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Manganese in PDB 4uxa: Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria

Protein crystallography data

The structure of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria, PDB code: 4uxa was solved by T.Pavkov-Keller, R.Wiedner, B.Kothbauer, M.Gruber-Khadjawi, H.Schwab, K.Steiner, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.28 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.806, 93.174, 146.671, 90.00, 111.93, 90.00
R / Rfree (%) 18.082 / 23.397

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Manganese atom in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria (pdb code 4uxa). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 20 binding sites of Manganese where determined in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria, PDB code: 4uxa:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 20 in 4uxa

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Manganese binding site 1 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn200

b:44.5
occ:1.00
 OE1 A:GLN59 2.2 44.1 1.0
NE2 A:HIS53 2.4 40.7 1.0
NE2 A:HIS94 2.4 45.5 1.0
NE2 A:HIS96 2.5 34.9 1.0
NE2 A:HIS55 2.6 37.2 1.0
O A:HOH2045 2.9 30.2 1.0
CD A:GLN59 3.0 39.8 1.0
NE2 A:GLN59 3.3 36.8 1.0
CE1 A:HIS96 3.3 35.8 1.0
CE1 A:HIS94 3.3 45.0 1.0
CD2 A:HIS53 3.3 40.5 1.0
CD2 A:HIS55 3.4 40.5 1.0
CE1 A:HIS53 3.4 45.0 1.0
CD2 A:HIS94 3.4 42.1 1.0
CD2 A:HIS96 3.5 36.6 1.0
CE1 A:HIS55 3.6 39.7 1.0
CG A:GLN59 4.4 40.1 1.0
ND1 A:HIS94 4.4 45.4 1.0
ND1 A:HIS96 4.5 35.4 1.0
CG A:HIS53 4.5 41.2 1.0
ND1 A:HIS53 4.5 43.4 1.0
CG A:HIS94 4.5 40.8 1.0
CG A:HIS55 4.6 38.1 1.0
CG A:HIS96 4.6 38.1 1.0
CB A:GLN59 4.7 39.8 1.0
ND1 A:HIS55 4.7 43.5 1.0
CD2 A:PHE88 4.7 40.1 1.0
CE2 A:PHE88 4.9 41.8 1.0

Manganese binding site 2 out of 20 in 4uxa

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Manganese binding site 2 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn200

b:39.7
occ:1.00
 OE1 B:GLN59 2.2 32.9 1.0
NE2 B:HIS53 2.3 33.5 1.0
NE2 B:HIS94 2.5 33.8 1.0
NE2 B:HIS96 2.5 31.6 1.0
NE2 B:HIS55 2.5 38.2 1.0
O B:HOH2055 2.7 31.9 1.0
CD B:GLN59 3.0 30.8 1.0
CE1 B:HIS53 3.2 34.5 1.0
CE1 B:HIS94 3.2 32.5 1.0
CD2 B:HIS53 3.3 33.7 1.0
CD2 B:HIS96 3.4 29.4 1.0
CD2 B:HIS55 3.4 36.6 1.0
CE1 B:HIS55 3.4 38.8 1.0
NE2 B:GLN59 3.4 30.9 1.0
CE1 B:HIS96 3.4 32.6 1.0
CD2 B:HIS94 3.5 30.4 1.0
ND1 B:HIS53 4.3 33.0 1.0
CG B:GLN59 4.3 34.3 1.0
ND1 B:HIS94 4.4 35.2 1.0
CG B:HIS53 4.4 33.4 1.0
CG B:HIS94 4.5 33.6 1.0
ND1 B:HIS55 4.5 38.8 1.0
ND1 B:HIS96 4.6 33.3 1.0
CG B:HIS96 4.6 30.7 1.0
CG B:HIS55 4.6 37.1 1.0
CB B:GLN59 4.6 33.3 1.0
CD2 B:PHE88 4.7 37.4 1.0
CE2 B:PHE88 4.8 36.9 1.0

