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Magnesium in PDB 2gge: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A, PDB code: 2gge was solved by V.N.Malashkevich, J.M.Sauder, K.D.Schwinn, S.Emtage, D.A.Thompson, M.E.Rutter, M.Dickey, C.Groshong, K.T.Bain, J.M.Adams, C.Reyes, I.Rooney, A.Powell, A.Boice, T.Gheyi, S.Ozyurt, S.Atwell, S.R.Wasserman, S.K.Burley, A.Sali, P.Babbitt, U.Pieper, J.A.Gerlt, S.C.Almo, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.95 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 112.417, 110.654, 129.308, 90.00, 105.77, 90.00
R / Rfree (%) 18.9 / 25.3

Other elements in 2gge:

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A (pdb code 2gge). 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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A, PDB code: 2gge:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2gge

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Magnesium binding site 1 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:23.4
occ:1.00
 OE2 A:GLU217 2.0 15.6 1.0
OE2 A:GLU243 2.1 22.2 1.0
O A:HOH622 2.2 14.4 1.0
O A:HOH618 2.2 12.6 1.0
NE2 A:HIS293 2.3 21.4 1.0
O A:HOH621 2.3 16.5 1.0
CD A:GLU217 3.0 12.8 1.0
CE1 A:HIS293 3.2 23.4 1.0
CD2 A:HIS293 3.2 23.8 1.0
CD A:GLU243 3.3 21.8 1.0
CG A:GLU217 3.6 12.4 1.0
OD2 A:ASP190 3.6 19.1 1.0
NZ A:LYS159 4.0 14.4 1.0
OD1 A:ASP190 4.1 17.0 1.0
CG A:ASP190 4.1 14.9 1.0
OE1 A:GLU243 4.1 27.9 1.0
O A:HOH619 4.1 22.6 1.0
OE1 A:GLU217 4.1 14.7 1.0
O A:HOH607 4.1 39.7 1.0
ND1 A:HIS293 4.2 22.6 1.0
OE2 A:GLU218 4.3 25.5 1.0
OE1 A:GLN264 4.3 18.5 1.0
CG A:HIS293 4.3 19.8 1.0
CB A:GLU243 4.3 18.1 1.0
CG A:GLU243 4.3 20.7 1.0
O A:HOH482 4.4 22.2 1.0
CD A:GLU218 4.5 21.1 1.0
CG A:GLU218 4.7 17.7 1.0
ND2 A:ASN192 4.8 15.0 1.0
CB A:GLU217 4.9 15.5 1.0
CE A:LYS159 4.9 14.3 1.0
NE2 A:GLN264 5.0 12.3 1.0
CD A:GLN264 5.0 14.3 1.0

Magnesium binding site 2 out of 8 in 2gge

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Magnesium binding site 2 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg400

b:15.3
occ:1.00
 OE2 B:GLU243 2.0 20.7 1.0
O B:HOH647 2.1 17.3 1.0
OE2 B:GLU217 2.2 14.8 1.0
O B:HOH628 2.2 23.4 1.0
O B:HOH403 2.2 16.1 1.0
NE2 B:HIS293 2.3 23.3 1.0
CD2 B:HIS293 3.0 21.0 1.0
CD B:GLU243 3.2 26.1 1.0
CD B:GLU217 3.3 16.5 1.0
CE1 B:HIS293 3.3 22.1 1.0
O B:HOH476 3.7 31.3 1.0
OD2 B:ASP190 3.8 13.2 1.0
CG B:GLU217 3.8 14.8 1.0
CG B:GLU243 4.1 21.6 1.0
NZ B:LYS159 4.1 14.1 1.0
OE1 B:GLU243 4.1 28.0 1.0
CB B:GLU243 4.2 19.6 1.0
OD1 B:ASP190 4.2 13.0 1.0
OE2 B:GLU218 4.2 23.7 1.0
CG B:HIS293 4.2 21.8 1.0
CG B:ASP190 4.3 17.4 1.0
OE1 B:GLN264 4.3 17.3 1.0
OE1 B:GLU217 4.3 15.8 1.0
ND1 B:HIS293 4.3 23.1 1.0
O B:HOH437 4.4 20.9 1.0
CD B:GLU218 4.5 21.1 1.0
O B:HOH458 4.7 17.6 1.0
ND2 B:ASN192 4.8 23.1 1.0
CG B:GLU218 4.8 16.9 1.0
CE B:LYS159 4.9 15.0 1.0
CD B:GLN264 4.9 16.9 1.0
NE2 B:GLN264 5.0 17.1 1.0

