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Magnesium in PDB 4k2s: Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate

Enzymatic activity of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate

All present enzymatic activity of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate, PDB code: 4k2s 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) 44.25 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.334, 85.790, 195.638, 90.00, 110.47, 90.00
R / Rfree (%) 16.9 / 20.3

Other elements in 4k2s:

The structure of Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate also contains other interesting chemical elements:

Chlorine (Cl) 6 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate (pdb code 4k2s). 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate, PDB code: 4k2s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 4k2s

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Magnesium binding site 1 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:9.6
occ:1.00
 O A:HOH987 2.0 13.1 1.0
OD2 A:ASP213 2.0 10.1 1.0
OE1 A:GLU239 2.0 8.4 1.0
O11 A:GCO501 2.1 12.6 1.0
OE1 A:GLU265 2.2 8.7 1.0
O2 A:GCO501 2.3 11.5 1.0
C1 A:GCO501 2.9 18.8 1.0
C2 A:GCO501 3.0 14.1 1.0
CG A:ASP213 3.0 11.4 1.0
CD A:GLU265 3.1 10.6 1.0
CD A:GLU239 3.1 8.2 1.0
OE2 A:GLU265 3.4 9.8 1.0
OD1 A:ASP213 3.4 8.4 1.0
NH2 A:ARG286 3.8 9.1 1.0
OE2 A:GLU239 3.8 10.2 1.0
O A:HOH613 4.0 12.7 1.0
CD2 A:HIS215 4.0 14.4 1.0
CG A:GLU239 4.0 8.5 1.0
O12 A:GCO501 4.1 15.1 1.0
OD2 A:ASP240 4.1 8.9 1.0
O A:HOH601 4.2 8.1 1.0
CB A:ASP213 4.2 8.9 1.0
OH A:TYR161 4.3 31.6 1.0
CG A:GLU265 4.4 7.8 1.0
C3 A:GCO501 4.4 15.1 1.0
NE2 A:HIS215 4.5 16.5 1.0
NH1 A:ARG149 4.5 22.1 1.0
CG A:ASP240 4.7 9.8 1.0
O3 A:GCO501 4.7 21.4 1.0
CZ A:ARG286 4.8 10.9 1.0
OH B:TYR77 4.8 12.9 1.0
NE A:ARG286 4.9 9.1 1.0

Magnesium binding site 2 out of 13 in 4k2s

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Magnesium binding site 2 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:9.1
occ:1.00
 OE1 B:GLU239 2.0 8.3 1.0
O B:HOH1002 2.0 6.9 1.0
OD2 B:ASP213 2.1 9.4 1.0
O11 B:GCO501 2.1 10.5 1.0
OE1 B:GLU265 2.1 10.1 1.0
O2 B:GCO501 2.2 12.2 1.0
C1 B:GCO501 2.9 15.9 1.0
C2 B:GCO501 3.0 15.2 1.0
CG B:ASP213 3.0 10.3 1.0
CD B:GLU265 3.0 9.3 1.0
CD B:GLU239 3.1 7.4 1.0
OE2 B:GLU265 3.3 11.3 1.0
OD1 B:ASP213 3.4 8.7 1.0
NH2 B:ARG286 3.8 10.4 1.0
OE2 B:GLU239 3.8 8.7 1.0
O B:HOH601 4.0 7.7 1.0
CG B:GLU239 4.0 7.2 1.0
CD2 B:HIS215 4.0 10.6 1.0
OD2 B:ASP240 4.1 9.2 1.0
O12 B:GCO501 4.1 13.5 1.0
OH B:TYR161 4.2 33.5 1.0
CB B:ASP213 4.3 10.7 1.0
O B:HOH616 4.3 10.2 1.0
C3 B:GCO501 4.3 16.5 1.0
CG B:GLU265 4.4 12.1 1.0
NE2 B:HIS215 4.5 12.7 1.0
NH1 B:ARG149 4.5 16.9 1.0
O3 B:GCO501 4.6 20.9 1.0
CG B:ASP240 4.7 10.7 1.0
OH A:TYR77 4.7 10.3 1.0
CZ B:ARG286 4.8 10.3 1.0
NE B:ARG286 4.9 8.3 1.0
CZ B:TYR161 5.0 33.8 1.0