Manganese binding site 3 out of 20 in 4uxa

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Manganese binding site 3 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn200

b:46.9
occ:1.00
 OE1 C:GLN59 2.3 32.7 1.0
NE2 C:HIS94 2.4 33.7 1.0
NE2 C:HIS53 2.4 42.3 1.0
NE2 C:HIS96 2.5 36.6 1.0
NE2 C:HIS55 2.5 38.2 1.0
O C:HOH2051 2.6 37.5 1.0
CD C:GLN59 3.1 33.0 1.0
CD2 C:HIS55 3.2 39.3 1.0
CE1 C:HIS94 3.2 36.4 1.0
CD2 C:HIS53 3.3 41.4 1.0
CE1 C:HIS96 3.4 35.5 1.0
CE1 C:HIS53 3.4 41.9 1.0
CD2 C:HIS94 3.4 32.8 1.0
NE2 C:GLN59 3.4 33.8 1.0
CD2 C:HIS96 3.5 34.4 1.0
CE1 C:HIS55 3.7 39.0 1.0
CG C:GLN59 4.4 33.5 1.0
ND1 C:HIS94 4.4 39.5 1.0
CG C:HIS53 4.5 41.9 1.0
CG C:HIS55 4.5 37.7 1.0
ND1 C:HIS53 4.5 43.4 1.0
CG C:HIS94 4.5 35.2 1.0
ND1 C:HIS96 4.5 37.8 1.0
CB C:GLN59 4.6 34.0 1.0
CG C:HIS96 4.6 34.8 1.0
ND1 C:HIS55 4.7 39.4 1.0
CD2 C:PHE88 4.7 32.4 1.0
CE2 C:PHE88 4.8 32.6 1.0

Manganese binding site 4 out of 20 in 4uxa

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Manganese binding site 4 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn200

b:30.7
occ:1.00
 OE1 D:GLN59 2.2 26.3 1.0
NE2 D:HIS53 2.3 31.0 1.0
NE2 D:HIS96 2.3 27.3 1.0
NE2 D:HIS55 2.4 30.4 1.0
NE2 D:HIS94 2.5 28.2 1.0
O D:HOH2064 2.5 26.3 1.0
CD D:GLN59 3.1 27.1 1.0
CE1 D:HIS96 3.2 26.6 1.0
CD2 D:HIS55 3.2 29.9 1.0
CD2 D:HIS53 3.2 29.3 1.0
CE1 D:HIS53 3.3 30.9 1.0
CE1 D:HIS94 3.3 28.5 1.0
CE1 D:HIS55 3.4 30.5 1.0
CD2 D:HIS96 3.4 27.4 1.0
CD2 D:HIS94 3.5 27.7 1.0
NE2 D:GLN59 3.5 28.6 1.0
ND1 D:HIS96 4.3 25.4 1.0
ND1 D:HIS53 4.4 30.3 1.0
CG D:HIS53 4.4 29.7 1.0
CG D:HIS55 4.4 29.5 1.0
CG D:GLN59 4.4 30.5 1.0
ND1 D:HIS94 4.5 29.8 1.0
ND1 D:HIS55 4.5 31.9 1.0
CG D:HIS96 4.5 26.1 1.0
CG D:HIS94 4.6 26.8 1.0
CB D:GLN59 4.6 29.2 1.0
CD2 D:PHE88 4.6 31.1 1.0
CE2 D:PHE88 4.8 31.2 1.0

Manganese binding site 5 out of 20 in 4uxa

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Manganese binding site 5 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn200

b:40.9
occ:1.00
 OE1 E:GLN59 2.2 33.5 1.0
NE2 E:HIS55 2.3 42.0 1.0
NE2 E:HIS53 2.4 39.4 1.0
NE2 E:HIS96 2.4 37.2 1.0
NE2 E:HIS94 2.5 42.8 1.0
O E:HOH2039 2.6 41.5 1.0
CD E:GLN59 3.0 32.6 1.0
CE1 E:HIS96 3.2 39.7 1.0
CD2 E:HIS53 3.2 39.1 1.0
NE2 E:GLN59 3.3 33.5 1.0
CE1 E:HIS55 3.3 39.9 1.0
CE1 E:HIS94 3.3 40.0 1.0
CD2 E:HIS55 3.4 42.2 1.0
CE1 E:HIS53 3.4 42.6 1.0
CD2 E:HIS96 3.5 38.4 1.0
CD2 E:HIS94 3.6 39.9 1.0
CG E:GLN59 4.3 36.3 1.0
ND1 E:HIS96 4.4 37.4 1.0
ND1 E:HIS55 4.4 40.3 1.0
CG E:HIS53 4.4 39.7 1.0
ND1 E:HIS94 4.4 40.9 1.0
ND1 E:HIS53 4.4 43.0 1.0
CG E:HIS55 4.5 39.6 1.0
CG E:HIS96 4.6 35.7 1.0
CG E:HIS94 4.6 39.8 1.0
CB E:GLN59 4.6 36.7 1.0
CD2 E:PHE88 4.7 40.8 1.0
CE2 E:PHE88 4.9 40.9 1.0

