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Magnesium in PDB 3p93: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate

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: 3p93 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 / 1.80
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 (%) 19.9 / 24.1

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 3p93). 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: 3p93:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3p93

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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:Mg406

b:17.8
occ:1.00
 OD2 A:ASP213 2.1 15.2 1.0
OE1 A:GLU265 2.1 18.3 1.0
OE1 A:GLU239 2.2 16.9 1.0
O A:HOH1933 2.2 17.6 1.0
O1B A:CS2407 2.3 16.5 1.0
O2 A:CS2407 2.3 20.6 1.0
C1 A:CS2407 3.0 23.8 1.0
CD A:GLU265 3.0 13.8 1.0
CG A:ASP213 3.1 17.0 1.0
C2 A:CS2407 3.1 28.6 1.0
CD A:GLU239 3.2 17.5 1.0
OE2 A:GLU265 3.4 17.4 1.0
OD1 A:ASP213 3.4 14.9 1.0
NH2 A:ARG286 3.8 13.6 1.0
OE2 A:GLU239 3.9 15.3 1.0
O A:HOH442 3.9 16.7 1.0
CD2 A:HIS215 4.0 18.8 1.0
CG A:GLU239 4.1 14.6 1.0
OD2 A:ASP240 4.3 16.6 1.0
NE2 A:HIS215 4.3 22.9 1.0
O A:HOH450 4.3 15.9 1.0
O1A A:CS2407 4.3 27.5 1.0
CB A:ASP213 4.3 19.2 1.0
CG A:GLU265 4.3 13.4 1.0
NH1 A:ARG149 4.4 28.3 1.0
C3 A:CS2407 4.4 27.8 1.0
CG A:ASP240 4.7 16.6 1.0
OH H:TYR77 4.8 15.7 1.0
CZ A:ARG286 4.8 15.3 1.0
NE A:ARG286 4.9 17.3 1.0
CD2 A:HIS315 4.9 16.8 1.0

Magnesium binding site 2 out of 8 in 3p93

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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:Mg406

b:18.8
occ:1.00
 OE1 B:GLU239 2.1 17.5 1.0
OD2 B:ASP213 2.1 18.0 1.0
OE1 B:GLU265 2.2 15.5 1.0
O B:HOH1935 2.2 18.3 1.0
O1B B:CS2407 2.3 15.1 1.0
O2 B:CS2407 2.3 18.8 1.0
C1 B:CS2407 3.0 22.2 1.0
CG B:ASP213 3.0 17.3 1.0
CD B:GLU239 3.1 18.7 1.0
CD B:GLU265 3.1 20.0 1.0
C2 B:CS2407 3.1 26.0 1.0
OE2 B:GLU265 3.3 16.4 1.0
OD1 B:ASP213 3.4 18.4 1.0
OE2 B:GLU239 3.8 18.1 1.0
NH2 B:ARG286 3.8 14.2 1.0
CD2 B:HIS215 4.0 19.4 1.0
O B:HOH412 4.0 17.2 1.0
CG B:GLU239 4.0 15.6 1.0
O B:HOH414 4.0 15.8 1.0
OD2 B:ASP240 4.1 14.7 1.0
CB B:ASP213 4.3 19.8 1.0
O1A B:CS2407 4.3 24.1 1.0
NH1 B:ARG149 4.4 29.8 1.0
CG B:GLU265 4.4 16.8 1.0
C3 B:CS2407 4.4 26.6 1.0
NE2 B:HIS215 4.5 20.5 1.0
CG B:ASP240 4.7 16.9 1.0
OH D:TYR77 4.7 12.3 1.0
CZ B:ARG286 4.8 16.6 1.0
NE B:ARG286 4.8 17.3 1.0
CD2 B:HIS315 5.0 18.6 1.0

Magnesium binding site 3 out of 8 in 3p93

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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:Mg406

b:18.9
occ:1.00
 OD2 C:ASP213 2.2 19.8 1.0
OE1 C:GLU239 2.2 14.6 1.0
OE1 C:GLU265 2.2 16.9 1.0
O6A C:KDG407 2.3 18.1 1.0
O5 C:KDG407 2.3 15.5 1.0
O C:HOH408 2.4 16.0 1.0
C5 C:KDG407 2.8 25.4 1.0
C6 C:KDG407 2.9 18.9 1.0
CD C:GLU265 3.1 15.8 1.0
CG C:ASP213 3.1 20.7 1.0
CD C:GLU239 3.2 18.3 1.0
OE2 C:GLU265 3.3 15.1 1.0
OD1 C:ASP213 3.4 16.4 1.0
NH2 C:ARG286 3.7 18.7 1.0
OE2 C:GLU239 3.9 18.2 1.0
O C:HOH412 3.9 15.5 1.0
O6B C:KDG407 4.0 28.9 1.0
CD2 C:HIS215 4.1 17.7 1.0
CG C:GLU239 4.2 15.2 1.0
OD2 C:ASP240 4.2 13.0 1.0
O C:HOH420 4.3 17.1 1.0
C4 C:KDG407 4.3 22.6 1.0
NH1 C:ARG149 4.4 25.6 1.0
CB C:ASP213 4.4 19.0 1.0
CG C:GLU265 4.4 12.6 1.0
NE2 C:HIS215 4.5 21.7 1.0
OH G:TYR77 4.6 15.9 1.0
CZ C:ARG286 4.7 18.9 1.0
CG C:ASP240 4.8 17.1 1.0
CD2 C:HIS315 4.8 17.0 1.0
NE C:ARG286 4.9 18.6 1.0
C3 C:KDG407 5.0 22.1 1.0