Magnesium binding site 3 out of 13 in 4k2s

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Magnesium binding site 3 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:6.0
occ:0.36
 O B:HOH1013 2.0 13.9 0.5
O B:HOH1009 2.0 10.3 0.5
O B:HOH1013 2.0 17.8 0.5
O B:HOH1009 2.1 8.4 0.5
O B:HOH819 4.1 32.0 1.0
O B:HOH713 4.3 17.6 1.0
O F:HOH720 4.3 16.5 1.0
O F:HOH809 4.4 33.0 1.0
OE2 F:GLU255 4.5 26.4 1.0
CD F:GLU255 4.6 23.3 1.0
CD B:GLU255 4.6 20.5 1.0
OE2 B:GLU255 4.7 21.6 1.0
CG B:GLU255 4.8 9.5 1.0
OE1 B:GLU255 4.8 19.2 1.0
OE1 F:GLU255 4.9 23.8 1.0
CG F:GLU255 4.9 11.6 1.0
CB B:GLU255 4.9 9.6 1.0

Magnesium binding site 4 out of 13 in 4k2s

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Magnesium binding site 4 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:12.3
occ:1.00
 OE1 C:GLU239 1.9 13.9 1.0
OD2 C:ASP213 2.0 14.6 1.0
O C:HOH946 2.1 14.7 1.0
O11 C:GCO501 2.1 12.9 1.0
O2 C:GCO501 2.1 13.6 1.0
OE1 C:GLU265 2.2 13.2 1.0
C1 C:GCO501 2.9 19.3 1.0
C2 C:GCO501 2.9 18.5 1.0
CD C:GLU239 3.0 15.4 1.0
CG C:ASP213 3.0 14.2 1.0
CD C:GLU265 3.1 13.1 1.0
OE2 C:GLU265 3.3 13.4 1.0
OD1 C:ASP213 3.4 13.8 1.0
OE2 C:GLU239 3.7 16.1 1.0
NH2 C:ARG286 3.7 14.2 1.0
O C:HOH601 3.9 10.4 1.0
CG C:GLU239 4.0 13.0 1.0
CD2 C:HIS215 4.0 18.9 1.0
O12 C:GCO501 4.1 16.8 1.0
OD2 C:ASP240 4.1 13.1 1.0
CB C:ASP213 4.2 14.5 1.0
O C:HOH627 4.3 14.7 1.0
C3 C:GCO501 4.3 19.3 1.0
OH C:TYR161 4.4 31.2 1.0
CG C:GLU265 4.4 13.9 1.0
NH1 C:ARG149 4.4 25.0 1.0
NE2 C:HIS215 4.4 18.0 1.0
O3 C:GCO501 4.6 20.2 1.0
CG C:ASP240 4.7 15.6 1.0
CZ C:ARG286 4.7 13.1 1.0
NE C:ARG286 4.8 12.7 1.0
OH E:TYR77 4.8 14.2 1.0

Magnesium binding site 5 out of 13 in 4k2s

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Magnesium binding site 5 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:5.3
occ:0.28
 O C:HOH965 1.9 11.3 0.5
O D:HOH975 2.0 34.3 1.0
O C:HOH965 2.1 16.6 0.5
O D:HOH976 2.2 36.2 1.0
O C:HOH828 4.2 33.9 1.0
O C:HOH719 4.3 20.6 1.0
O D:HOH678 4.3 16.5 1.0
CD D:GLU255 4.5 27.4 1.0
OE2 D:GLU255 4.5 29.9 1.0
OE2 C:GLU255 4.6 26.1 1.0
CD C:GLU255 4.6 22.5 1.0
CG D:GLU255 4.8 15.5 1.0
OE1 D:GLU255 4.8 25.9 1.0
CG C:GLU255 4.9 14.7 1.0
OE1 C:GLU255 4.9 25.2 1.0

