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Magnesium in PDB 3nfu: Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium

Enzymatic activity of Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium

All present enzymatic activity of Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium:
4.2.1.40;

Protein crystallography data

The structure of Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium, PDB code: 3nfu was solved by Y.Patskovsky, R.Toro, M.Rutter, J.M.Sauder, J.A.Gerlt, S.C.Almo, S.K.Burley, New York Structural Genomix Research Consortium(Nysgxrc), New York Sgx Research Center For Structural Genomics(Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.009, 105.731, 87.991, 90.00, 128.97, 90.00
R / Rfree (%) 19.7 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium (pdb code 3nfu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium, PDB code: 3nfu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3nfu

Go back to Magnesium Binding Sites List in 3nfu
Magnesium binding site 1 out of 2 in the Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium


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 Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg451

b:46.7
occ:1.00
OE2 A:GLU256 2.3 35.9 1.0
OD1 A:ASP231 2.3 39.4 1.0
OD1 A:ASN285 2.4 37.7 1.0
OD2 A:ASP257 2.5 29.6 1.0
OD2 A:ASP231 2.9 36.1 1.0
CG A:ASP231 2.9 28.3 1.0
CD A:GLU256 3.0 43.4 1.0
ND2 A:ASN233 3.1 30.6 1.0
CG A:GLU256 3.2 30.1 1.0
CG A:ASP257 3.5 29.4 1.0
CG A:ASN285 3.6 35.8 1.0
O A:HOH655 3.7 40.8 1.0
O A:HOH515 3.7 46.4 1.0
CB A:ASP257 3.8 29.1 1.0
CG A:ASN233 3.9 42.0 1.0
N A:ASN285 4.1 31.4 1.0
OE1 A:GLU256 4.2 40.7 1.0
CA A:ASN233 4.3 34.5 1.0
CB A:ASP231 4.3 26.3 1.0
CB A:ASN285 4.3 36.6 1.0
CB A:GLU256 4.4 25.4 1.0
OD1 A:ASN233 4.5 41.1 1.0
N A:ASN233 4.5 37.3 1.0
SD A:MET286 4.6 20.2 1.0
C A:GLU256 4.6 33.8 1.0
N A:ASP257 4.6 33.4 1.0
ND2 A:ASN285 4.6 42.8 1.0
CB A:ASN233 4.6 37.1 1.0
OD1 A:ASP257 4.6 30.5 1.0
O A:GLU256 4.7 32.7 1.0
CA A:ASN285 4.7 29.4 1.0
CA A:ASP257 4.9 33.0 1.0
CG A:MET286 4.9 32.9 1.0
C A:THR284 4.9 32.2 1.0
NZ A:LYS203 4.9 35.9 1.0
CA A:ASP231 5.0 30.8 1.0

Magnesium binding site 2 out of 2 in 3nfu

Go back to Magnesium Binding Sites List in 3nfu
Magnesium binding site 2 out of 2 in the Crystal Structure of Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium


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 Probable Glucarate Dehydratase From Chromohalobacter Salexigens Dsm 3043 Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg451

b:49.6
occ:1.00
OD1 B:ASN285 2.2 37.0 1.0
OE2 B:GLU256 2.3 35.7 1.0
OD2 B:ASP231 2.6 32.9 1.0
OD2 B:ASP257 2.6 27.0 1.0
OD1 B:ASN233 2.9 33.6 1.0
OD1 B:ASP231 2.9 37.0 1.0
CG B:ASP231 3.1 27.2 1.0
CD B:GLU256 3.2 30.3 1.0
O B:HOH607 3.3 38.4 1.0
CG B:ASN285 3.3 27.8 1.0
CG B:GLU256 3.5 21.3 1.0
O B:HOH628 3.6 38.0 1.0
CG B:ASP257 3.7 28.4 1.0
CG B:ASN233 3.7 42.6 1.0
CB B:ASP257 4.1 30.9 1.0
N B:ASN285 4.1 29.6 1.0
ND2 B:ASN285 4.2 36.1 1.0
OE1 B:GLU256 4.3 37.0 1.0
CB B:ASN285 4.3 33.1 1.0
CA B:ASN233 4.3 33.1 1.0
CG B:MET286 4.4 22.6 1.0
CB B:ASP231 4.5 21.8 1.0
ND2 B:ASN233 4.5 27.9 1.0
SD B:MET286 4.5 18.1 1.0
CB B:ASN233 4.6 36.8 1.0
N B:ASN233 4.7 31.3 1.0
CA B:ASN285 4.7 24.7 1.0
OD1 B:ASP257 4.8 30.1 1.0
CB B:GLU256 4.8 18.6 1.0
O B:GLU256 4.9 29.8 1.0
C B:GLU256 4.9 35.1 1.0
NZ B:LYS203 5.0 35.0 1.0
C B:THR284 5.0 32.4 1.0

Reference:

Y.Patskovsky, R.Toro, M.Rutter, J.M.Sauder, J.A.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of Glucarate Dehydratase From Chromohalobacter Salexigens To Be Published.
Page generated: Mon Dec 14 08:28:25 2020

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