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Magnesium in PDB 2o56: Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium

Protein crystallography data

The structure of Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium, PDB code: 2o56 was solved by Y.Patskovsky, J.M.Sauder, M.Dickey, J.M.Adams, S.Ozyurt, S.R.Wasserman, J.Gerlt, S.K.Burley, S.C.Almo, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.662, 140.818, 126.838, 90.00, 105.94, 90.00
R / Rfree (%) 20.9 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium (pdb code 2o56). 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 A Member of the Enolase Superfamily From Salmonella Typhimurium, PDB code: 2o56:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2o56

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Magnesium binding site 1 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:38.1
occ:1.00
 OE2 A:GLU245 2.2 39.7 1.0
O A:HOH2200 2.2 49.6 1.0
OE1 A:GLU271 2.3 38.0 1.0
OE1 A:GLU219 2.3 43.1 1.0
O A:HOH2074 2.4 40.1 1.0
CD A:GLU271 3.1 38.1 1.0
CD A:GLU219 3.3 44.5 1.0
OE2 A:GLU271 3.3 38.2 1.0
CD A:GLU245 3.4 35.5 1.0
OE2 A:GLU219 3.5 36.3 1.0
NZ A:LYS170 3.7 26.6 1.0
O A:HOH2014 4.0 29.5 1.0
OE1 A:GLU246 4.1 37.6 1.0
NE2 A:GLN134 4.2 46.7 1.0
OE1 A:GLU245 4.2 40.7 1.0
CG A:GLU245 4.2 25.8 1.0
CD2 A:HIS321 4.3 28.9 1.0
O A:HOH2112 4.4 48.7 1.0
NE2 A:HIS321 4.5 29.0 1.0
CG A:GLU271 4.6 29.9 1.0
CE A:LYS170 4.6 26.4 1.0
O A:HOH2018 4.6 26.8 1.0
CD2 A:HIS221 4.7 35.6 1.0
CG A:GLU219 4.7 26.9 1.0
NE2 A:HIS221 4.9 34.2 1.0
OE2 A:GLU346 4.9 34.0 1.0
CD A:GLU246 5.0 40.8 1.0

Magnesium binding site 2 out of 8 in 2o56

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Magnesium binding site 2 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:37.2
occ:1.00
 OE2 B:GLU245 2.1 41.1 1.0
O B:HOH2237 2.3 41.4 1.0
OE1 B:GLU219 2.3 43.4 1.0
OE1 B:GLU271 2.4 36.7 1.0
O B:HOH2145 2.5 39.5 1.0
CD B:GLU271 3.2 37.7 1.0
CD B:GLU219 3.2 44.9 1.0
CD B:GLU245 3.3 35.2 1.0
OE2 B:GLU271 3.4 37.1 1.0
OE2 B:GLU219 3.4 33.7 1.0
NZ B:LYS170 3.8 24.6 1.0
CG B:GLU245 4.1 28.4 1.0
O B:HOH2047 4.1 29.9 1.0
OE1 B:GLU245 4.1 40.3 1.0
O B:HOH2058 4.2 43.1 1.0
OE1 B:GLU246 4.2 37.0 1.0
NE2 B:GLN134 4.3 23.0 0.5
CD2 B:HIS321 4.4 28.6 1.0
NE2 B:HIS321 4.5 28.1 1.0
O B:HOH2023 4.5 22.1 1.0
CE B:LYS170 4.6 26.1 1.0
CG B:GLU219 4.6 22.4 1.0
CG B:GLU271 4.6 30.3 1.0
CD2 B:HIS221 4.8 38.6 1.0
CG B:GLU246 4.8 26.9 1.0
CD B:GLU246 4.8 40.5 1.0

Magnesium binding site 3 out of 8 in 2o56

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Magnesium binding site 3 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:34.2
occ:1.00
 OE2 C:GLU245 2.1 40.4 1.0
OE1 C:GLU271 2.2 34.8 1.0
O C:HOH2073 2.3 42.2 1.0
OE1 C:GLU219 2.3 43.0 1.0
O C:HOH2192 2.4 47.9 1.0
CD C:GLU271 3.1 38.1 1.0
CD C:GLU219 3.2 45.2 1.0
OE2 C:GLU271 3.2 39.3 1.0
CD C:GLU245 3.3 35.0 1.0
OE2 C:GLU219 3.3 35.3 1.0
O C:HOH2193 3.8 56.8 1.0
NZ C:LYS170 3.9 25.8 1.0
O C:HOH2087 4.0 31.1 1.0
OE1 C:GLU246 4.0 38.0 1.0
OE1 C:GLU245 4.1 39.2 1.0
CG C:GLU245 4.2 25.6 1.0
NE2 C:GLN134 4.3 40.1 1.0
CD2 C:HIS321 4.3 30.0 1.0
O C:HOH2035 4.5 34.0 1.0
CG C:GLU271 4.5 30.3 1.0
NE2 C:HIS321 4.6 26.2 1.0
CG C:GLU219 4.6 23.8 1.0
CD2 C:HIS221 4.6 36.6 1.0
CE C:LYS170 4.7 26.4 1.0
CD C:GLU246 4.7 41.5 1.0
CG C:GLU246 4.9 30.1 1.0
NE2 C:HIS221 4.9 36.1 1.0