Manganese binding site 6 out of 20 in 4uxa

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Manganese binding site 6 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn200

b:39.6
occ:1.00
 OE1 F:GLN59 2.0 35.6 1.0
NE2 F:HIS53 2.4 35.1 1.0
NE2 F:HIS55 2.4 40.0 1.0
NE2 F:HIS96 2.5 32.9 1.0
NE2 F:HIS94 2.5 40.9 1.0
O F:HOH2048 2.7 33.0 1.0
CD F:GLN59 3.0 35.2 1.0
CD2 F:HIS53 3.3 33.0 1.0
CE1 F:HIS96 3.3 34.9 1.0
CD2 F:HIS55 3.3 37.3 1.0
CE1 F:HIS53 3.3 36.6 1.0
CE1 F:HIS94 3.4 38.8 1.0
NE2 F:GLN59 3.4 37.7 1.0
CE1 F:HIS55 3.5 41.2 1.0
CD2 F:HIS94 3.5 38.6 1.0
CD2 F:HIS96 3.5 33.3 1.0
CG F:GLN59 4.3 36.7 1.0
CG F:HIS53 4.4 33.7 1.0
ND1 F:HIS53 4.4 37.3 1.0
ND1 F:HIS96 4.5 36.6 1.0
CG F:HIS55 4.5 39.2 1.0
ND1 F:HIS94 4.5 40.3 1.0
CB F:GLN59 4.5 36.0 1.0
ND1 F:HIS55 4.6 42.6 1.0
CD2 F:PHE88 4.6 35.1 1.0
CG F:HIS94 4.6 35.6 1.0
CG F:HIS96 4.6 34.1 1.0
CE2 F:PHE88 4.8 37.6 1.0

Manganese binding site 7 out of 20 in 4uxa

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Manganese binding site 7 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn200

b:45.0
occ:1.00
 OE1 G:GLN59 2.1 38.3 1.0
NE2 G:HIS53 2.3 28.8 1.0
NE2 G:HIS94 2.5 27.5 1.0
NE2 G:HIS55 2.5 38.3 1.0
NE2 G:HIS96 2.5 27.9 1.0
O G:HOH2041 2.9 28.9 1.0
CD G:GLN59 3.0 38.0 1.0
CD2 G:HIS55 3.2 38.9 1.0
CE1 G:HIS53 3.3 31.8 1.0
CD2 G:HIS53 3.3 29.9 1.0
CE1 G:HIS94 3.4 29.4 1.0
NE2 G:GLN59 3.4 34.4 1.0
CD2 G:HIS94 3.4 27.5 1.0
CD2 G:HIS96 3.5 28.9 1.0
CE1 G:HIS96 3.5 29.0 1.0
CE1 G:HIS55 3.6 37.4 1.0
CG G:GLN59 4.3 38.5 1.0
ND1 G:HIS53 4.4 31.7 1.0
CG G:HIS53 4.4 31.4 1.0
ND1 G:HIS94 4.5 29.0 1.0
CG G:HIS55 4.5 35.5 1.0
CB G:GLN59 4.5 36.0 1.0
CG G:HIS94 4.5 26.8 1.0
CD2 G:PHE88 4.6 32.0 1.0
ND1 G:HIS96 4.6 29.1 1.0
ND1 G:HIS55 4.6 38.6 1.0
CG G:HIS96 4.6 27.3 1.0
CE2 G:PHE88 4.8 32.5 1.0

Manganese binding site 8 out of 20 in 4uxa

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Manganese binding site 8 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn200

b:38.7
occ:1.00
 OE1 H:GLN59 2.1 37.2 1.0
NE2 H:HIS53 2.2 38.2 1.0
NE2 H:HIS55 2.4 37.8 1.0
NE2 H:HIS94 2.5 39.8 1.0
NE2 H:HIS96 2.5 33.4 1.0
O H:HOH2044 2.5 33.5 1.0
CD H:GLN59 3.1 37.8 1.0
CE1 H:HIS53 3.2 40.0 1.0
CD2 H:HIS53 3.2 36.3 1.0
CE1 H:HIS94 3.2 37.6 1.0
CD2 H:HIS55 3.3 35.5 1.0
CD2 H:HIS96 3.4 35.7 1.0
CE1 H:HIS55 3.4 37.0 1.0
NE2 H:GLN59 3.5 38.2 1.0
CE1 H:HIS96 3.5 38.1 1.0
CD2 H:HIS94 3.5 38.9 1.0
ND1 H:HIS53 4.3 38.6 1.0
CG H:HIS53 4.3 36.7 1.0
CG H:GLN59 4.4 38.4 1.0
ND1 H:HIS94 4.4 38.4 1.0
CG H:HIS55 4.5 37.3 1.0
ND1 H:HIS55 4.5 39.6 1.0
CG H:HIS94 4.6 35.6 1.0
CB H:GLN59 4.6 35.0 1.0
ND1 H:HIS96 4.6 34.8 1.0
CG H:HIS96 4.6 33.5 1.0
CD2 H:PHE88 4.7 37.0 1.0
CE2 H:PHE88 5.0 35.4 1.0

