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Magnesium in PDB 4kws: 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: 4kws 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) 40.05 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 195.273, 85.762, 195.097, 90.00, 110.31, 90.00
R / Rfree (%) 13.9 / 16.3

Other elements in 4kws:

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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

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 4kws). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and Glycerol, PDB code: 4kws:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 4kws

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Magnesium binding site 1 out of 13 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:Mg501

b:15.1
occ:1.00
 OD2 A:ASP213 2.0 14.6 1.0
OE1 A:GLU239 2.1 14.5 1.0
OE1 A:GLU265 2.1 14.7 1.0
O A:HOH964 2.1 15.9 1.0
O A:HOH959 2.1 13.2 1.0
O A:HOH960 2.2 15.7 1.0
CD A:GLU265 3.0 13.3 1.0
CG A:ASP213 3.1 15.1 1.0
CD A:GLU239 3.1 14.4 1.0
OE2 A:GLU265 3.3 15.8 1.0
OD1 A:ASP213 3.5 13.4 1.0
NH2 A:ARG286 3.7 15.5 1.0
OE2 A:GLU239 3.8 13.7 1.0
O A:HOH619 4.0 16.0 1.0
CG A:GLU239 4.0 13.0 1.0
CD2 A:HIS215 4.0 21.4 1.0
OD2 A:ASP240 4.2 15.3 1.0
O A:HOH631 4.3 19.6 1.0
O A:HOH612 4.3 15.2 1.0
CB A:ASP213 4.3 15.6 1.0
CG A:GLU265 4.4 12.4 1.0
NH1 A:ARG149 4.4 22.7 1.0
NE2 A:HIS215 4.4 22.6 1.0
OH A:TYR161 4.5 27.5 1.0
OH B:TYR77 4.8 14.3 1.0
CZ A:ARG286 4.8 19.0 1.0
CG A:ASP240 4.8 15.2 1.0
NE2 A:HIS315 4.9 20.4 1.0
CD2 A:HIS315 4.9 16.0 1.0
NE A:ARG286 4.9 23.2 1.0

Magnesium binding site 2 out of 13 in 4kws

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Magnesium binding site 2 out of 13 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
A:Mg504

b:12.9
occ:0.41
 O A:HOH965 2.0 32.0 1.0
O A:HOH966 2.0 36.2 1.0
O A:HOH968 2.1 45.4 0.5
O F:HOH750 4.3 21.2 1.0
O F:HOH846 4.3 41.9 1.0
OE2 A:GLU255 4.3 30.8 1.0
O A:HOH752 4.3 23.8 1.0
O A:HOH793 4.4 36.0 1.0
OE2 F:GLU255 4.5 32.4 1.0
CD F:GLU255 4.5 28.2 1.0
CD A:GLU255 4.5 28.1 1.0
CG F:GLU255 4.8 15.7 1.0
OE1 F:GLU255 4.8 26.3 1.0
OE1 A:GLU255 4.9 29.7 1.0
CG A:GLU255 4.9 16.8 1.0

Magnesium binding site 3 out of 13 in 4kws

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Magnesium binding site 3 out of 13 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
B:Mg501

b:13.1
occ:1.00
 OD2 B:ASP213 2.1 11.7 1.0
O B:HOH958 2.1 13.9 1.0
O B:HOH956 2.1 13.5 1.0
O B:HOH957 2.1 13.3 1.0
OE1 B:GLU239 2.1 13.2 1.0
OE1 B:GLU265 2.1 12.9 1.0
CD B:GLU265 3.0 12.6 1.0
CG B:ASP213 3.1 11.9 1.0
CD B:GLU239 3.1 12.5 1.0
OE2 B:GLU265 3.3 14.3 1.0
OD1 B:ASP213 3.5 12.4 1.0
NH2 B:ARG286 3.8 14.1 1.0
OE2 B:GLU239 3.9 12.3 1.0
O B:HOH613 4.0 14.3 1.0
CD2 B:HIS215 4.0 29.6 1.0
CG B:GLU239 4.1 11.7 1.0
OD2 B:ASP240 4.1 13.8 1.0
O B:HOH633 4.3 13.8 1.0
O B:HOH664 4.3 18.9 1.0
OH B:TYR161 4.3 41.4 1.0
CB B:ASP213 4.3 13.7 1.0
CG B:GLU265 4.4 11.0 1.0
NE2 B:HIS215 4.4 30.5 1.0
NH1 B:ARG149 4.4 25.2 1.0
OH A:TYR77 4.7 15.3 1.0
CG B:ASP240 4.8 14.2 1.0
CZ B:ARG286 4.9 19.5 1.0
NE2 B:HIS315 4.9 16.9 1.0
CD2 B:HIS315 4.9 14.4 1.0
CZ B:TYR161 5.0 40.2 1.0
NE B:ARG286 5.0 20.3 1.0