Magnesium binding site 3 out of 8 in 2gge

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Magnesium binding site 3 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg400

b:23.5
occ:1.00
 O C:HOH588 2.0 16.0 1.0
OE2 C:GLU217 2.0 24.5 1.0
OE2 C:GLU243 2.1 28.7 1.0
O C:HOH589 2.1 18.7 1.0
O C:HOH587 2.2 15.8 1.0
NE2 C:HIS293 2.4 26.9 1.0
CD C:GLU217 3.1 18.2 1.0
CE1 C:HIS293 3.2 24.2 1.0
CD C:GLU243 3.3 27.8 1.0
CD2 C:HIS293 3.4 24.8 1.0
CG C:GLU217 3.5 18.6 1.0
OD2 C:ASP190 3.8 21.4 1.0
OD1 C:ASP190 4.0 17.1 1.0
OE1 C:GLU243 4.0 29.4 1.0
CG C:ASP190 4.2 21.4 1.0
OE1 C:GLU217 4.2 21.7 1.0
OE1 C:GLN264 4.2 18.8 1.0
NZ C:LYS159 4.3 11.6 1.0
O C:HOH578 4.3 18.5 1.0
OE2 C:GLU218 4.3 25.0 1.0
CG C:GLU243 4.3 24.2 1.0
ND1 C:HIS293 4.4 22.3 1.0
CD C:GLU218 4.4 26.3 1.0
CB C:GLU243 4.4 25.7 1.0
CG C:HIS293 4.5 20.9 1.0
CG C:GLU218 4.5 20.1 1.0
ND2 C:ASN192 4.6 19.2 1.0
O C:HOH516 4.7 21.8 1.0
CB C:GLU217 4.8 15.1 1.0
OE1 C:GLU218 4.9 26.9 1.0
CD C:GLN264 4.9 24.4 1.0
NE2 C:GLN264 5.0 16.4 1.0

Magnesium binding site 4 out of 8 in 2gge

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Magnesium binding site 4 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg400

b:14.3
occ:1.00
 O D:HOH2026 1.9 16.5 1.0
O D:HOH1878 2.0 15.7 1.0
OE2 D:GLU217 2.0 13.6 1.0
OE2 D:GLU243 2.1 22.2 1.0
O D:HOH1847 2.1 8.4 1.0
NE2 D:HIS293 2.3 14.6 1.0
CD D:GLU217 3.1 14.1 1.0
CD2 D:HIS293 3.2 14.4 1.0
CE1 D:HIS293 3.3 16.4 1.0
CD D:GLU243 3.3 24.2 1.0
CG D:GLU217 3.5 11.5 1.0
OD2 D:ASP190 3.8 13.2 1.0
NZ D:LYS159 4.0 13.8 1.0
OD1 D:ASP190 4.0 13.1 1.0
OE1 D:GLU243 4.1 27.3 1.0
OE1 D:GLU217 4.1 16.0 1.0
CG D:ASP190 4.2 16.3 1.0
CB D:GLU243 4.2 20.9 1.0
CG D:GLU243 4.3 22.4 1.0
OE2 D:GLU218 4.3 24.7 1.0
O D:HOH1817 4.3 34.8 1.0
CG D:HIS293 4.3 13.6 1.0
O D:HOH2007 4.3 16.3 1.0
ND1 D:HIS293 4.3 14.5 1.0
OE1 D:GLN264 4.4 13.3 1.0
CD D:GLU218 4.5 25.6 1.0
O D:HOH1854 4.6 21.6 1.0
CG D:GLU218 4.7 17.3 1.0
ND2 D:ASN192 4.8 17.1 1.0
NE2 D:GLN264 4.9 12.9 1.0
CB D:GLU217 4.9 8.0 1.0
CE D:LYS159 4.9 9.0 1.0
CD D:GLN264 4.9 10.5 1.0

