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Magnesium in PDB 3ow1: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg, PDB code: 3ow1 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 (%) 16.1 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg (pdb code 3ow1). 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, PDB code: 3ow1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:22.9
occ:1.00
 OE1 A:GLU265 2.1 17.6 1.0
O A:HOH2097 2.2 18.8 1.0
OE1 A:GLU239 2.2 17.8 1.0
OD2 A:ASP213 2.2 19.3 1.0
O A:HOH2093 2.3 24.9 1.0
O A:HOH441 2.3 23.9 1.0
CD A:GLU265 3.0 19.2 1.0
CG A:ASP213 3.2 23.3 1.0
CD A:GLU239 3.2 18.6 1.0
OE2 A:GLU265 3.3 18.6 1.0
OD1 A:ASP213 3.5 19.1 1.0
NH2 A:ARG286 3.7 16.9 1.0
OE2 A:GLU239 3.9 19.3 1.0
O A:HOH443 4.0 19.4 1.0
CD2 A:HIS215 4.0 24.6 1.0
OD2 A:ASP240 4.1 20.2 1.0
CG A:GLU239 4.1 18.0 1.0
O A:HOH437 4.2 16.9 1.0
NE2 A:HIS215 4.3 31.1 1.0
O A:HOH1626 4.3 23.1 1.0
CG A:GLU265 4.3 18.5 1.0
CB A:ASP213 4.4 22.3 1.0
NH1 A:ARG149 4.5 31.4 1.0
OH B:TYR77 4.6 20.6 1.0
CG A:ASP240 4.7 21.0 1.0
CZ A:ARG286 4.7 20.8 1.0
NE A:ARG286 4.8 19.9 1.0
CD2 A:HIS315 4.9 19.4 1.0
NE2 A:HIS315 4.9 19.2 1.0
CB A:GLU265 4.9 17.3 1.0
O A:HOH1642 5.0 31.0 1.0

Magnesium binding site 2 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:25.3
occ:1.00
 O B:HOH2134 2.2 20.8 1.0
O B:HOH2142 2.2 23.9 1.0
OE1 B:GLU265 2.2 19.4 1.0
OE1 B:GLU239 2.2 16.7 1.0
OD2 B:ASP213 2.3 20.9 1.0
O B:HOH627 2.3 24.6 1.0
CD B:GLU265 3.0 17.3 1.0
OE2 B:GLU265 3.2 18.1 1.0
CG B:ASP213 3.2 20.3 1.0
CD B:GLU239 3.2 18.6 1.0
OD1 B:ASP213 3.5 17.6 1.0
NH2 B:ARG286 3.7 17.7 1.0
OE2 B:GLU239 3.9 16.3 1.0
O B:HOH455 3.9 20.2 1.0
CD2 B:HIS215 4.0 19.5 1.0
CG B:GLU239 4.1 17.7 1.0
OD2 B:ASP240 4.2 17.3 1.0
O B:HOH444 4.3 16.7 1.0
O B:HOH452 4.3 21.2 1.0
CG B:GLU265 4.3 15.5 1.0
NE2 B:HIS215 4.4 20.1 1.0
CB B:ASP213 4.4 17.5 1.0
NH1 B:ARG149 4.5 27.3 1.0
OH A:TYR77 4.7 16.9 1.0
CZ B:ARG286 4.8 18.2 1.0
CG B:ASP240 4.8 21.6 1.0
NE2 B:HIS315 4.8 15.5 1.0
CD2 B:HIS315 4.8 17.3 1.0
NE B:ARG286 4.9 22.8 1.0

Magnesium binding site 3 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg406

b:19.8
occ:1.00
 O C:HOH2096 2.1 19.8 1.0
OD2 C:ASP213 2.1 17.0 1.0
OE1 C:GLU239 2.2 17.7 1.0
OE1 C:GLU265 2.2 15.5 1.0
O C:HOH1608 2.3 19.6 1.0
O C:HOH684 2.3 20.4 1.0
CD C:GLU265 3.0 17.8 1.0
CG C:ASP213 3.1 21.4 1.0
CD C:GLU239 3.2 21.2 1.0
OE2 C:GLU265 3.3 16.9 1.0
OD1 C:ASP213 3.4 15.9 1.0
NH2 C:ARG286 3.8 18.3 1.0
OE2 C:GLU239 3.9 17.8 1.0
CD2 C:HIS215 4.0 22.7 1.0
OD2 C:ASP240 4.0 16.9 1.0
O C:HOH424 4.0 16.5 1.0
CG C:GLU239 4.1 17.2 1.0
O C:HOH453 4.2 16.4 1.0
NH1 C:ARG149 4.3 23.1 1.0
NE2 C:HIS215 4.3 25.8 1.0
CB C:ASP213 4.3 16.7 1.0
CG C:GLU265 4.4 14.7 1.0
O C:HOH1607 4.4 20.9 1.0
CG C:ASP240 4.7 19.6 1.0
OH D:TYR77 4.7 16.1 1.0
CZ C:ARG286 4.8 17.4 1.0
NE C:ARG286 4.9 21.3 1.0
CD2 C:HIS315 5.0 15.1 1.0
NE2 C:HIS315 5.0 15.9 1.0
O C:HOH2155 5.0 32.5 1.0

