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Magnesium in PDB 4kt2: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol

Enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol

All present enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol, PDB code: 4kt2 was solved by A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.17 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.585, 177.787, 109.993, 90.00, 102.62, 90.00
R / Rfree (%) 14.9 / 18.2

Other elements in 4kt2:

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol (pdb code 4kt2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol, PDB code: 4kt2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4kt2

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Magnesium binding site 1 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:24.6
occ:1.00
 O A:HOH865 2.2 18.7 1.0
OE1 A:GLU265 2.2 18.4 1.0
OD2 A:ASP213 2.2 17.7 1.0
OE1 A:GLU239 2.2 22.4 1.0
O A:HOH867 2.3 25.7 1.0
O A:HOH806 2.3 19.6 1.0
CD A:GLU265 3.0 19.8 1.0
CG A:ASP213 3.1 21.0 1.0
CD A:GLU239 3.2 21.5 1.0
OE2 A:GLU265 3.3 19.7 1.0
OD1 A:ASP213 3.5 19.2 1.0
NH2 A:ARG286 3.8 17.4 1.0
OE2 A:GLU239 3.9 19.1 1.0
CD2 A:HIS215 4.0 26.9 1.0
O A:HOH630 4.0 20.1 1.0
OD2 A:ASP240 4.1 18.0 1.0
CG A:GLU239 4.1 17.5 1.0
O A:HOH871 4.1 36.3 1.0
NE2 A:HIS215 4.3 32.8 1.0
O A:HOH604 4.3 15.7 1.0
CG A:GLU265 4.3 13.8 1.0
O A:HOH691 4.4 22.9 1.0
CB A:ASP213 4.4 19.5 1.0
OH E:TYR77 4.6 18.6 1.0
CG A:ASP240 4.7 21.8 1.0
NE2 A:HIS315 4.9 14.4 1.0
CZ A:ARG286 4.9 18.9 1.0
O A:HOH812 4.9 38.0 1.0
CD2 A:HIS315 4.9 12.2 1.0
NE A:ARG286 5.0 22.8 1.0

Magnesium binding site 2 out of 8 in 4kt2

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Magnesium binding site 2 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:27.2
occ:1.00
 O B:HOH865 2.2 21.5 1.0
OE1 B:GLU239 2.2 17.1 1.0
OE1 B:GLU265 2.2 21.0 1.0
O B:HOH867 2.3 27.3 1.0
OD2 B:ASP213 2.3 23.0 1.0
O B:HOH866 2.4 28.2 1.0
CD B:GLU265 3.0 17.0 1.0
CG B:ASP213 3.2 21.9 1.0
OE2 B:GLU265 3.2 20.4 1.0
CD B:GLU239 3.2 21.1 1.0
OD1 B:ASP213 3.5 17.5 1.0
NH2 B:ARG286 3.7 16.6 1.0
OE2 B:GLU239 3.9 15.8 1.0
O B:HOH627 4.0 18.8 1.0
CD2 B:HIS215 4.0 21.4 1.0
CG B:GLU239 4.1 17.4 1.0
OD2 B:ASP240 4.2 18.1 1.0
O B:HOH618 4.3 21.3 1.0
O B:HOH615 4.3 17.1 1.0
CG B:GLU265 4.3 16.1 1.0
NE2 B:HIS215 4.4 20.8 1.0
NH1 B:ARG149 4.4 28.9 1.0
CB B:ASP213 4.5 17.1 1.0
OH D:TYR77 4.7 16.7 1.0
CZ B:ARG286 4.8 16.6 1.0
CG B:ASP240 4.8 21.7 1.0
NE2 B:HIS315 4.8 16.1 1.0
CD2 B:HIS315 4.8 15.3 1.0
O3 B:GOL503 4.9 33.2 1.0
NE B:ARG286 4.9 24.4 1.0

Magnesium binding site 3 out of 8 in 4kt2

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Magnesium binding site 3 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:25.3
occ:1.00
 OD2 C:ASP213 2.2 17.9 1.0
OE1 C:GLU265 2.2 21.0 1.0
OE1 C:GLU239 2.2 17.4 1.0
O C:HOH854 2.3 19.8 1.0
O C:HOH641 2.3 20.0 1.0
O C:HOH679 2.4 22.8 1.0
CD C:GLU265 3.1 19.7 1.0
CG C:ASP213 3.1 23.9 1.0
CD C:GLU239 3.1 22.1 1.0
OE2 C:GLU265 3.3 17.4 1.0
OD1 C:ASP213 3.4 20.1 1.0
NH2 C:ARG286 3.7 20.1 1.0
OE2 C:GLU239 3.8 20.7 1.0
CG C:GLU239 4.0 18.0 1.0
O C:HOH621 4.1 18.0 1.0
OD2 C:ASP240 4.1 20.4 1.0
CD2 C:HIS215 4.2 33.0 1.0
O C:HOH630 4.2 17.7 1.0
O C:HOH617 4.3 21.6 1.0
CG C:GLU265 4.4 16.3 1.0
CB C:ASP213 4.4 20.4 1.0
NH1 C:ARG149 4.5 32.6 1.0
NE2 C:HIS215 4.6 29.0 1.0
OH G:TYR77 4.7 21.0 1.0
CZ C:ARG286 4.7 23.4 1.0
CG C:ASP240 4.8 20.2 1.0
NE2 C:HIS315 4.8 14.9 1.0
NE C:ARG286 4.8 22.2 1.0
CD2 C:HIS315 4.9 18.1 1.0

