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Magnesium in PDB 4kpl: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate

Enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate

All present enzymatic activity of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate, PDB code: 4kpl 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) 41.82 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.242, 167.263, 168.863, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.3

Other elements in 4kpl:

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate 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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate (pdb code 4kpl). 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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate, PDB code: 4kpl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:22.1
occ:1.00
 OE1 A:GLU239 2.2 16.9 1.0
OD2 A:ASP213 2.2 15.5 1.0
O2 A:CS2501 2.2 17.5 1.0
O A:HOH829 2.2 18.6 1.0
OE1 A:GLU265 2.2 13.5 1.0
O1B A:CS2501 2.3 26.9 1.0
C1 A:CS2501 3.0 33.7 1.0
CD A:GLU265 3.1 15.5 1.0
C2 A:CS2501 3.1 29.2 1.0
CG A:ASP213 3.1 11.3 1.0
CD A:GLU239 3.3 16.1 1.0
OE2 A:GLU265 3.3 15.2 1.0
OD1 A:ASP213 3.5 12.3 1.0
NH2 A:ARG286 3.8 9.8 1.0
O A:HOH618 3.9 21.0 1.0
OE2 A:GLU239 4.0 15.1 1.0
CD2 A:HIS215 4.0 19.3 1.0
O A:HOH615 4.1 11.5 1.0
OD2 A:ASP240 4.1 15.8 1.0
CG A:GLU239 4.2 12.3 1.0
C3 A:CS2501 4.3 32.7 1.0
NH1 A:ARG149 4.3 30.5 1.0
O1A A:CS2501 4.3 39.2 1.0
NE2 A:HIS215 4.4 25.2 1.0
CB A:ASP213 4.4 11.5 1.0
CG A:GLU265 4.4 9.6 1.0
OH E:TYR77 4.6 12.3 1.0
CG A:ASP240 4.8 18.0 1.0
C4 A:CS2501 4.8 24.7 1.0
CD2 A:HIS315 4.9 12.0 1.0
CZ A:ARG286 4.9 15.4 1.0
NE2 A:HIS315 4.9 21.0 1.0

Magnesium binding site 2 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:21.4
occ:1.00
 OD2 B:ASP213 2.2 17.1 1.0
OE1 B:GLU239 2.2 18.3 1.0
O B:HOH838 2.2 17.8 1.0
O1B B:CS2501 2.3 13.1 1.0
OE1 B:GLU265 2.3 17.4 1.0
O2 B:CS2501 2.3 17.6 1.0
CG B:ASP213 2.9 16.8 1.0
C1 B:CS2501 3.1 24.1 1.0
CD B:GLU239 3.1 18.0 1.0
CD B:GLU265 3.1 19.4 1.0
C2 B:CS2501 3.2 28.3 1.0
OD1 B:ASP213 3.2 19.0 1.0
OE2 B:GLU265 3.3 15.8 1.0
OE2 B:GLU239 3.8 12.5 1.0
NH2 B:ARG286 3.8 10.2 1.0
CD2 B:HIS215 3.9 19.8 1.0
OD2 B:ASP240 4.0 14.6 1.0
O B:HOH608 4.0 12.6 1.0
CG B:GLU239 4.0 13.6 1.0
O B:HOH620 4.0 15.2 1.0
NH1 B:ARG149 4.2 36.7 1.0
CB B:ASP213 4.3 19.0 1.0
O1A B:CS2501 4.3 26.3 1.0
NE2 B:HIS215 4.4 22.9 1.0
CG B:GLU265 4.4 14.0 1.0
C3 B:CS2501 4.5 31.4 1.0
CG B:ASP240 4.6 19.1 1.0
OH D:TYR77 4.7 12.9 1.0
CZ B:ARG286 4.9 14.0 1.0
NE B:ARG286 4.9 19.0 1.0
CG B:HIS215 5.0 21.4 1.0
C4 B:CS2501 5.0 27.5 1.0

Magnesium binding site 3 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:19.9
occ:1.00
 OD2 C:ASP213 2.2 21.9 1.0
OE1 C:GLU265 2.2 19.2 1.0
O6A C:KDG501 2.2 10.6 1.0
OE1 C:GLU239 2.2 13.7 1.0
O C:HOH824 2.3 12.6 1.0
O5 C:KDG501 2.4 14.8 1.0
C6 C:KDG501 2.9 16.9 1.0
C5 C:KDG501 2.9 23.5 1.0
CD C:GLU265 3.0 10.3 1.0
CG C:ASP213 3.1 18.6 1.0
OE2 C:GLU265 3.2 12.2 1.0
CD C:GLU239 3.2 14.8 1.0
OD1 C:ASP213 3.5 15.3 1.0
NH2 C:ARG286 3.7 18.8 1.0
O C:HOH602 3.9 13.7 1.0
OE2 C:GLU239 4.0 17.4 1.0
O6B C:KDG501 4.0 32.4 1.0
OD2 C:ASP240 4.1 9.5 1.0
CG C:GLU239 4.2 10.9 1.0
CD2 C:HIS215 4.2 22.6 1.0
O C:HOH603 4.3 12.2 1.0
C4 C:KDG501 4.4 24.0 1.0
CB C:ASP213 4.4 13.3 1.0
CG C:GLU265 4.4 7.9 1.0
NH1 C:ARG149 4.5 22.4 1.0
NE2 C:HIS215 4.7 22.4 1.0
OH G:TYR77 4.7 15.4 1.0
CZ C:ARG286 4.7 18.1 1.0
CG C:ASP240 4.8 12.9 1.0
CD2 C:HIS315 4.8 16.3 1.0
NE C:ARG286 4.8 17.3 1.0
NE2 C:HIS315 4.9 13.9 1.0
C3 C:KDG501 5.0 21.7 1.0