Manganese binding site 9 out of 20 in 4uxa

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Manganese binding site 9 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn200

b:48.2
occ:1.00
 OE1 I:GLN59 2.0 38.1 1.0
NE2 I:HIS53 2.4 40.5 1.0
NE2 I:HIS96 2.4 40.2 1.0
NE2 I:HIS55 2.5 45.4 1.0
NE2 I:HIS94 2.5 44.0 1.0
O I:HOH2044 2.6 42.0 1.0
CD I:GLN59 3.0 40.8 1.0
CD2 I:HIS53 3.3 37.5 1.0
CE1 I:HIS96 3.3 39.8 1.0
CD2 I:HIS55 3.3 42.6 1.0
CE1 I:HIS53 3.4 41.1 1.0
NE2 I:GLN59 3.4 39.7 1.0
CE1 I:HIS94 3.4 45.8 1.0
CD2 I:HIS96 3.5 40.3 1.0
CD2 I:HIS94 3.5 43.4 1.0
CE1 I:HIS55 3.5 42.4 1.0
CG I:GLN59 4.3 41.7 1.0
ND1 I:HIS53 4.4 41.1 1.0
CG I:HIS53 4.4 40.0 1.0
ND1 I:HIS96 4.5 41.6 1.0
ND1 I:HIS94 4.5 42.9 1.0
CG I:HIS55 4.5 41.6 1.0
CG I:HIS96 4.6 38.7 1.0
ND1 I:HIS55 4.6 41.8 1.0
CG I:HIS94 4.6 43.8 1.0
CB I:GLN59 4.6 45.0 1.0
CD2 I:PHE88 4.6 38.0 1.0
CE2 I:PHE88 4.8 36.4 1.0

Manganese binding site 10 out of 20 in 4uxa

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Manganese binding site 10 out of 20 in the Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Improved Variant of (R)-Selective Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn200

b:39.6
occ:1.00
 OE1 J:GLN59 2.1 37.9 1.0
NE2 J:HIS53 2.3 36.6 1.0
NE2 J:HIS94 2.5 36.3 1.0
NE2 J:HIS96 2.5 36.4 1.0
NE2 J:HIS55 2.5 43.2 1.0
O J:HOH2036 2.7 33.1 1.0
CD J:GLN59 3.0 37.3 1.0
CE1 J:HIS53 3.2 37.3 1.0
CD2 J:HIS53 3.2 37.2 1.0
CD2 J:HIS55 3.3 41.2 1.0
NE2 J:GLN59 3.4 40.1 1.0
CD2 J:HIS94 3.4 36.6 1.0
CE1 J:HIS94 3.4 38.1 1.0
CD2 J:HIS96 3.4 33.3 1.0
CE1 J:HIS96 3.5 37.5 1.0
CE1 J:HIS55 3.6 41.7 1.0
ND1 J:HIS53 4.3 37.4 1.0
CG J:GLN59 4.4 35.2 1.0
CG J:HIS53 4.4 36.2 1.0
CG J:HIS55 4.5 41.0 1.0
ND1 J:HIS94 4.5 35.9 1.0
CG J:HIS94 4.5 37.0 1.0
ND1 J:HIS96 4.6 37.4 1.0
CG J:HIS96 4.6 34.0 1.0
ND1 J:HIS55 4.7 43.0 1.0
CB J:GLN59 4.7 33.8 1.0
CD2 J:PHE88 4.7 39.7 1.0
CE2 J:PHE88 4.8 40.2 1.0

Reference:

R.Wiedner, B.Kothbauer, T.Pavkov-Keller, M.Gruber-Khadjawi, K.Grube, H.Schwab, K.Steiner. Improving the Properties of Bacterial R-Selective Hydroxynitrile Lyases For Industrial Applications Chemcatchem 2015.
ISSN: ESSN 1867-3899
DOI: 10.1002/CCTC.201402742
Page generated: Sat Oct 5 21:28:01 2024

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