Magnesium binding site 5 out of 8 in 2gge

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Magnesium binding site 5 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg400

b:20.1
occ:1.00
 OE2 E:GLU243 1.9 26.0 1.0
O E:HOH478 2.0 20.0 1.0
O E:HOH535 2.1 18.3 1.0
OE2 E:GLU217 2.2 14.2 1.0
O E:HOH465 2.2 16.1 1.0
NE2 E:HIS293 2.4 30.2 1.0
CD E:GLU243 3.1 25.6 1.0
CE1 E:HIS293 3.2 32.1 1.0
CD E:GLU217 3.2 14.6 1.0
CD2 E:HIS293 3.3 25.2 1.0
OD2 E:ASP190 3.6 12.4 1.0
CG E:GLU217 3.7 11.7 1.0
OE1 E:GLU243 3.9 27.5 1.0
NZ E:LYS159 3.9 11.2 1.0
CG E:ASP190 4.1 15.4 1.0
O E:HOH598 4.2 29.4 1.0
OD1 E:ASP190 4.2 12.1 1.0
CG E:GLU243 4.2 22.6 1.0
ND1 E:HIS293 4.3 29.5 1.0
OE1 E:GLU217 4.3 16.6 1.0
OE1 E:GLN264 4.3 16.8 1.0
CG E:HIS293 4.4 26.8 1.0
OE2 E:GLU218 4.4 24.4 1.0
O E:HOH518 4.4 23.2 1.0
CB E:GLU243 4.4 24.4 1.0
CG E:GLU218 4.5 21.0 1.0
CD E:GLU218 4.5 28.3 1.0
O E:HOH488 4.6 22.1 1.0
CE E:LYS159 4.8 14.6 1.0
ND2 E:ASN192 4.8 18.1 1.0
CD E:GLN264 4.9 17.7 1.0
NE2 E:GLN264 5.0 16.2 1.0

Magnesium binding site 6 out of 8 in 2gge

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Magnesium binding site 6 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg400

b:25.5
occ:1.00
 OE2 F:GLU243 1.9 28.9 1.0
OE2 F:GLU217 2.0 19.9 1.0
O F:HOH445 2.0 20.5 1.0
O F:HOH550 2.0 21.3 1.0
O F:HOH408 2.2 16.9 1.0
NE2 F:HIS293 2.4 28.0 1.0
CD F:GLU243 3.0 26.9 1.0
CD F:GLU217 3.1 20.3 1.0
CE1 F:HIS293 3.2 25.9 1.0
CD2 F:HIS293 3.4 26.7 1.0
CG F:GLU217 3.6 17.2 1.0
OD2 F:ASP190 3.6 21.4 1.0
OE1 F:GLU243 3.6 30.3 1.0
OD1 F:ASP190 3.8 21.8 1.0
CG F:ASP190 4.0 24.5 1.0
NZ F:LYS159 4.1 18.1 1.0
OE1 F:GLU217 4.2 20.4 1.0
CG F:GLU243 4.2 25.0 1.0
CB F:GLU243 4.3 24.9 1.0
ND1 F:HIS293 4.3 23.6 1.0
O F:HOH419 4.4 17.9 1.0
CG F:HIS293 4.4 26.6 1.0
OE1 F:GLN264 4.5 17.3 1.0
OE2 F:GLU218 4.5 30.6 1.0
O F:HOH482 4.6 27.9 1.0
ND2 F:ASN192 4.7 25.4 1.0
CD F:GLU218 4.7 26.3 1.0
CG F:GLU218 4.8 22.6 1.0
CE F:LYS159 4.8 20.8 1.0
CB F:GLU217 4.8 15.7 1.0