Magnesium binding site 4 out of 8 in 3p93

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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:Mg406

b:18.6
occ:1.00
 OD2 D:ASP213 2.1 16.1 1.0
OE1 D:GLU239 2.1 15.8 1.0
OE1 D:GLU265 2.2 16.2 1.0
O D:HOH1934 2.2 14.6 1.0
O6A D:KDG407 2.3 16.1 1.0
O5 D:KDG407 2.4 20.6 1.0
C6 D:KDG407 3.0 25.2 1.0
C5 D:KDG407 3.0 26.2 1.0
CD D:GLU265 3.0 18.6 1.0
CD D:GLU239 3.1 17.8 1.0
CG D:ASP213 3.1 17.6 1.0
OE2 D:GLU265 3.3 14.3 1.0
OD1 D:ASP213 3.5 17.6 1.0
NH2 D:ARG286 3.8 14.4 1.0
OE2 D:GLU239 3.9 18.2 1.0
CD2 D:HIS215 3.9 18.4 1.0
CG D:GLU239 4.0 16.0 1.0
O D:HOH423 4.1 17.9 1.0
OD2 D:ASP240 4.1 14.3 1.0
O D:HOH408 4.1 15.1 1.0
O6B D:KDG407 4.2 30.1 1.0
CB D:ASP213 4.4 16.3 1.0
CG D:GLU265 4.4 16.8 1.0
NE2 D:HIS215 4.4 21.3 1.0
C4 D:KDG407 4.4 28.7 1.0
NH1 D:ARG149 4.5 29.8 1.0
OH B:TYR77 4.6 17.9 1.0
CG D:ASP240 4.7 17.1 1.0
CD2 D:HIS315 4.8 14.8 1.0
CZ D:ARG286 4.8 15.4 1.0
NE D:ARG286 4.9 18.0 1.0
NE2 D:HIS315 4.9 17.6 1.0
C3 D:KDG407 4.9 21.7 1.0

Magnesium binding site 5 out of 8 in 3p93

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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:Mg406

b:19.9
occ:1.00
 OE1 E:GLU239 2.1 12.8 1.0
OE1 E:GLU265 2.1 13.8 1.0
O E:HOH1932 2.2 14.2 1.0
OD2 E:ASP213 2.2 15.8 1.0
O1B E:CS2407 2.3 19.2 1.0
O2 E:CS2407 2.3 15.7 1.0
CD E:GLU265 3.0 16.3 1.0
C1 E:CS2407 3.0 23.4 1.0
CD E:GLU239 3.1 15.9 1.0
C2 E:CS2407 3.1 24.4 1.0
CG E:ASP213 3.1 15.4 1.0
OE2 E:GLU265 3.2 17.5 1.0
OD1 E:ASP213 3.4 12.8 1.0
NH2 E:ARG286 3.7 17.0 1.0
OE2 E:GLU239 3.8 14.6 1.0
O E:HOH424 3.9 17.6 1.0
CG E:GLU239 4.0 15.7 1.0
OD2 E:ASP240 4.0 15.9 1.0
O E:HOH425 4.1 14.4 1.0
CD2 E:HIS215 4.2 15.3 1.0
O1A E:CS2407 4.3 27.1 1.0
CG E:GLU265 4.3 14.3 1.0
C3 E:CS2407 4.3 26.2 1.0
CB E:ASP213 4.4 16.3 1.0
NH1 E:ARG149 4.5 22.0 1.0
NE2 E:HIS215 4.6 16.9 1.0
OH F:TYR77 4.7 15.4 1.0
CZ E:ARG286 4.7 15.3 1.0
CG E:ASP240 4.7 16.9 1.0
NE E:ARG286 4.8 15.4 1.0
CD2 E:HIS315 4.9 16.7 1.0
CB E:GLU265 5.0 13.8 1.0
NE2 E:HIS315 5.0 17.6 1.0

