Atomistry » Magnesium » PDB 4knx-4kvi » 4kt2
Atomistry »
  Magnesium »
    PDB 4knx-4kvi »
      4kt2 »

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

Go back to Magnesium Binding Sites List in 4kt2
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

Go back to Magnesium Binding Sites List in 4kt2
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

Go back to Magnesium Binding Sites List in 4kt2
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

Go back to Magnesium Binding Sites List in 4kt2
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

Go back to Magnesium Binding Sites List in 4kt2
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

Go back to Magnesium Binding Sites List in 4kt2
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

Go back to Magnesium Binding Sites List in 4kt2
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

Go back to Magnesium Binding Sites List in 4kt2
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy