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Manganese in PDB 6k1g: Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ From Raoultella Sp.

Enzymatic activity of Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ From Raoultella Sp.

All present enzymatic activity of Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ From Raoultella Sp.:
5.3.1.25;

Protein crystallography data

The structure of Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ From Raoultella Sp., PDB code: 6k1g 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) 30.00 / 2.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.274, 163.278, 196.343, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 25.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ From Raoultella Sp. (pdb code 6k1g). 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 Soaked with MN2+ From Raoultella Sp., PDB code: 6k1g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6k1g

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Manganese binding site 1 out of 6 in the Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ 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 Soaked with MN2+ From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:69.4
occ:1.00
 NE2 A:HIS528 2.5 42.6 1.0
OE1 A:GLU337 2.6 68.8 1.0
OE2 A:GLU337 2.7 66.3 1.0
OD2 A:ASP361 2.8 74.7 1.0
OD1 A:ASP361 2.8 70.7 1.0
O A:HOH719 2.8 24.7 1.0
CD A:GLU337 3.0 57.1 1.0
CG A:ASP361 3.1 63.4 1.0
CD2 A:HIS528 3.4 41.3 1.0
CE1 A:HIS528 3.5 39.3 1.0
ND2 A:ASN527 4.3 30.4 1.0
OG A:SER393 4.4 61.9 1.0
CG A:GLU337 4.5 47.4 1.0
CG A:HIS528 4.6 38.0 1.0
CB A:ASP361 4.6 54.2 1.0
ND1 A:HIS528 4.6 37.8 1.0
CB A:SER393 4.7 57.1 1.0

Manganese binding site 2 out of 6 in 6k1g

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Manganese binding site 2 out of 6 in the Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ 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 Soaked with MN2+ From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:64.0
occ:1.00
 NE2 B:HIS528 2.6 71.1 1.0
OE1 B:GLU337 2.6 65.9 1.0
OE2 B:GLU337 2.6 56.7 1.0
OD1 B:ASP361 2.7 62.8 1.0
OD2 B:ASP361 2.7 56.1 1.0
CD B:GLU337 2.9 61.3 1.0
CG B:ASP361 3.0 57.0 1.0
CE1 B:HIS528 3.5 74.7 1.0
ND2 B:ASN527 3.5 54.7 1.0
CD2 B:HIS528 3.6 69.1 1.0
CG B:GLU337 4.5 56.6 1.0
CB B:ASP361 4.5 54.4 1.0
ND1 B:HIS528 4.6 67.0 1.0
CG B:HIS528 4.7 63.7 1.0
CG B:ASN527 4.8 57.3 1.0

Manganese binding site 3 out of 6 in 6k1g

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Manganese binding site 3 out of 6 in the Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ 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 Soaked with MN2+ From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:74.7
occ:1.00
 NE2 C:HIS528 2.5 70.0 1.0
OE1 C:GLU337 2.6 61.2 1.0
OE2 C:GLU337 2.7 70.7 1.0
OD2 C:ASP361 2.7 76.1 1.0
OD1 C:ASP361 2.7 72.1 1.0
CD C:GLU337 3.0 59.5 1.0
O C:HOH712 3.0 29.3 1.0
CG C:ASP361 3.0 73.2 1.0
CE1 C:HIS528 3.3 68.1 1.0
CD2 C:HIS528 3.5 68.3 1.0
OG C:SER393 4.2 77.5 1.0
ND2 C:ASN527 4.3 63.8 1.0
CG C:GLU337 4.5 57.7 1.0
ND1 C:HIS528 4.5 66.3 1.0
CB C:ASP361 4.5 70.7 1.0
CG C:HIS528 4.6 68.3 1.0
OD1 C:ASN392 4.8 68.8 1.0
CB C:SER393 4.8 74.9 1.0
CD1 C:ILE187 4.9 65.4 1.0
CG2 C:THR336 4.9 61.3 1.0

Manganese binding site 4 out of 6 in 6k1g

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Manganese binding site 4 out of 6 in the Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ 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 Soaked with MN2+ From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:73.0
occ:1.00
 NE2 D:HIS528 2.5 56.4 1.0
OE1 D:GLU337 2.6 68.0 1.0
O D:HOH714 2.7 44.0 1.0
OE2 D:GLU337 2.7 62.2 1.0
OD1 D:ASP361 2.7 68.6 1.0
OD2 D:ASP361 2.7 62.2 1.0
CD D:GLU337 3.0 58.1 1.0
CG D:ASP361 3.1 61.2 1.0
CE1 D:HIS528 3.3 48.7 1.0
OG D:SER393 3.3 62.7 1.0
CD2 D:HIS528 3.5 51.8 1.0
ND2 D:ASN527 3.7 50.2 1.0
ND1 D:HIS528 4.5 46.8 1.0
CG D:GLU337 4.5 51.6 1.0
CG D:HIS528 4.6 46.2 1.0
CB D:ASP361 4.6 54.3 1.0
CB D:SER393 4.7 59.9 1.0
OD1 D:ASN392 4.7 47.7 1.0

Manganese binding site 5 out of 6 in 6k1g

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Manganese binding site 5 out of 6 in the Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ 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 Soaked with MN2+ From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn601

b:81.2
occ:1.00
 NE2 E:HIS528 2.5 54.5 1.0
OE1 E:GLU337 2.7 78.9 1.0
OE2 E:GLU337 2.7 75.0 1.0
OD2 E:ASP361 2.7 76.0 1.0
OD1 E:ASP361 2.7 77.9 1.0
CD E:GLU337 3.0 71.7 1.0
CG E:ASP361 3.1 74.2 1.0
CE1 E:HIS528 3.2 53.8 1.0
CD2 E:HIS528 3.6 49.0 1.0
ND2 E:ASN527 4.3 48.2 1.0
CG E:GLU337 4.4 68.8 1.0
ND1 E:HIS528 4.4 55.0 1.0
CD1 E:ILE187 4.6 50.3 1.0
CB E:SER393 4.7 87.4 1.0
CB E:ASP361 4.7 66.2 1.0
CG E:HIS528 4.7 51.1 1.0
CB E:GLU337 4.9 61.9 1.0

Manganese binding site 6 out of 6 in 6k1g

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Manganese binding site 6 out of 6 in the Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ 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 Soaked with MN2+ From Raoultella Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn601

b:90.1
occ:1.00
 NE2 F:HIS528 2.5 82.2 1.0
OE2 F:GLU337 2.6 84.0 1.0
OE1 F:GLU337 2.6 82.9 1.0
OD2 F:ASP361 2.7 79.3 1.0
OD1 F:ASP361 2.7 80.8 1.0
CD F:GLU337 2.9 81.0 1.0
CG F:ASP361 3.1 79.8 1.0
CD2 F:HIS528 3.5 77.9 1.0
CE1 F:HIS528 3.5 76.2 1.0
ND2 F:ASN527 3.9 81.4 1.0
CG F:GLU337 4.4 76.5 1.0
CB F:ASP361 4.6 80.2 1.0
ND1 F:HIS528 4.6 73.3 1.0
CG F:HIS528 4.7 75.5 1.0
CD1 F:ILE187 4.9 91.8 1.0
CB F:SER393 4.9 83.0 1.0
CG F:ASN527 5.0 82.1 1.0

Reference:

I.J.Kim, D.H.Kim, K.H.Nam, K.H.Kim. Crystal Structure of the L-Fucose Isomerase Soaked with MN2+ From Raoultella Sp. To Be Published.
Page generated: Sun Oct 6 05:13:47 2024

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