Magnesium binding site 6 out of 13 in 4k2s

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Magnesium binding site 6 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:11.7
occ:1.00
 OD2 D:ASP213 2.0 13.6 1.0
OE1 D:GLU239 2.0 13.9 1.0
O11 D:GCO501 2.1 11.1 1.0
O D:HOH971 2.1 11.6 1.0
OE1 D:GLU265 2.1 14.1 1.0
O2 D:GCO501 2.2 14.9 1.0
C1 D:GCO501 2.9 20.4 1.0
C2 D:GCO501 2.9 19.5 1.0
CG D:ASP213 3.0 12.7 1.0
CD D:GLU265 3.1 14.1 1.0
CD D:GLU239 3.1 12.1 1.0
OE2 D:GLU265 3.4 13.7 1.0
OD1 D:ASP213 3.4 14.2 1.0
NH2 D:ARG286 3.8 13.2 1.0
OE2 D:GLU239 3.8 12.3 1.0
O D:HOH601 3.9 10.9 1.0
CG D:GLU239 4.0 11.8 1.0
CD2 D:HIS215 4.0 19.1 1.0
O12 D:GCO501 4.1 17.5 1.0
OD2 D:ASP240 4.2 12.4 1.0
CB D:ASP213 4.2 13.1 1.0
O D:HOH604 4.3 11.6 1.0
C3 D:GCO501 4.3 21.3 1.0
CG D:GLU265 4.4 11.9 1.0
NH1 D:ARG149 4.4 25.5 1.0
NE2 D:HIS215 4.5 19.8 1.0
OH D:TYR161 4.5 39.5 1.0
O3 D:GCO501 4.6 21.1 1.0
CG D:ASP240 4.7 14.1 1.0
CZ D:ARG286 4.8 11.9 1.0
OH H:TYR77 4.8 13.9 1.0
NE D:ARG286 4.9 11.6 1.0

Magnesium binding site 7 out of 13 in 4k2s

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Magnesium binding site 7 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:15.8
occ:0.50
 O D:HOH741 2.1 39.6 1.0
O D:HOH851 2.1 35.9 1.0
O D:HOH910 2.1 31.6 1.0
O D:HOH712 2.2 23.7 1.0
O D:HOH898 2.3 33.4 1.0
O D:HOH886 2.3 43.2 1.0
O D:HOH943 3.9 36.4 1.0
OD1 D:ASP376 4.1 30.3 1.0
O D:PRO371 4.2 19.7 1.0
O D:HOH905 4.2 31.6 1.0
O D:HOH847 4.3 44.9 1.0
OD2 D:ASP376 4.3 35.1 1.0
O D:HOH695 4.3 19.9 1.0
OG D:SER370 4.4 24.3 1.0
O D:HOH903 4.6 28.1 1.0
CG D:ASP376 4.6 29.4 1.0
CB D:SER370 4.7 21.6 1.0
CE D:LYS101 4.7 15.0 1.0