Magnesium binding site 4 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg406

b:23.1
occ:1.00
 OD2 D:ASP213 2.2 19.5 1.0
O D:HOH2099 2.2 19.4 1.0
O D:HOH2131 2.2 21.6 1.0
OE1 D:GLU265 2.2 14.3 1.0
OE1 D:GLU239 2.2 17.5 1.0
O D:HOH2138 2.3 23.5 1.0
CD D:GLU265 3.0 17.5 1.0
CG D:ASP213 3.1 19.8 1.0
OE2 D:GLU265 3.2 17.5 1.0
CD D:GLU239 3.2 20.1 1.0
OD1 D:ASP213 3.4 15.8 1.0
NH2 D:ARG286 3.7 18.1 1.0
OE2 D:GLU239 3.9 18.4 1.0
O D:HOH417 4.0 19.7 1.0
CD2 D:HIS215 4.0 21.7 1.0
CG D:GLU239 4.2 16.4 1.0
OD2 D:ASP240 4.2 16.9 1.0
NH1 D:ARG149 4.2 24.0 1.0
O D:HOH420 4.3 21.0 1.0
NE2 D:HIS215 4.4 24.3 1.0
CG D:GLU265 4.4 16.2 1.0
CB D:ASP213 4.4 18.9 1.0
O D:HOH466 4.4 16.6 1.0
OH C:TYR77 4.6 18.2 1.0
O D:HOH2291 4.7 34.5 1.0
NE2 D:HIS315 4.8 13.8 1.0
CZ D:ARG286 4.8 19.3 1.0
CG D:ASP240 4.8 17.6 1.0
CD2 D:HIS315 4.9 15.5 1.0
NE D:ARG286 4.9 21.6 1.0

Magnesium binding site 5 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg406

b:27.4
occ:1.00
 O E:HOH2128 2.1 20.1 1.0
O E:HOH2140 2.2 22.2 1.0
OD2 E:ASP213 2.2 19.1 1.0
OE1 E:GLU239 2.2 16.1 1.0
OE1 E:GLU265 2.2 18.7 1.0
O E:HOH2151 2.4 26.4 1.0
CD E:GLU265 3.0 16.2 1.0
CG E:ASP213 3.2 20.9 1.0
OE2 E:GLU265 3.2 19.1 1.0
CD E:GLU239 3.3 19.3 1.0
OD1 E:ASP213 3.5 17.1 1.0
NH2 E:ARG286 3.7 16.8 1.0
CD2 E:HIS215 3.9 18.6 1.0
O E:HOH454 3.9 20.6 1.0
OE2 E:GLU239 3.9 18.7 1.0
OD2 E:ASP240 4.1 18.5 1.0
CG E:GLU239 4.2 15.9 1.0
O E:HOH1641 4.3 23.5 1.0
O E:HOH442 4.3 16.3 1.0
NE2 E:HIS215 4.3 20.7 1.0
CB E:ASP213 4.4 17.9 1.0
CG E:GLU265 4.4 15.7 1.0
NH1 E:ARG149 4.5 28.3 1.0
OH F:TYR77 4.7 16.5 1.0
CG E:ASP240 4.7 17.8 1.0
CZ E:ARG286 4.8 15.8 1.0
CD2 E:HIS315 4.8 15.8 1.0
NE2 E:HIS315 4.8 16.4 1.0
NE E:ARG286 4.9 18.6 1.0
O3 E:GOL407 4.9 30.4 1.0