Magnesium binding site 4 out of 8 in 2o56

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Magnesium binding site 4 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:36.6
occ:1.00
 OE2 D:GLU245 2.2 39.8 1.0
OE1 D:GLU271 2.2 35.9 1.0
O D:HOH2205 2.3 51.2 1.0
O D:HOH2053 2.3 40.0 1.0
OE1 D:GLU219 2.3 43.8 1.0
CD D:GLU271 3.1 38.0 1.0
CD D:GLU219 3.3 45.2 1.0
CD D:GLU245 3.3 35.7 1.0
OE2 D:GLU271 3.4 38.1 1.0
OE2 D:GLU219 3.5 39.4 1.0
NZ D:LYS170 3.8 25.7 1.0
O D:HOH2029 3.9 31.1 1.0
OE1 D:GLU246 4.0 39.8 1.0
CG D:GLU245 4.1 28.2 1.0
OE1 D:GLU245 4.2 41.7 1.0
CD2 D:HIS321 4.3 31.5 1.0
NE2 D:GLN134 4.3 45.5 1.0
O D:HOH2201 4.4 50.9 1.0
O D:HOH2202 4.4 51.7 1.0
NE2 D:HIS321 4.5 30.0 1.0
CG D:GLU271 4.5 29.6 1.0
O D:HOH2023 4.6 29.1 1.0
CE D:LYS170 4.6 26.2 1.0
CG D:GLU219 4.7 26.6 1.0
CD2 D:HIS221 4.7 35.8 1.0
CD D:GLU246 4.8 42.0 1.0
CG D:GLU246 4.9 31.3 1.0
NE2 D:HIS221 4.9 34.9 1.0

Magnesium binding site 5 out of 8 in 2o56

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Magnesium binding site 5 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2005

b:37.3
occ:1.00
 OE2 E:GLU245 2.2 41.8 1.0
O E:HOH2234 2.3 44.8 1.0
OE1 E:GLU219 2.3 42.1 1.0
OE1 E:GLU271 2.4 37.1 1.0
O E:HOH2175 2.5 41.6 1.0
O E:HOH2202 3.0 59.4 1.0
CD E:GLU219 3.2 44.5 1.0
CD E:GLU271 3.2 39.6 1.0
OE2 E:GLU271 3.3 39.1 1.0
OE2 E:GLU219 3.4 32.6 1.0
CD E:GLU245 3.4 35.3 1.0
NZ E:LYS170 3.9 23.7 1.0
OE1 E:GLU246 4.0 38.8 1.0
CG E:GLU245 4.2 28.4 1.0
OE1 E:GLU245 4.2 40.7 1.0
O E:HOH2094 4.3 29.6 1.0
NE2 E:GLN134 4.3 41.5 1.0
O E:HOH2055 4.3 52.0 1.0
CD2 E:HIS321 4.4 29.7 1.0
O E:HOH2014 4.5 25.2 1.0
NE2 E:HIS321 4.5 30.0 1.0
CD2 E:HIS221 4.6 37.1 1.0
CG E:GLU219 4.6 22.8 1.0
CG E:GLU271 4.6 30.0 1.0
CE E:LYS170 4.7 28.0 1.0
CD E:GLU246 4.7 41.0 1.0
CG E:GLU246 4.8 29.0 1.0
NE2 E:HIS221 4.9 33.6 1.0