Magnesium binding site 7 out of 8 in 2gge

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Magnesium binding site 7 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg400

b:20.2
occ:1.00
 OE2 G:GLU217 2.0 18.2 1.0
OE2 G:GLU243 2.0 25.8 1.0
O G:HOH1805 2.1 18.4 1.0
O G:HOH2005 2.1 14.5 1.0
O G:HOH1998 2.2 20.4 1.0
NE2 G:HIS293 2.2 18.0 1.0
CE1 G:HIS293 3.0 18.6 1.0
CD G:GLU217 3.1 16.5 1.0
CD2 G:HIS293 3.2 19.7 1.0
CD G:GLU243 3.2 24.1 1.0
OD2 G:ASP190 3.7 12.5 1.0
CG G:GLU217 3.8 15.9 1.0
NZ G:LYS159 3.9 20.3 1.0
ND1 G:HIS293 4.1 19.6 1.0
OE1 G:GLU217 4.1 18.8 1.0
OE1 G:GLU243 4.1 26.3 1.0
CG G:GLU243 4.1 21.5 1.0
CB G:GLU243 4.2 21.6 1.0
O G:HOH1867 4.2 34.9 1.0
CG G:HIS293 4.2 20.1 1.0
OD1 G:ASP190 4.2 18.3 1.0
O G:HOH1845 4.2 22.7 1.0
OE1 G:GLN264 4.2 21.1 1.0
CG G:ASP190 4.3 16.0 1.0
OE2 G:GLU218 4.3 20.4 1.0
CD G:GLU218 4.5 21.8 1.0
O G:HOH1898 4.5 22.4 1.0
CG G:GLU218 4.7 19.3 1.0
CD G:GLN264 4.8 19.3 1.0
ND2 G:ASN192 4.8 17.3 1.0
OE1 G:GLU218 4.9 21.7 1.0
NE2 G:GLN264 4.9 19.9 1.0
CE G:LYS159 5.0 19.1 1.0

Magnesium binding site 8 out of 8 in 2gge

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Magnesium binding site 8 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A


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 Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg400

b:23.4
occ:1.00
 OE2 H:GLU243 1.9 24.2 1.0
O H:HOH402 2.0 19.7 1.0
O H:HOH626 2.1 21.2 1.0
OE2 H:GLU217 2.1 17.6 1.0
O H:HOH605 2.2 19.7 1.0
NE2 H:HIS293 2.3 23.6 1.0
CE1 H:HIS293 3.1 26.9 1.0
CD H:GLU217 3.2 16.3 1.0
CD H:GLU243 3.2 23.9 1.0
CD2 H:HIS293 3.3 23.3 1.0
CG H:GLU217 3.7 12.2 1.0
OD2 H:ASP190 3.7 15.6 1.0
OE2 H:GLU218 4.0 24.0 1.0
OE1 H:GLU243 4.0 23.9 1.0
NZ H:LYS159 4.1 15.5 1.0
OD1 H:ASP190 4.1 11.9 1.0
CG H:GLU243 4.2 19.8 1.0
ND1 H:HIS293 4.2 23.0 1.0
OE1 H:GLU217 4.2 14.7 1.0
CG H:ASP190 4.2 13.9 1.0
CB H:GLU243 4.3 21.6 1.0
O H:HOH620 4.3 37.2 1.0
OE1 H:GLN264 4.3 16.5 1.0
O H:HOH444 4.3 24.1 1.0
CG H:HIS293 4.3 22.3 1.0
CD H:GLU218 4.4 26.9 1.0
CG H:GLU218 4.6 20.4 1.0
O H:HOH500 4.9 22.4 1.0
CD H:GLN264 4.9 19.7 1.0
CB H:GLU217 5.0 16.5 1.0
CB H:GLU218 5.0 17.7 1.0
CE H:LYS159 5.0 11.2 1.0
ND2 H:ASN192 5.0 19.2 1.0

Reference:

V.N.Malashkevich, J.M.Sauder, K.D.Schwinn, S.Emtage, D.A.Thompson, M.E.Rutter, M.Dickey, C.Groshong, K.T.Bain, J.M.Adams, C.Reyes, I.Rooney, A.Powell, A.Boice, T.Gheyi, S.Ozyurt, S.Atwell, S.R.Wasserman, S.K.Burley, A.Sali, P.Babbitt, U.Pieper, J.A.Gerlt, S.C.Almo. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme From Bacillus Subtilis Complexed with Mg++ at 1.8 A To Be Published.
Page generated: Tue Aug 13 23:28:38 2024

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