYS200 4.9 40.4 1.0
CA A:THR199 5.0 36.2 1.0
N A:CYS127 5.0 36.9 1.0

Iron binding site 2 out of 8 in 9evv

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Iron binding site 2 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:37.8
occ:0.73
 FE2 A:FES602 0.0 37.8 0.7
S2 A:FES602 2.2 36.9 0.7
S1 A:FES602 2.2 42.4 0.7
O A:HOH763 2.3 37.4 1.0
SG A:CYS200 2.4 49.0 1.0
FE1 A:FES602 2.7 40.6 0.7
O A:HOH723 3.4 39.2 1.0
OD1 A:ASP128 3.6 45.5 1.0
CB A:CYS200 3.7 35.6 1.0
OD2 A:ASP128 4.1 37.5 1.0
CG A:ASP128 4.1 39.0 1.0
NE1 B:TRP30 4.2 45.8 1.0
N A:CYS200 4.3 40.4 1.0
SG A:CYS59 4.4 43.1 1.0
CA A:CYS200 4.6 37.8 1.0
O B:HOH791 4.6 46.0 1.0
SG A:CYS127 4.7 42.5 1.0
CB A:GLU91 4.8 38.8 1.0
O A:HOH743 4.9 37.3 1.0
CD1 B:TRP30 4.9 43.3 1.0
OH B:TYR26 4.9 49.4 1.0
CG A:GLU91 4.9 43.0 1.0

Iron binding site 3 out of 8 in 9evv

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Iron binding site 3 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:38.6
occ:0.78
 FE1 B:FES602 0.0 38.6 0.8
S2 B:FES602 2.2 41.0 0.8
S1 B:FES602 2.2 45.9 0.8
SG B:CYS59 2.3 43.1 1.0
SG B:CYS127 2.4 43.4 1.0
FE2 B:FES602 2.7 44.4 0.8
CB B:CYS59 3.3 33.7 1.0
CB B:CYS127 3.6 32.1 1.0
CA B:CYS127 3.8 35.1 1.0
O B:HOH780 4.1 36.0 1.0
ND2 B:ASN92 4.3 34.1 1.0
O B:HOH727 4.3 45.4 1.0
N B:ASP128 4.4 37.0 1.0
CB B:GLU91 4.5 44.3 1.0
OD1 B:ASP128 4.5 36.6 1.0
CD1 A:TRP30 4.6 44.6 1.0
SG B:CYS200 4.6 54.9 1.0
NE1 A:TRP30 4.7 47.9 1.0
C B:CYS127 4.7 36.8 1.0
CA B:CYS59 4.8 32.7 1.0
CG2 B:THR199 4.8 32.3 1.0
N B:CYS127 4.8 31.9 1.0
N B:CYS200 4.8 42.6 1.0
CA B:THR199 4.9 36.8 1.0
CG B:ASP128 4.9 36.5 1.0
CB B:THR199 5.0 36.5 1.0

Iron binding site 4 out of 8 in 9evv

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Iron binding site 4 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:44.4
occ:0.78
 FE2 B:FES602 0.0 44.4 0.8
S1 B:FES602 2.2 45.9 0.8
S2 B:FES602 2.2 41.0 0.8
O B:HOH727 2.3 45.4 1.0
SG B:CYS200 2.4 54.9 1.0
FE1 B:FES602 2.7 38.6 0.8
O B:HOH712 3.5 35.4 1.0
CB B:CYS200 3.5 42.6 1.0
OD1 B:ASP128 3.7 36.6 1.0
NE1 A:TRP30 3.9 47.9 1.0
N B:CYS200 4.1 42.6 1.0
OD2 B:ASP128 4.2 42.1 1.0
CG B:ASP128 4.3 36.5 1.0
SG B:CYS59 4.3 43.1 1.0
CA B:CYS200 4.4 42.4 1.0
CD1 A:TRP30 4.6 44.6 1.0
SG B:CYS127 4.8 43.4 1.0
OH A:TYR26 4.8 51.5 1.0
O B:HOH793 4.9 47.6 1.0
CE2 A:TRP30 4.9 45.0 1.0
CB B:GLU91 4.9 44.3 1.0

Iron binding site 5 out of 8 in 9evv

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Iron binding site 5 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe602

b:43.5
occ:0.80
 FE1 C:FES602 0.0 43.5 0.8
S1 C:FES602 2.2 44.4 0.8
S2 C:FES602 2.2 39.3 0.8
SG C:CYS59 2.3 37.3 1.0
SG C:CYS127 2.3 44.7 1.0
FE2 C:FES602 2.7 42.9 0.8
CB C:CYS59 3.4 38.0 1.0
CB C:CYS127 3.6 33.9 1.0
CA C:CYS127 3.9 36.5 1.0
ND2 C:ASN92 4.2 38.3 1.0
O C:HOH793 4.2 39.7 1.0
N C:ASP128 4.4 38.1 1.0
SG C:CYS200 4.4 57.4 1.0
OD1 C:ASP128 4.4 40.5 1.0
CG2 C:THR199 4.6 26.2 1.0
C C:CYS127 4.7 37.3 1.0
O C:HOH812 4.7 43.3 1.0
CB C:GLU91 4.7 41.7 1.0
CD1 D:TRP30 4.8 50.0 1.0
CA C:CYS59 4.8 40.5 1.0
CA C:THR199 4.8 38.2 1.0
CG C:ASP128 4.8 45.1 1.0
N C:CYS200 4.9 39.0 1.0
NE1 D:TRP30 4.9 50.4 1.0
CB C:THR199 4.9 33.2 1.0