Magnesium binding site 4 out of 13 in 4kws

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Magnesium binding site 4 out of 13 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
B:Mg503

b:13.4
occ:0.41
 O G:HOH602 2.0 31.4 1.0
O B:HOH859 2.1 31.6 1.0
O G:HOH697 4.3 17.7 1.0
O B:HOH723 4.3 20.8 1.0
OE2 G:GLU255 4.5 29.9 1.0
CD G:GLU255 4.5 25.2 1.0
CD B:GLU255 4.5 22.9 1.0
OE2 B:GLU255 4.6 28.5 1.0
OE1 B:GLU255 4.8 26.8 1.0
CG G:GLU255 4.8 13.2 1.0
CG B:GLU255 4.8 12.7 1.0
OE1 G:GLU255 4.8 25.6 1.0

Magnesium binding site 5 out of 13 in 4kws

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Magnesium binding site 5 out of 13 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
C:Mg501

b:13.0
occ:1.00
 OE1 C:GLU239 2.1 11.9 1.0
OD2 C:ASP213 2.1 12.3 1.0
O C:HOH981 2.1 13.6 1.0
OE1 C:GLU265 2.1 13.1 1.0
O C:HOH985 2.1 15.1 1.0
O C:HOH982 2.1 15.6 1.0
CD C:GLU265 3.0 12.6 1.0
CG C:ASP213 3.1 13.4 1.0
CD C:GLU239 3.1 13.8 1.0
OE2 C:GLU265 3.3 14.0 1.0
OD1 C:ASP213 3.5 12.5 1.0
NH2 C:ARG286 3.8 12.8 1.0
OE2 C:GLU239 3.8 12.8 1.0
O C:HOH628 3.9 14.2 1.0
CD2 C:HIS215 4.0 19.2 1.0
CG C:GLU239 4.1 11.3 1.0
OD2 C:ASP240 4.1 14.0 1.0
O C:HOH601 4.3 13.4 1.0
O C:HOH653 4.3 18.2 1.0
CB C:ASP213 4.3 13.0 1.0
NH1 C:ARG149 4.3 18.4 1.0
CG C:GLU265 4.4 13.8 1.0
NE2 C:HIS215 4.4 22.3 1.0
OH C:TYR161 4.5 30.0 1.0
CG C:ASP240 4.7 15.2 1.0
OH D:TYR77 4.8 14.1 1.0
CZ C:ARG286 4.8 18.9 1.0
NE2 C:HIS315 4.9 17.1 1.0
CD2 C:HIS315 4.9 15.1 1.0
NE C:ARG286 5.0 22.1 1.0

Magnesium binding site 6 out of 13 in 4kws

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Magnesium binding site 6 out of 13 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
C:Mg504

b:12.9
occ:0.41
 O E:HOH980 2.0 38.9 0.5
O E:HOH978 2.0 34.9 1.0
O C:HOH776 2.1 28.6 1.0
O C:HOH692 4.3 20.4 1.0
O E:HOH959 4.4 38.5 1.0
O E:HOH681 4.4 18.1 1.0
O E:HOH951 4.4 33.8 1.0
OE2 E:GLU255 4.5 31.2 1.0
CD E:GLU255 4.5 27.6 1.0
CD C:GLU255 4.5 25.5 1.0
OE2 C:GLU255 4.6 33.8 1.0
OE1 E:GLU255 4.8 26.2 1.0
CG C:GLU255 4.8 14.3 1.0
OE1 C:GLU255 4.8 24.2 1.0
CG E:GLU255 4.9 15.3 1.0

Magnesium binding site 7 out of 13 in 4kws

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Magnesium binding site 7 out of 13 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
D:Mg501

