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Manganese in PDB 6k1f: Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.

Enzymatic activity of Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.

All present enzymatic activity of Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.:
5.3.1.25;

Protein crystallography data

The structure of Crystal Structure of the L-Fucose Isomerase From Raoultella Sp., PDB code: 6k1f was solved by I.J.Kim, D.H.Kim, K.H.Nam, K.H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.987, 127.611, 257.298, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp. (pdb code 6k1f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp., PDB code: 6k1f:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6k1f

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Manganese binding site 1 out of 6 in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.


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 the L-Fucose Isomerase From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:68.3
occ:1.00
 NE2 A:HIS528 2.5 40.8 1.0
OE1 A:GLU337 2.7 50.4 1.0
OD1 A:ASP361 2.8 51.7 1.0
OG A:SER393 3.2 38.7 1.0
CD2 A:HIS528 3.4 36.7 1.0
CE1 A:HIS528 3.4 37.1 1.0
OD2 A:ASP361 3.5 42.5 1.0
CG A:ASP361 3.5 42.9 1.0
CD A:GLU337 3.5 46.5 1.0
OE2 A:GLU337 3.7 47.5 1.0
CB A:SER393 4.1 39.6 1.0
OD1 A:ASN392 4.2 40.4 1.0
ND2 A:ASN527 4.4 38.2 1.0
ND1 A:HIS528 4.6 34.0 1.0
CG A:HIS528 4.6 33.8 1.0
N A:SER393 4.8 35.7 1.0
CG A:GLU337 4.9 43.8 1.0
CB A:ASP361 5.0 40.2 1.0

Manganese binding site 2 out of 6 in 6k1f

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Manganese binding site 2 out of 6 in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.


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 the L-Fucose Isomerase From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:72.0
occ:1.00
 NE2 B:HIS528 2.6 48.6 1.0
OE1 B:GLU337 2.7 48.2 1.0
OD1 B:ASP361 2.8 56.8 1.0
O B:HOH721 2.8 32.8 1.0
ND2 B:ASN527 3.3 33.9 1.0
CE1 B:HIS528 3.4 42.5 1.0
CD B:GLU337 3.5 36.5 1.0
OE2 B:GLU337 3.5 36.7 1.0
CD2 B:HIS528 3.6 41.5 1.0
CG B:ASP361 3.8 46.1 1.0
OD2 B:ASP361 4.0 53.6 1.0
CG B:ASN527 4.5 34.1 1.0
ND1 B:HIS528 4.6 40.3 1.0
CD1 B:ILE187 4.7 32.8 1.0
CG B:HIS528 4.7 38.5 1.0
CH2 A:TRP90 4.7 33.6 1.0
CZ2 A:TRP90 4.8 34.5 1.0
OG B:SER393 4.8 40.4 1.0

Manganese binding site 3 out of 6 in 6k1f

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Manganese binding site 3 out of 6 in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.


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 the L-Fucose Isomerase From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:67.4
occ:1.00
 NE2 C:HIS528 2.5 44.9 1.0
OE1 C:GLU337 2.7 46.3 1.0
OD1 C:ASP361 2.7 53.1 1.0
O C:HOH844 2.9 25.1 1.0
CD C:GLU337 3.3 40.7 1.0
OE2 C:GLU337 3.3 40.3 1.0
CD2 C:HIS528 3.3 40.7 1.0
OG C:SER393 3.3 32.0 1.0
CE1 C:HIS528 3.4 42.5 1.0
CG C:ASP361 3.5 44.5 1.0
OD2 C:ASP361 3.7 50.7 1.0
OD1 C:ASN392 3.8 31.3 1.0
CB C:SER393 4.1 33.0 1.0
CG C:HIS528 4.4 38.2 1.0
ND1 C:HIS528 4.5 38.5 1.0
ND2 C:ASN527 4.5 33.0 1.0
N C:SER393 4.6 33.3 1.0
CG C:GLU337 4.7 35.5 1.0
CE1 C:PHE359 4.7 25.8 1.0
CG2 C:THR336 4.7 26.7 1.0
CB C:ASP361 4.8 41.3 1.0

Manganese binding site 4 out of 6 in 6k1f

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Manganese binding site 4 out of 6 in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.