Magnesium binding site 4 out of 8 in 4kt2

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Magnesium binding site 4 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:24.1
occ:1.00
 OE1 D:GLU265 2.2 17.5 1.0
OE1 D:GLU239 2.2 17.2 1.0
O D:HOH618 2.2 19.3 1.0
OD2 D:ASP213 2.2 21.2 1.0
O D:HOH854 2.3 23.4 1.0
O D:HOH665 2.3 24.4 1.0
CD D:GLU265 3.0 20.5 1.0
CG D:ASP213 3.2 26.0 1.0
CD D:GLU239 3.2 22.8 1.0
OE2 D:GLU265 3.3 18.2 1.0
OD1 D:ASP213 3.5 18.9 1.0
NH2 D:ARG286 3.7 18.1 1.0
OE2 D:GLU239 3.8 19.3 1.0
O D:HOH615 4.0 17.7 1.0
OD2 D:ASP240 4.0 20.5 1.0
CD2 D:HIS215 4.1 30.6 1.0
CG D:GLU239 4.2 19.5 1.0
O D:HOH621 4.2 15.9 1.0
CG D:GLU265 4.3 18.4 1.0
O D:HOH663 4.4 20.2 1.0
NE2 D:HIS215 4.4 38.4 1.0
CB D:ASP213 4.4 24.4 1.0
NH1 D:ARG149 4.6 37.7 1.0
OH B:TYR77 4.6 20.3 1.0
CG D:ASP240 4.7 21.2 1.0
CZ D:ARG286 4.7 22.9 1.0
NE D:ARG286 4.8 22.4 1.0
NE2 D:HIS315 4.9 20.3 1.0
CD2 D:HIS315 4.9 19.1 1.0
CB D:GLU265 4.9 16.6 1.0

Magnesium binding site 5 out of 8 in 4kt2

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Magnesium binding site 5 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:30.9
occ:1.00
 O E:HOH654 2.1 20.1 1.0
OE1 E:GLU265 2.2 18.5 1.0
O E:HOH879 2.2 25.2 1.0
OE1 E:GLU239 2.2 16.5 1.0
OD2 E:ASP213 2.3 19.7 1.0
O E:HOH758 2.4 29.9 1.0
CD E:GLU265 3.0 16.0 1.0
CG E:ASP213 3.2 20.9 1.0
OE2 E:GLU265 3.2 16.7 1.0
CD E:GLU239 3.3 23.1 1.0
OD1 E:ASP213 3.5 18.4 1.0
NH2 E:ARG286 3.8 16.4 1.0
CD2 E:HIS215 3.9 21.1 1.0
OE2 E:GLU239 3.9 19.1 1.0
O E:HOH610 4.0 19.8 1.0
OD2 E:ASP240 4.1 19.1 1.0
CG E:GLU239 4.2 18.7 1.0
O E:HOH636 4.3 16.4 1.0
O E:HOH678 4.3 24.6 1.0
NE2 E:HIS215 4.4 21.2 1.0
CG E:GLU265 4.4 16.8 1.0
CB E:ASP213 4.4 16.6 1.0
OH E:TYR161 4.5 33.4 1.0
NH1 E:ARG149 4.5 31.1 1.0
OH A:TYR77 4.7 16.8 1.0
CG E:ASP240 4.7 20.3 1.0
CZ E:ARG286 4.8 15.7 1.0
NE E:ARG286 4.9 20.9 1.0
NE2 E:HIS315 4.9 15.6 1.0
CD2 E:HIS315 4.9 15.0 1.0
CZ E:TYR161 4.9 39.3 1.0