b:18.0
occ:1.00
 OE1 D:GLU239 2.1 17.4 1.0
OE1 D:GLU265 2.1 16.7 1.0
OD2 D:ASP213 2.1 16.1 1.0
O D:HOH953 2.1 17.7 1.0
O D:HOH952 2.2 18.1 1.0
O D:HOH951 2.2 16.4 1.0
CD D:GLU265 3.0 14.3 1.0
CG D:ASP213 3.1 16.8 1.0
CD D:GLU239 3.1 17.9 1.0
OE2 D:GLU265 3.3 17.1 1.0
OD1 D:ASP213 3.5 16.5 1.0
NH2 D:ARG286 3.7 17.2 1.0
OE2 D:GLU239 3.8 17.5 1.0
CD2 D:HIS215 4.0 29.4 1.0
O D:HOH617 4.0 17.6 1.0
CG D:GLU239 4.1 13.6 1.0
OD2 D:ASP240 4.1 16.3 1.0
O D:HOH652 4.2 22.5 1.0
O D:HOH605 4.3 16.6 1.0
NE2 D:HIS215 4.3 32.8 1.0
CG D:GLU265 4.3 14.9 1.0
CB D:ASP213 4.4 17.7 1.0
OH D:TYR161 4.4 42.1 1.0
NH1 D:ARG149 4.5 33.7 1.0
OH C:TYR77 4.7 16.0 1.0
CG D:ASP240 4.8 16.9 1.0
CZ D:ARG286 4.8 21.5 1.0
NE2 D:HIS315 4.8 20.4 1.0
CD2 D:HIS315 4.9 17.8 1.0
NE D:ARG286 4.9 22.8 1.0
CB D:GLU265 5.0 13.9 1.0

Magnesium binding site 8 out of 13 in 4kws

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Magnesium binding site 8 out of 13 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
D:Mg503

b:15.1
occ:0.38
 O H:HOH936 2.0 39.9 1.0
O D:HOH955 2.1 39.8 1.0
O H:HOH729 4.3 23.1 1.0
O D:HOH714 4.3 22.1 1.0
O H:HOH810 4.3 34.4 1.0
OE2 D:GLU255 4.5 37.6 1.0
CD D:GLU255 4.5 32.2 1.0
OE2 H:GLU255 4.6 37.2 1.0
CD H:GLU255 4.6 28.1 1.0
OE1 D:GLU255 4.8 29.8 1.0
CG D:GLU255 4.9 21.6 1.0
OE1 H:GLU255 4.9 27.2 1.0
CG H:GLU255 4.9 16.8 1.0

Magnesium binding site 9 out of 13 in 4kws

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Magnesium binding site 9 out of 13 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 9 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:Mg504

b:24.8
occ:0.51
 O D:HOH959 2.0 37.1 1.0
O D:HOH961 2.0 40.2 1.0
O D:HOH912 2.0 39.3 1.0
O D:HOH937 2.1 34.2 1.0
O D:HOH886 2.2 42.0 1.0
O D:HOH782 2.3 31.1 1.0
O D:HOH925 4.0 41.3 1.0
OD1 D:ASP376 4.1 31.5 1.0
OD2 D:ASP376 4.1 36.0 1.0
O D:PRO371 4.2 23.8 1.0
OG D:SER370 4.3 29.0 1.0
O D:HOH697 4.4 24.7 1.0
O D:HOH906 4.5 40.3 1.0
CG D:ASP376 4.5 33.4 1.0
O D:HOH845 4.6 33.7 1.0
CB D:SER370 4.7 25.1 1.0
CE D:LYS101 4.9 20.0 1.0

Magnesium binding site 10 out of 13 in 4kws

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Magnesium binding site 10 out of 13 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 10 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:13.6
occ:1.00
 OE1 E:GLU265 2.1 12.5 1.0
O E:HOH973 2.1 15.0 1.0
OD2 E:ASP213 2.1 12.5 1.0
OE1 E:GLU239 2.1 13.2 1.0
O E:HOH974 2.1 14.8 1.0
O E:HOH975 2.1 16.2 1.0
CD E:GLU265 3.0 14.0 1.0
CG E:ASP213 3.1 14.4 1.0
CD E:GLU239 3.1 13.8 1.0
OE2 E:GLU265 3.3 15.4 1.0
OD1 E:ASP213 3.5 13.0 1.0
NH2 E:ARG286 3.8 14.0 1.0
OE2 E:GLU239 3.9 13.7 1.0
O E:HOH609 4.0 13.9 1.0
CD2 E:HIS215 4.0 21.2 1.0
CG E:GLU239 4.1 12.4 1.0
OD2 E:ASP240 4.1 13.5 1.0
O E:HOH603 4.3 14.3 1.0
O E:HOH675 4.3 18.0 1.0
CG E:GLU265 4.3 13.6 1.0
CB E:ASP213 4.4 13.5 1.0
NH1 E:ARG149 4.4 19.2 1.0
NE2 E:HIS215 4.4 21.6 1.0
OH E:TYR161 4.4 31.7 1.0
CG E:ASP240 4.7 14.1 1.0
OH H:TYR77 4.7 15.5 1.0
CZ E:ARG286 4.8 19.5 1.0
NE2 E:HIS315 4.9 17.7 1.0
CD2 E:HIS315 4.9 14.5 1.0
NE E:ARG286 4.9 22.1 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: Mon Aug 11 18:08:00 2025

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