Magnesium binding site 8 out of 13 in 4k2s

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Magnesium binding site 8 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and 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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:12.0
occ:1.00
 OE1 E:GLU239 2.0 11.9 1.0
OD2 E:ASP213 2.0 9.4 1.0
O E:HOH987 2.1 13.5 1.0
O11 E:GCO501 2.1 11.8 1.0
O2 E:GCO501 2.2 11.2 1.0
OE1 E:GLU265 2.2 10.2 1.0
C1 E:GCO501 2.9 16.4 1.0
C2 E:GCO501 3.0 16.1 1.0
CG E:ASP213 3.0 11.1 1.0
CD E:GLU265 3.1 10.4 1.0
CD E:GLU239 3.1 9.4 1.0
OD1 E:ASP213 3.4 11.4 1.0
OE2 E:GLU265 3.4 11.4 1.0
NH2 E:ARG286 3.8 10.6 1.0
OE2 E:GLU239 3.8 9.1 1.0
O E:HOH603 3.9 11.0 1.0
CG E:GLU239 4.0 8.9 1.0
CD2 E:HIS215 4.0 15.7 1.0
OD2 E:ASP240 4.1 9.6 1.0
O12 E:GCO501 4.1 13.7 1.0
O E:HOH601 4.2 10.8 1.0
CB E:ASP213 4.2 10.9 1.0
OH E:TYR161 4.3 27.8 1.0
C3 E:GCO501 4.3 18.4 1.0
CG E:GLU265 4.4 9.6 1.0
NH1 E:ARG149 4.5 20.0 1.0
NE2 E:HIS215 4.5 13.2 1.0
O3 E:GCO501 4.6 22.4 1.0
CG E:ASP240 4.7 9.7 1.0
CZ E:ARG286 4.8 12.7 1.0
OH C:TYR77 4.8 12.3 1.0
NE E:ARG286 4.9 12.6 1.0

Magnesium binding site 9 out of 13 in 4k2s

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Magnesium binding site 9 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate


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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:9.0
occ:0.38
 O E:HOH997 2.0 13.5 0.5
O H:HOH978 2.1 29.5 1.0
O E:HOH997 2.1 18.5 0.5
O E:HOH688 4.2 16.9 1.0
O H:HOH682 4.3 17.6 1.0
O E:HOH967 4.4 32.9 1.0
CD E:GLU255 4.6 20.5 1.0
CD H:GLU255 4.6 21.0 1.0
OE2 E:GLU255 4.7 22.1 1.0
OE2 H:GLU255 4.7 21.7 1.0
CG E:GLU255 4.8 11.5 1.0
OE1 E:GLU255 4.8 19.9 1.0
CG H:GLU255 4.8 8.6 1.0
OE1 H:GLU255 4.9 20.1 1.0

Magnesium binding site 10 out of 13 in 4k2s

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Magnesium binding site 10 out of 13 in the Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate


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 the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:10.0
occ:1.00
 OD2 F:ASP213 2.0 9.8 1.0
OE1 F:GLU239 2.0 9.7 1.0
O F:HOH990 2.1 9.1 1.0
OE1 F:GLU265 2.1 9.9 1.0
O11 F:GCO501 2.2 10.0 1.0
O2 F:GCO501 2.2 11.1 1.0
C1 F:GCO501 2.9 15.2 1.0
C2 F:GCO501 3.0 15.4 1.0
CG F:ASP213 3.0 10.3 1.0
CD F:GLU265 3.0 7.9 1.0
CD F:GLU239 3.1 10.3 1.0
OE2 F:GLU265 3.3 10.2 1.0
OD1 F:ASP213 3.4 10.3 1.0
NH2 F:ARG286 3.8 9.1 1.0
OE2 F:GLU239 3.8 9.8 1.0
O F:HOH602 4.0 9.6 1.0
CG F:GLU239 4.0 9.2 1.0
CD2 F:HIS215 4.0 11.5 1.0
OD2 F:ASP240 4.1 10.2 1.0
O12 F:GCO501 4.1 15.0 1.0
CB F:ASP213 4.2 8.6 1.0
O F:HOH630 4.3 9.1 1.0
C3 F:GCO501 4.3 15.9 1.0
CG F:GLU265 4.4 7.5 1.0
OH F:TYR161 4.4 26.6 1.0
NH1 F:ARG149 4.5 18.2 1.0
NE2 F:HIS215 4.5 13.3 1.0
CG F:ASP240 4.7 9.1 1.0
O3 F:GCO501 4.7 15.2 1.0
OH G:TYR77 4.8 9.8 1.0
CZ F:ARG286 4.8 11.1 1.0
NE F:ARG286 4.9 7.4 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Crystal Structure of the Mutant P317A of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg and D-Gluconate To Be Published.
Page generated: Mon Dec 14 19:01:40 2020

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