Magnesium binding site 6 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg406

b:23.3
occ:1.00
 O F:HOH2088 2.2 17.9 1.0
OE1 F:GLU239 2.2 20.3 1.0
OD2 F:ASP213 2.2 18.7 1.0
OE1 F:GLU265 2.2 18.5 1.0
O F:HOH2157 2.3 25.0 1.0
O F:HOH1622 2.3 19.9 1.0
CD F:GLU265 3.0 20.0 1.0
CG F:ASP213 3.1 21.2 1.0
CD F:GLU239 3.2 20.5 1.0
OE2 F:GLU265 3.3 18.9 1.0
OD1 F:ASP213 3.4 18.8 1.0
NH2 F:ARG286 3.9 17.6 1.0
OE2 F:GLU239 3.9 18.8 1.0
CD2 F:HIS215 4.0 22.2 1.0
O F:HOH442 4.0 20.7 1.0
CG F:GLU239 4.1 18.1 1.0
OD2 F:ASP240 4.1 18.8 1.0
NE2 F:HIS215 4.2 27.2 1.0
O F:HOH428 4.3 15.4 1.0
CG F:GLU265 4.3 14.9 1.0
CB F:ASP213 4.4 18.3 1.0
O F:HOH1620 4.4 21.6 1.0
OH E:TYR77 4.6 19.9 1.0
NH1 F:ARG149 4.6 34.0 1.0
CG F:ASP240 4.7 18.4 1.0
CZ F:ARG286 4.9 17.9 1.0
NE2 F:HIS315 4.9 16.3 1.0
CD2 F:HIS315 5.0 14.8 1.0
NE F:ARG286 5.0 20.2 1.0

Magnesium binding site 7 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg406

b:23.1
occ:1.00
 OD2 G:ASP213 2.1 19.0 1.0
OE1 G:GLU239 2.2 18.6 1.0
O G:HOH2098 2.2 19.1 1.0
OE1 G:GLU265 2.2 18.9 1.0
O G:HOH1610 2.2 20.3 1.0
O G:HOH440 2.4 23.4 1.0
CD G:GLU265 3.1 20.2 1.0
CG G:ASP213 3.1 23.1 1.0
CD G:GLU239 3.1 20.8 1.0
OE2 G:GLU265 3.3 17.6 1.0
OD1 G:ASP213 3.5 19.8 1.0
NH2 G:ARG286 3.7 18.9 1.0
OE2 G:GLU239 3.8 20.3 1.0
O G:HOH421 4.1 18.0 1.0
CG G:GLU239 4.1 17.6 1.0
CD2 G:HIS215 4.1 25.9 1.0
OD2 G:ASP240 4.1 19.4 1.0
O G:HOH448 4.2 17.8 1.0
O G:HOH2130 4.2 22.3 1.0
CB G:ASP213 4.4 19.9 1.0
CG G:GLU265 4.4 17.1 1.0
NE2 G:HIS215 4.4 26.4 1.0
NH1 G:ARG149 4.5 32.1 1.0
CZ G:ARG286 4.7 20.6 1.0
OH H:TYR77 4.8 21.5 1.0
NE2 G:HIS315 4.8 14.9 1.0
CG G:ASP240 4.8 19.4 1.0
NE G:ARG286 4.8 19.5 1.0
CD2 G:HIS315 4.8 16.8 1.0

Magnesium binding site 8 out of 8 in 3ow1

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg406

b:18.7
occ:1.00
 O H:HOH2091 2.1 15.3 1.0
OE1 H:GLU239 2.1 16.9 1.0
OD2 H:ASP213 2.1 15.0 1.0
OE1 H:GLU265 2.2 15.3 1.0
O H:HOH2087 2.2 18.0 1.0
O H:HOH2129 2.3 20.0 1.0
CD H:GLU265 3.0 16.1 1.0
CG H:ASP213 3.1 19.2 1.0
CD H:GLU239 3.2 19.1 1.0
OE2 H:GLU265 3.3 16.7 1.0
OD1 H:ASP213 3.5 16.9 1.0
NH2 H:ARG286 3.7 16.7 1.0
OE2 H:GLU239 3.9 16.1 1.0
O H:HOH439 4.0 17.8 1.0
OD2 H:ASP240 4.1 14.8 1.0
CG H:GLU239 4.1 16.8 1.0
CD2 H:HIS215 4.1 21.4 1.0
O H:HOH416 4.1 15.7 1.0
O H:HOH602 4.3 21.2 1.0
CG H:GLU265 4.4 13.1 1.0
CB H:ASP213 4.4 17.1 1.0
NE2 H:HIS215 4.4 25.5 1.0
NH1 H:ARG149 4.5 29.9 1.0
OH G:TYR77 4.7 17.2 1.0
CG H:ASP240 4.7 16.9 1.0
CZ H:ARG286 4.8 16.2 1.0
CD2 H:HIS315 4.9 16.0 1.0
NE2 H:HIS315 4.9 15.1 1.0
NE H:ARG286 4.9 17.0 1.0
CB H:GLU265 5.0 17.2 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 To Be Published.
Page generated: Thu Aug 15 08:30:44 2024

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