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Magnesium in PDB 3fyy: Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg

Protein crystallography data

The structure of Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg, PDB code: 3fyy was solved by A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo, Newyork 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) 24.72 / 1.80
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 121.162, 121.162, 120.876, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg (pdb code 3fyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg, PDB code: 3fyy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3fyy

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Magnesium binding site 1 out of 4 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis 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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:17.8
occ:1.00
OE1 A:GLU221 2.0 28.7 1.0
NE2 A:HIS246 2.0 28.6 1.0
OD2 A:ASP193 2.1 30.5 1.0
O A:HOH565 2.1 32.3 1.0
O A:HOH557 2.1 29.9 1.0
CE1 A:HIS246 2.9 26.0 1.0
CD A:GLU221 3.0 30.6 1.0
CD2 A:HIS246 3.0 25.9 1.0
CG A:ASP193 3.1 27.2 1.0
CG A:GLU221 3.4 27.1 1.0
OD1 A:ASP193 3.5 29.8 1.0
ND1 A:HIS246 4.1 27.7 1.0
OE2 A:GLU221 4.1 29.0 1.0
O A:HOH397 4.1 26.3 1.0
CG A:HIS246 4.1 27.8 1.0
O A:HOH451 4.2 28.3 1.0
OG A:SER222 4.2 24.9 1.0
CB A:GLU221 4.4 26.5 1.0
CE1 A:TYR164 4.4 34.0 1.0
OH A:TYR164 4.4 36.2 1.0
OH A:TYR89 4.4 37.3 1.0
CB A:ASP193 4.5 28.8 1.0
OD1 A:ASN266 4.7 29.8 1.0
O A:HOH571 4.7 52.2 1.0
O A:HOH392 4.9 28.4 1.0
CZ A:TYR164 4.9 36.0 1.0

Magnesium binding site 2 out of 4 in 3fyy

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Magnesium binding site 2 out of 4 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis 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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:28.7
occ:1.00
OD1 A:ASP42 2.1 30.6 1.0
O A:HOH632 2.1 47.2 1.0
O A:HOH631 2.1 43.0 1.0
OG1 A:THR297 2.1 29.7 1.0
NE2 A:HIS45 2.3 33.9 1.0
O A:THR297 2.3 31.6 1.0
C A:THR297 3.1 31.1 1.0
CE1 A:HIS45 3.1 36.3 1.0
CG A:ASP42 3.2 30.2 1.0
CB A:THR297 3.2 27.7 1.0
CA A:THR297 3.2 28.5 1.0
CD2 A:HIS45 3.3 34.3 1.0
CB A:ASP42 3.6 29.6 1.0
O A:HOH524 3.8 38.7 1.0
CG2 A:THR297 4.0 28.0 1.0
O A:HOH410 4.2 35.3 1.0
OD2 A:ASP42 4.2 31.1 1.0
ND1 A:HIS45 4.3 34.3 1.0
N A:GLN298 4.3 31.4 1.0
CG A:HIS45 4.4 33.3 1.0
NH2 A:ARG15 4.5 48.6 1.0
CG A:GLN298 4.6 34.8 1.0
CB A:GLN298 4.6 32.3 1.0
N A:THR297 4.7 28.6 1.0
O A:ASP42 4.9 33.6 1.0

Magnesium binding site 3 out of 4 in 3fyy

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Magnesium binding site 3 out of 4 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis 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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:16.7
occ:1.00
O B:HOH630 1.9 32.3 1.0
OE1 B:GLU221 1.9 27.5 1.0
NE2 B:HIS246 2.1 32.4 1.0
O B:HOH411 2.1 34.1 1.0
OD2 B:ASP193 2.1 31.1 1.0
CD B:GLU221 2.9 29.6 1.0
CE1 B:HIS246 3.0 31.4 1.0
CD2 B:HIS246 3.1 29.8 1.0
CG B:ASP193 3.2 30.9 1.0
CG B:GLU221 3.4 27.8 1.0
OD1 B:ASP193 3.5 32.2 1.0
O B:HOH410 3.7 47.5 1.0
OE2 B:GLU221 4.1 28.1 1.0
O B:HOH429 4.1 26.8 1.0
ND1 B:HIS246 4.1 31.3 1.0
O B:HOH476 4.1 33.9 1.0
CG B:HIS246 4.2 29.5 1.0
OH B:TYR164 4.3 33.4 1.0
O B:HOH541 4.3 47.9 1.0
OG B:SER222 4.3 28.6 1.0
CB B:GLU221 4.4 27.6 1.0
CE1 B:TYR164 4.4 33.7 1.0
CB B:ASP193 4.5 29.9 1.0
OH B:TYR89 4.6 34.3 1.0
OD1 B:ASN266 4.6 32.6 1.0
CZ B:TYR164 4.8 34.0 1.0
O B:HOH395 4.8 29.0 1.0

Magnesium binding site 4 out of 4 in 3fyy

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Magnesium binding site 4 out of 4 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis 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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:31.9
occ:1.00
O B:HOH634 2.0 46.2 1.0
OD1 B:ASP42 2.0 31.1 1.0
OG1 B:THR297 2.2 31.5 1.0
O B:THR297 2.3 28.7 1.0
NE2 B:HIS45 2.4 36.1 1.0
O B:HOH633 2.8 47.2 1.0
CG B:ASP42 3.1 31.6 1.0
C B:THR297 3.1 28.7 1.0
CE1 B:HIS45 3.2 36.6 1.0
CB B:THR297 3.3 28.6 1.0
CA B:THR297 3.4 28.2 1.0
CD2 B:HIS45 3.5 36.4 1.0
CB B:ASP42 3.6 30.9 1.0
O B:HOH420 4.1 30.6 1.0
CG2 B:THR297 4.1 28.6 1.0
O B:HOH615 4.1 43.2 1.0
OD2 B:ASP42 4.2 33.2 1.0
N B:GLN298 4.4 29.1 1.0
ND1 B:HIS45 4.4 35.9 1.0
NH2 B:ARG15 4.4 44.7 1.0
CG B:HIS45 4.5 36.3 1.0
CG B:GLN298 4.6 30.4 1.0
CB B:GLN298 4.7 27.6 1.0
N B:THR297 4.8 26.2 1.0
O B:ASP42 4.9 32.1 1.0

Reference:

J.F.Rakus, C.Kalyanaraman, A.A.Fedorov, E.V.Fedorov, F.P.Mills-Groninger, R.Toro, J.Bonanno, K.Bain, J.M.Sauder, S.K.Burley, S.C.Almo, M.P.Jacobson, J.A.Gerlt. Computation-Facilitated Assignment of the Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase From Oceanobacillus Iheyensis . Biochemistry V. 48 11546 2009.
ISSN: ISSN 0006-2960
PubMed: 19883118
DOI: 10.1021/BI901731C
Page generated: Mon Dec 14 08:09:35 2020

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