Magnesium binding site 4 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:20.7
occ:1.00
 OE1 D:GLU265 2.2 16.1 1.0
OD2 D:ASP213 2.2 16.2 1.0
O6A D:KDG501 2.3 18.2 1.0
OE1 D:GLU239 2.3 18.6 1.0
O D:HOH820 2.3 16.1 1.0
O5 D:KDG501 2.3 16.2 1.0
C5 D:KDG501 2.9 26.7 1.0
C6 D:KDG501 2.9 26.8 1.0
CD D:GLU265 3.0 14.6 1.0
OE2 D:GLU265 3.2 14.7 1.0
CG D:ASP213 3.2 16.5 1.0
CD D:GLU239 3.3 22.1 1.0
OD1 D:ASP213 3.6 15.9 1.0
NH2 D:ARG286 3.8 9.9 1.0
O D:HOH621 3.9 14.7 1.0
CD2 D:HIS215 3.9 16.8 1.0
OE2 D:GLU239 4.1 20.1 1.0
O6B D:KDG501 4.1 39.0 1.0
OD2 D:ASP240 4.1 15.1 1.0
O D:HOH601 4.1 10.1 1.0
CG D:GLU239 4.1 17.3 1.0
C4 D:KDG501 4.3 30.7 1.0
CG D:GLU265 4.4 11.3 1.0
CB D:ASP213 4.4 13.7 1.0
NE2 D:HIS215 4.4 15.9 1.0
NH1 D:ARG149 4.5 34.8 1.0
OH B:TYR77 4.5 12.4 1.0
CG D:ASP240 4.7 18.9 1.0
CD2 D:HIS315 4.7 12.1 1.0
CZ D:ARG286 4.8 11.4 1.0
C3 D:KDG501 4.8 24.0 1.0
NE2 D:HIS315 4.9 15.4 1.0
NE D:ARG286 4.9 15.7 1.0
CB D:GLU265 5.0 17.9 1.0

Magnesium binding site 5 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:22.0
occ:1.00
 OE1 E:GLU265 2.1 11.9 1.0
OE1 E:GLU239 2.2 13.2 1.0
OD2 E:ASP213 2.2 16.9 1.0
O E:HOH849 2.2 11.9 1.0
O1B E:CS2501 2.3 19.7 1.0
O2 E:CS2501 2.4 20.1 1.0
CD E:GLU265 3.0 14.6 1.0
C1 E:CS2501 3.1 26.8 1.0
CD E:GLU239 3.1 17.5 1.0
CG E:ASP213 3.1 13.9 1.0
OE2 E:GLU265 3.2 16.2 1.0
C2 E:CS2501 3.2 28.4 1.0
OD1 E:ASP213 3.4 15.5 1.0
NH2 E:ARG286 3.8 19.1 1.0
OE2 E:GLU239 3.9 19.2 1.0
O E:HOH606 3.9 14.2 1.0
CG E:GLU239 4.0 20.7 1.0
CD2 E:HIS215 4.2 11.6 1.0
OD2 E:ASP240 4.2 17.1 1.0
O E:HOH604 4.2 9.0 1.0
CG E:GLU265 4.3 15.1 1.0
NH1 E:ARG149 4.3 22.1 1.0
O1A E:CS2501 4.3 35.5 1.0
CB E:ASP213 4.4 15.8 1.0
C3 E:CS2501 4.4 34.3 1.0
NE2 E:HIS215 4.6 18.7 1.0
OH A:TYR77 4.7 12.0 1.0
CG E:ASP240 4.8 19.2 1.0
CZ E:ARG286 4.8 17.0 1.0
NE E:ARG286 4.8 17.4 1.0
CB E:GLU265 5.0 11.7 1.0
CD2 E:HIS315 5.0 9.9 1.0