Magnesium binding site 6 out of 8 in 2o56

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Magnesium binding site 6 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2006

b:37.1
occ:1.00
 OE2 F:GLU245 2.2 39.1 1.0
OE1 F:GLU271 2.3 35.4 1.0
OE1 F:GLU219 2.3 43.0 1.0
O F:HOH2072 2.3 37.4 1.0
CD F:GLU271 3.1 37.6 1.0
CD F:GLU219 3.2 45.7 1.0
OE2 F:GLU271 3.3 36.5 1.0
CD F:GLU245 3.4 34.7 1.0
OE2 F:GLU219 3.4 35.5 1.0
NZ F:LYS170 3.8 24.2 1.0
O F:HOH2137 3.9 51.7 1.0
OE1 F:GLU246 4.0 39.4 1.0
O F:HOH2065 4.1 32.6 1.0
OE1 F:GLU245 4.2 40.9 1.0
NE2 F:GLN134 4.2 37.8 1.0
CG F:GLU245 4.3 27.0 1.0
CD2 F:HIS321 4.3 29.6 1.0
O F:HOH2038 4.5 27.7 1.0
NE2 F:HIS321 4.5 28.3 1.0
CG F:GLU271 4.5 31.0 1.0
CG F:GLU219 4.6 24.5 1.0
CD2 F:HIS221 4.6 37.4 1.0
CE F:LYS170 4.7 26.5 1.0
CD F:GLU246 4.8 41.4 1.0
CG F:GLU246 4.9 29.4 1.0
NE2 F:HIS221 4.9 35.1 1.0
OE2 F:GLU346 5.0 33.2 1.0

Magnesium binding site 7 out of 8 in 2o56

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Magnesium binding site 7 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg2007

b:27.6
occ:1.00
 OE2 G:GLU245 2.1 38.7 1.0
OE1 G:GLU219 2.3 40.5 1.0
O G:HOH2227 2.3 47.1 1.0
OE1 G:GLU271 2.3 36.3 1.0
O G:HOH2191 2.3 50.4 1.0
O G:HOH2107 2.4 33.3 1.0
CD G:GLU219 3.1 44.3 1.0
CD G:GLU245 3.2 33.7 1.0
CD G:GLU271 3.2 38.6 1.0
OE2 G:GLU219 3.2 34.2 1.0
OE2 G:GLU271 3.5 35.5 1.0
NZ G:LYS170 3.9 24.9 1.0
OE1 G:GLU246 4.0 38.1 1.0
O G:HOH2063 4.0 28.4 1.0
OE1 G:GLU245 4.0 39.8 1.0
CG G:GLU245 4.0 27.0 1.0
NE2 G:GLN134 4.3 35.2 1.0
CD2 G:HIS321 4.4 28.0 1.0
O G:HOH2144 4.4 49.0 1.0
NE2 G:HIS321 4.5 28.8 1.0
CG G:GLU219 4.5 25.6 1.0
CD2 G:HIS221 4.5 36.7 1.0
CG G:GLU271 4.6 27.9 1.0
CE G:LYS170 4.6 24.1 1.0
O G:HOH2036 4.7 24.6 1.0
CD G:GLU246 4.8 40.4 1.0
NE2 G:HIS221 4.8 34.9 1.0
CG G:GLU246 4.9 27.1 1.0

Magnesium binding site 8 out of 8 in 2o56

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Magnesium binding site 8 out of 8 in the Crystal Structure of A Member of the Enolase Superfamily From Salmonella Typhimurium


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 A Member of the Enolase Superfamily From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg2008

b:30.6
occ:1.00
 OE2 H:GLU245 2.1 39.0 1.0
OE1 H:GLU271 2.3 37.4 1.0
O H:HOH2115 2.3 35.3 1.0
OE1 H:GLU219 2.3 41.4 1.0
O H:HOH2215 2.7 46.9 1.0
CD H:GLU219 3.2 43.6 1.0
CD H:GLU245 3.2 34.5 1.0
CD H:GLU271 3.2 38.4 1.0
OE2 H:GLU219 3.4 35.8 1.0
OE2 H:GLU271 3.5 34.8 1.0
NZ H:LYS170 3.8 22.1 1.0
OE1 H:GLU246 3.9 36.3 1.0
O H:HOH2098 4.0 31.5 1.0
OE1 H:GLU245 4.0 40.0 1.0
CG H:GLU245 4.1 25.6 1.0
CD2 H:HIS321 4.3 29.3 1.0
NE2 H:GLN134 4.3 29.4 1.0
NE2 H:HIS321 4.5 30.3 1.0
CG H:GLU219 4.6 26.6 1.0
CG H:GLU271 4.6 29.9 1.0
O H:HOH2216 4.6 45.4 1.0
CE H:LYS170 4.6 26.8 1.0
CD2 H:HIS221 4.7 37.6 1.0
CD H:GLU246 4.7 39.6 1.0
O H:HOH2035 4.7 25.2 1.0
CG H:GLU246 4.9 27.6 1.0
NE2 H:HIS221 5.0 33.6 1.0

Reference:

Y.Patskovsky, J.M.Sauder, M.Dickey, J.M.Adams, S.Ozyurt, S.R.Wasserman, J.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of Putative Enolase From Salmonella Typhimurium LT2 To Be Published.
Page generated: Wed Aug 14 01:23:04 2024

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