Magnesium binding site 6 out of 8 in 3p93

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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:Mg406

b:19.2
occ:1.00
 OE1 F:GLU239 2.2 15.8 1.0
O F:HOH1936 2.2 17.5 1.0
OD2 F:ASP213 2.2 16.1 1.0
OE1 F:GLU265 2.2 14.0 1.0
O2 F:CS2407 2.2 19.9 1.0
O1B F:CS2407 2.3 22.6 1.0
C1 F:CS2407 3.0 25.4 1.0
CD F:GLU265 3.1 18.2 1.0
CG F:ASP213 3.1 15.5 1.0
C2 F:CS2407 3.1 26.4 1.0
CD F:GLU239 3.2 17.3 1.0
OE2 F:GLU265 3.3 15.6 1.0
OD1 F:ASP213 3.5 17.9 1.0
NH2 F:ARG286 3.9 15.4 1.0
CD2 F:HIS215 4.0 16.2 1.0
O F:HOH430 4.0 19.1 1.0
OE2 F:GLU239 4.0 17.8 1.0
CG F:GLU239 4.1 14.1 1.0
O F:HOH428 4.1 14.3 1.0
OD2 F:ASP240 4.2 17.4 1.0
O1A F:CS2407 4.3 31.2 1.0
C3 F:CS2407 4.3 26.7 1.0
NE2 F:HIS215 4.4 22.3 1.0
CG F:GLU265 4.4 14.6 1.0
CB F:ASP213 4.4 17.6 1.0
NH1 F:ARG149 4.4 27.3 1.0
OH E:TYR77 4.5 15.6 1.0
CG F:ASP240 4.7 18.5 1.0
CD2 F:HIS315 4.8 15.7 1.0
CZ F:ARG286 4.9 17.0 1.0
NE2 F:HIS315 4.9 20.5 1.0
C4 F:CS2407 5.0 22.6 1.0
NE F:ARG286 5.0 16.3 1.0

Magnesium binding site 7 out of 8 in 3p93

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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:Mg406

b:19.2
occ:1.00
 O G:HOH1931 2.2 16.7 1.0
OE1 G:GLU239 2.2 14.5 1.0
OD2 G:ASP213 2.2 18.7 1.0
O5 G:KDG407 2.3 20.6 1.0
OE1 G:GLU265 2.3 17.7 1.0
O6A G:KDG407 2.3 20.1 1.0
C5 G:KDG407 2.9 26.0 1.0
C6 G:KDG407 3.0 22.3 1.0
CD G:GLU265 3.1 17.9 1.0
CG G:ASP213 3.1 20.1 1.0
CD G:GLU239 3.2 15.6 1.0
OE2 G:GLU265 3.3 16.9 1.0
OD1 G:ASP213 3.4 15.7 1.0
NH2 G:ARG286 3.8 14.2 1.0
OE2 G:GLU239 3.9 15.6 1.0
CD2 G:HIS215 3.9 22.7 1.0
O G:HOH409 4.1 13.6 1.0
OD2 G:ASP240 4.1 17.6 1.0
O6B G:KDG407 4.2 26.9 1.0
CG G:GLU239 4.2 14.4 1.0
O G:HOH451 4.3 13.5 1.0
NH1 G:ARG149 4.3 29.1 1.0
NE2 G:HIS215 4.3 19.9 1.0
CB G:ASP213 4.4 17.1 1.0
CG G:GLU265 4.4 17.4 1.0
C4 G:KDG407 4.4 23.5 1.0
OH C:TYR77 4.7 17.6 1.0
CG G:ASP240 4.7 17.0 1.0
CZ G:ARG286 4.9 15.2 1.0
CD2 G:HIS315 5.0 19.2 1.0
C3 G:KDG407 5.0 23.1 1.0

Magnesium binding site 8 out of 8 in 3p93

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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:Mg406

b:17.4
occ:1.00
 OE1 H:GLU265 2.1 15.8 1.0
OE1 H:GLU239 2.1 15.2 1.0
OD2 H:ASP213 2.2 18.7 1.0
O6A H:KDG407 2.2 18.6 1.0
O H:HOH1361 2.3 13.3 1.0
O5 H:KDG407 2.3 14.3 1.0
C6 H:KDG407 2.9 21.4 1.0
C5 H:KDG407 3.0 23.0 1.0
CD H:GLU265 3.0 17.0 1.0
CG H:ASP213 3.1 16.6 1.0
CD H:GLU239 3.1 18.8 1.0
OE2 H:GLU265 3.2 14.4 1.0
OD1 H:ASP213 3.4 14.5 1.0
NH2 H:ARG286 3.8 16.0 1.0
OE2 H:GLU239 3.8 15.4 1.0
O H:HOH411 3.9 15.5 1.0
CG H:GLU239 4.1 15.8 1.0
CD2 H:HIS215 4.1 19.7 1.0
O H:HOH606 4.1 15.8 1.0
O6B H:KDG407 4.1 27.1 1.0
OD2 H:ASP240 4.2 13.6 1.0
CG H:GLU265 4.3 14.8 1.0
CB H:ASP213 4.3 16.4 1.0
C4 H:KDG407 4.4 21.9 1.0
NE2 H:HIS215 4.5 18.0 1.0
NH1 H:ARG149 4.6 23.8 1.0
OH A:TYR77 4.7 12.7 1.0
CG H:ASP240 4.7 18.7 1.0
CZ H:ARG286 4.7 16.3 1.0
NE H:ARG286 4.8 15.6 1.0
CD2 H:HIS315 4.9 20.6 1.0
C3 H:KDG407 5.0 22.4 1.0
CB H:GLU265 5.0 15.8 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,D-Mannonate and 2-Keto-3-Deoxy-D-Gluconate To Be Published.
Page generated: Thu Aug 15 09:09:32 2024

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