Iron binding site 6 out of 8 in 9evv

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Iron binding site 6 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe602

b:42.9
occ:0.80
 FE2 C:FES602 0.0 42.9 0.8
S2 C:FES602 2.2 39.3 0.8
S1 C:FES602 2.2 44.4 0.8
O C:HOH812 2.4 43.3 1.0
SG C:CYS200 2.4 57.4 1.0
FE1 C:FES602 2.7 43.5 0.8
O C:HOH773 3.4 35.1 1.0
OD1 C:ASP128 3.5 40.5 1.0
CB C:CYS200 3.7 40.6 1.0
CG C:ASP128 4.1 45.1 1.0
OD2 C:ASP128 4.1 49.7 1.0
N C:CYS200 4.3 39.0 1.0
NE1 D:TRP30 4.3 50.4 1.0
SG C:CYS59 4.5 37.3 1.0
CA C:CYS200 4.6 35.0 1.0
O C:HOH809 4.6 41.3 1.0
SG C:CYS127 4.7 44.7 1.0
OH D:TYR26 4.8 47.5 1.0
O C:HOH738 4.9 47.4 1.0
CD1 D:TRP30 4.9 50.0 1.0

Iron binding site 7 out of 8 in 9evv

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Iron binding site 7 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe602

b:39.0
occ:0.91
 FE1 D:FES602 0.0 39.0 0.9
S2 D:FES602 2.2 34.4 0.9
S1 D:FES602 2.2 39.6 0.9
SG D:CYS59 2.3 38.6 1.0
SG D:CYS127 2.4 38.1 1.0
FE2 D:FES602 2.7 42.8 0.9
CB D:CYS59 3.3 33.1 1.0
O D:HOH784 3.6 33.2 1.0
CB D:CYS127 3.7 33.7 1.0
CA D:CYS127 3.9 31.2 1.0
OD1 D:ASN92 4.2 35.2 1.0
CB D:GLU91 4.2 34.2 1.0
N D:ASP128 4.5 37.5 1.0
SG D:CYS200 4.5 43.3 1.0
CD1 C:TRP30 4.7 41.6 1.0
CA D:CYS59 4.7 31.9 1.0
C D:CYS127 4.8 35.5 1.0
CG2 D:THR199 4.8 27.5 1.0
OD1 D:ASP128 4.9 45.5 1.0
CA D:THR199 4.9 33.0 1.0
N D:CYS200 4.9 36.0 1.0
NE1 C:TRP30 5.0 40.6 1.0
N D:GLU91 5.0 40.7 1.0

Iron binding site 8 out of 8 in 9evv

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Iron binding site 8 out of 8 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe602

b:42.8
occ:0.91
 FE2 D:FES602 0.0 42.8 0.9
S1 D:FES602 2.2 39.6 0.9
S2 D:FES602 2.2 34.4 0.9
SG D:CYS200 2.3 43.3 1.0
FE1 D:FES602 2.7 39.0 0.9
O D:HOH707 3.1 39.6 1.0
H32 D:2KT603 3.5 58.7 1.0
CB D:CYS200 3.7 32.0 1.0
OD1 D:ASP128 3.8 45.5 1.0
OD2 D:ASP128 4.0 39.1 1.0
N D:CYS200 4.1 36.0 1.0
CG D:ASP128 4.1 42.0 1.0
NE1 C:TRP30 4.3 40.6 1.0
C3 D:2KT603 4.4 48.9 1.0
SG D:CYS59 4.5 38.6 1.0
CA D:CYS200 4.5 40.5 1.0
C2 D:2KT603 4.6 55.2 1.0
SG D:CYS127 4.6 38.1 1.0
CB D:GLU91 4.7 34.2 1.0
H43 D:2KT603 4.7 54.5 1.0
CG D:GLU91 4.7 34.8 1.0
CD1 C:TRP30 4.8 41.6 1.0
O3 D:2KT603 4.9 45.1 1.0
O D:2KT603 5.0 32.1 1.0

Reference:

Y.Ren, E.Vettenranta, L.Penttinen, M.Blomster Andberg, A.Koivula, J.Rouvinen, N.Hakulinen. Unveiling the Importance of the C-Terminus in the Sugar Acid Dehydratase of the Ilvd/Edd Superfamily. Appl.Microbiol.Biotechnol. V. 108 436 2024.
ISSN: ESSN 1432-0614
PubMed: 39126499
DOI: 10.1007/S00253-024-13270-8
Page generated: Thu Oct 31 21:02:03 2024

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