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 the L-Fucose Isomerase From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:66.2
occ:1.00
 NE2 D:HIS528 2.5 33.9 1.0
OE1 D:GLU337 2.7 38.0 1.0
OD1 D:ASP361 2.8 54.0 1.0
ND2 D:ASN527 3.1 22.8 1.0
O D:HOH891 3.1 30.4 1.0
CE1 D:HIS528 3.4 29.5 1.0
CD2 D:HIS528 3.5 29.8 1.0
CD D:GLU337 3.6 29.7 1.0
CG D:ASP361 3.7 41.6 1.0
OE2 D:GLU337 3.7 31.0 1.0
OD2 D:ASP361 3.8 47.3 1.0
CG D:ASN527 4.4 22.9 1.0
OG D:SER393 4.4 34.0 1.0
ND1 D:HIS528 4.6 27.0 1.0
CG D:HIS528 4.6 27.0 1.0
CH2 F:TRP90 4.7 23.5 1.0
CD1 D:ILE187 4.7 24.8 1.0
CZ2 F:TRP90 4.8 23.0 1.0
CZ3 F:TRP90 4.9 23.8 1.0

Manganese binding site 5 out of 6 in 6k1f

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Manganese binding site 5 out of 6 in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.


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 the L-Fucose Isomerase From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn601

b:75.3
occ:1.00
 NE2 E:HIS528 2.5 51.0 1.0
OE1 E:GLU337 2.7 55.7 1.0
OD1 E:ASP361 2.8 51.9 1.0
O E:HOH796 3.1 25.4 1.0
CE1 E:HIS528 3.3 47.6 1.0
OE2 E:GLU337 3.3 52.4 1.0
ND2 E:ASN527 3.3 36.1 1.0
CD E:GLU337 3.4 52.3 1.0
CG E:ASP361 3.6 44.6 1.0
CD2 E:HIS528 3.7 45.3 1.0
OD2 E:ASP361 3.7 50.7 1.0
ND1 E:HIS528 4.5 42.9 1.0
CD1 E:ILE187 4.5 36.4 1.0
CG E:ASN527 4.6 36.0 1.0
CG E:HIS528 4.7 39.6 1.0
CH2 D:TRP90 4.8 37.1 1.0
CZ2 D:TRP90 4.8 35.7 1.0
CG E:GLU337 4.9 48.4 1.0

Manganese binding site 6 out of 6 in 6k1f

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Manganese binding site 6 out of 6 in the Crystal Structure of the L-Fucose Isomerase From Raoultella Sp.


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 the L-Fucose Isomerase From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn601

b:74.0
occ:1.00
 NE2 F:HIS528 2.5 44.1 1.0
OE1 F:GLU337 2.7 42.4 1.0
OD1 F:ASP361 2.8 58.5 1.0
OE2 F:GLU337 2.9 40.0 1.0
CD F:GLU337 3.1 37.0 1.0
OD2 F:ASP361 3.4 56.9 1.0
CE1 F:HIS528 3.4 40.6 1.0
CG F:ASP361 3.5 49.2 1.0
CD2 F:HIS528 3.6 40.0 1.0
OG F:SER393 3.7 33.8 1.0
ND2 F:ASN527 4.1 34.8 1.0
CB F:SER393 4.5 34.0 1.0
ND1 F:HIS528 4.6 37.3 1.0
CG F:GLU337 4.6 33.3 1.0
CG F:HIS528 4.7 37.5 1.0
CD1 F:ILE187 4.9 27.4 1.0
OD1 F:ASN392 4.9 35.1 1.0
CB F:ASP361 4.9 43.2 1.0

Reference:

I.J.Kim, D.H.Kim, K.H.Nam, K.H.Kim. Crystal Structure of the L-Fucose Isomerase From Raoultella Sp. To Be Published.
Page generated: Sun Oct 6 05:13:26 2024

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