Magnesium binding site 6 out of 8 in 4kt2

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Magnesium binding site 6 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:20.0
occ:1.00
 O F:HOH876 2.1 20.0 1.0
OE1 F:GLU239 2.1 16.2 1.0
OD2 F:ASP213 2.1 17.1 1.0
OE1 F:GLU265 2.2 16.1 1.0
O F:HOH822 2.3 19.2 1.0
O F:HOH670 2.3 20.8 1.0
CD F:GLU265 3.1 17.1 1.0
CG F:ASP213 3.1 21.9 1.0
CD F:GLU239 3.2 19.9 1.0
OE2 F:GLU265 3.3 16.8 1.0
OD1 F:ASP213 3.4 15.3 1.0
NH2 F:ARG286 3.8 16.8 1.0
OE2 F:GLU239 3.9 16.4 1.0
OD2 F:ASP240 4.0 17.3 1.0
CD2 F:HIS215 4.0 25.5 1.0
O F:HOH612 4.0 15.3 1.0
CG F:GLU239 4.1 17.8 1.0
O F:HOH622 4.2 16.2 1.0
NH1 F:ARG149 4.3 25.2 1.0
CB F:ASP213 4.3 15.3 1.0
CG F:GLU265 4.4 14.1 1.0
NE2 F:HIS215 4.4 28.5 1.0
O F:HOH695 4.5 22.0 1.0
CG F:ASP240 4.6 20.4 1.0
OH H:TYR77 4.7 15.8 1.0
CZ F:ARG286 4.8 18.4 1.0
NE F:ARG286 4.9 26.7 1.0
NE2 F:HIS315 5.0 14.2 1.0
CD2 F:HIS315 5.0 12.1 1.0

Magnesium binding site 7 out of 8 in 4kt2

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Magnesium binding site 7 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:19.0
occ:1.00
 OD2 G:ASP213 2.1 13.9 1.0
OE1 G:GLU239 2.2 16.4 1.0
O G:HOH656 2.2 17.6 1.0
O G:HOH883 2.2 16.7 1.0
OE1 G:GLU265 2.2 13.8 1.0
O G:HOH712 2.3 19.9 1.0
CD G:GLU265 3.0 17.1 1.0
CG G:ASP213 3.1 18.5 1.0
CD G:GLU239 3.2 20.5 1.0
OE2 G:GLU265 3.3 15.4 1.0
OD1 G:ASP213 3.5 16.3 1.0
NH2 G:ARG286 3.7 17.2 1.0
O G:HOH616 3.9 18.0 1.0
OE2 G:GLU239 3.9 16.2 1.0
OD2 G:ASP240 4.1 15.2 1.0
CD2 G:HIS215 4.1 23.5 1.0
CG G:GLU239 4.1 18.8 1.0
O G:HOH605 4.2 16.5 1.0
O G:HOH693 4.2 21.3 1.0
CG G:GLU265 4.4 13.8 1.0
CB G:ASP213 4.4 16.4 1.0
NE2 G:HIS215 4.5 27.3 1.0
NH1 G:ARG149 4.5 36.9 1.0
OH C:TYR77 4.7 17.3 1.0
CG G:ASP240 4.7 17.7 1.0
CZ G:ARG286 4.8 19.0 1.0
CD2 G:HIS315 4.9 14.4 1.0
NE2 G:HIS315 4.9 15.3 1.0
NE G:ARG286 4.9 19.8 1.0
CB G:GLU265 5.0 16.7 1.0

Magnesium binding site 8 out of 8 in 4kt2

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Magnesium binding site 8 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:25.9
occ:1.00
 O H:HOH867 2.2 20.8 1.0
OD2 H:ASP213 2.2 18.8 1.0
O H:HOH868 2.2 19.6 1.0
OE1 H:GLU265 2.2 13.7 1.0
OE1 H:GLU239 2.3 18.0 1.0
O H:HOH869 2.3 22.7 1.0
CD H:GLU265 3.0 15.5 1.0
CG H:ASP213 3.1 21.8 1.0
OE2 H:GLU265 3.2 16.5 1.0
CD H:GLU239 3.2 20.9 1.0
OD1 H:ASP213 3.4 15.2 1.0
NH2 H:ARG286 3.7 17.5 1.0
OE2 H:GLU239 3.8 17.1 1.0
CD2 H:HIS215 4.0 25.4 1.0
O H:HOH605 4.0 18.4 1.0
CG H:GLU239 4.1 16.8 1.0
OD2 H:ASP240 4.2 15.1 1.0
NH1 H:ARG149 4.3 25.8 1.0
O H:HOH645 4.3 20.6 1.0
CG H:GLU265 4.3 16.8 1.0
O H:HOH629 4.4 18.3 1.0
NE2 H:HIS215 4.4 25.5 1.0
CB H:ASP213 4.4 17.1 1.0
OH F:TYR77 4.6 19.5 1.0
CG H:ASP240 4.8 17.9 1.0
O H:HOH817 4.8 38.0 1.0
CZ H:ARG286 4.8 22.5 1.0
NE2 H:HIS315 4.9 12.9 1.0
CD2 H:HIS315 4.9 15.2 1.0
NE H:ARG286 4.9 25.8 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol To Be Published.
Page generated: Sat Aug 17 03:57:33 2024

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