Magnesium binding site 6 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:18.6
occ:1.00
 OD2 F:ASP213 2.1 10.5 1.0
OE1 F:GLU265 2.2 17.1 1.0
O F:HOH839 2.2 14.6 1.0
OE1 F:GLU239 2.3 22.3 1.0
O2 F:CS2501 2.3 15.7 1.0
O1B F:CS2501 2.4 22.8 1.0
CD F:GLU265 3.0 10.8 1.0
CG F:ASP213 3.0 12.8 1.0
C1 F:CS2501 3.1 31.1 1.0
C2 F:CS2501 3.2 32.9 1.0
CD F:GLU239 3.2 14.6 1.0
OE2 F:GLU265 3.3 15.7 1.0
OD1 F:ASP213 3.4 10.3 1.0
CD2 F:HIS215 3.9 19.0 1.0
NH2 F:ARG286 3.9 9.9 1.0
O F:HOH621 4.0 16.6 1.0
OE2 F:GLU239 4.0 14.6 1.0
OD2 F:ASP240 4.1 18.2 1.0
CG F:GLU239 4.1 9.8 1.0
O F:HOH671 4.1 15.6 1.0
NE2 F:HIS215 4.2 20.1 1.0
CB F:ASP213 4.3 15.5 1.0
CG F:GLU265 4.3 8.3 1.0
O1A F:CS2501 4.4 36.2 1.0
C3 F:CS2501 4.4 37.5 1.0
NH1 F:ARG149 4.4 26.7 1.0
CG F:ASP240 4.6 20.2 1.0
OH H:TYR77 4.7 13.7 1.0
CZ F:ARG286 4.9 15.7 1.0
CD2 F:HIS315 5.0 18.3 1.0
NE F:ARG286 5.0 15.3 1.0
C4 F:CS2501 5.0 27.4 1.0

Magnesium binding site 7 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg503

b:18.6
occ:1.00
 OD2 G:ASP213 2.1 14.5 1.0
O G:HOH846 2.2 14.0 1.0
OE1 G:GLU239 2.2 12.4 1.0
O5 G:KDG501 2.3 25.3 1.0
O6A G:KDG501 2.4 24.5 1.0
OE1 G:GLU265 2.4 18.3 1.0
C5 G:KDG501 3.0 30.7 1.0
CG G:ASP213 3.0 15.3 1.0
C6 G:KDG501 3.1 26.7 1.0
CD G:GLU265 3.1 16.9 1.0
CD G:GLU239 3.2 14.3 1.0
OE2 G:GLU265 3.2 17.4 1.0
OD1 G:ASP213 3.3 11.0 1.0
OE2 G:GLU239 3.8 13.1 1.0
NH2 G:ARG286 3.9 14.1 1.0
CD2 G:HIS215 3.9 22.2 1.0
O G:HOH602 4.0 13.6 1.0
OD2 G:ASP240 4.1 18.4 1.0
CG G:GLU239 4.1 11.4 1.0
NH1 G:ARG149 4.2 29.6 1.0
O6B G:KDG501 4.2 31.5 1.0
O G:HOH638 4.3 9.9 1.0
CB G:ASP213 4.3 11.6 1.0
NE2 G:HIS215 4.4 20.5 1.0
C4 G:KDG501 4.5 27.2 1.0
CG G:GLU265 4.5 16.5 1.0
CG G:ASP240 4.7 18.8 1.0
OH C:TYR77 4.7 16.9 1.0
CZ G:ARG286 4.9 16.8 1.0

Magnesium binding site 8 out of 8 in 4kpl

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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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate


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,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:17.6
occ:1.00
 OE1 H:GLU239 2.2 14.1 1.0
OE1 H:GLU265 2.2 14.4 1.0
OD2 H:ASP213 2.2 18.7 1.0
O6A H:KDG501 2.2 21.2 1.0
O H:HOH843 2.3 9.1 1.0
O5 H:KDG501 2.4 8.4 1.0
CD H:GLU265 2.9 16.5 1.0
C6 H:KDG501 3.0 28.5 1.0
C5 H:KDG501 3.0 22.6 1.0
OE2 H:GLU265 3.1 13.1 1.0
CG H:ASP213 3.1 16.2 1.0
CD H:GLU239 3.1 16.4 1.0
OD1 H:ASP213 3.4 14.2 1.0
OE2 H:GLU239 3.8 16.8 1.0
NH2 H:ARG286 3.9 17.3 1.0
O H:HOH630 4.0 13.8 1.0
OD2 H:ASP240 4.0 15.1 1.0
CD2 H:HIS215 4.1 20.9 1.0
O H:HOH668 4.1 16.5 1.0
CG H:GLU239 4.1 17.1 1.0
O6B H:KDG501 4.1 34.5 1.0
CG H:GLU265 4.2 11.4 1.0
NH1 H:ARG149 4.4 23.0 1.0
C4 H:KDG501 4.5 25.4 1.0
CB H:ASP213 4.5 14.4 1.0
NE2 H:HIS215 4.6 17.3 1.0
CG H:ASP240 4.7 18.1 1.0
OH F:TYR77 4.7 13.7 1.0
CZ H:ARG286 4.9 14.0 1.0
CD2 H:HIS315 4.9 23.5 1.0
NE H:ARG286 4.9 14.6 1.0
C3 H:KDG501 5.0 26.9 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,D-Mannonate and 2-Keto-3-Deoxy-D-Gluconate To Be Published.
Page generated: Mon Aug 11 17:47:28 2025

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