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Magnesium in PDB 3rcy: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035, PDB code: 3rcy was solved by V.N.Malashkevich, R.Toro, R.Seidel, S.Garrett, R.Foti, S.C.Almo, New Yorkstructural Genomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.978, 162.143, 141.954, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 18.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035 (pdb code 3rcy). 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- Like Protein From Roseovarius Sp. TM1035, PDB code: 3rcy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3rcy

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Magnesium binding site 1 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:19.3
occ:1.00
 OE1 A:GLU260 2.2 14.5 1.0
OE2 A:GLU234 2.2 17.1 1.0
O A:HOH800 2.2 17.3 1.0
O A:HOH578 2.3 25.6 1.0
O A:HOH1005 2.3 15.8 1.0
O A:HOH498 2.3 14.5 1.0
CD A:GLU260 3.2 15.0 1.0
CD A:GLU234 3.2 13.5 1.0
OE2 A:GLU260 3.5 14.4 1.0
NZ A:LYS165 3.8 11.8 1.0
OH A:TYR130 4.0 24.8 1.0
CG A:GLU234 4.0 16.4 1.0
OE1 A:GLU234 4.1 16.9 1.0
O A:HOH463 4.1 12.5 1.0
O A:HOH483 4.3 11.3 1.0
O A:HOH1982 4.3 47.1 1.0
CD2 A:HIS310 4.3 14.3 1.0
NE2 A:HIS310 4.4 14.5 1.0
O A:THR209 4.4 16.7 1.0
CE A:LYS165 4.5 13.0 1.0
OE1 A:GLU235 4.5 16.2 1.0
CG A:GLU260 4.5 13.8 1.0
NE2 A:HIS210 4.6 17.9 1.0
CD2 A:HIS210 4.7 17.2 1.0
O A:GLY208 4.9 16.2 1.0

Magnesium binding site 2 out of 8 in 3rcy

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Magnesium binding site 2 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:19.6
occ:1.00
 O B:HOH1923 2.1 28.9 1.0
OE2 B:GLU234 2.2 18.6 1.0
O B:HOH658 2.2 15.1 1.0
OE1 B:GLU260 2.2 16.5 1.0
O B:HOH508 2.3 14.9 1.0
O B:HOH735 2.4 17.5 1.0
CD B:GLU234 3.2 14.6 1.0
CD B:GLU260 3.2 14.0 1.0
OE2 B:GLU260 3.6 16.6 1.0
NZ B:LYS165 3.8 12.3 1.0
CG B:GLU234 3.9 17.6 1.0
OH B:TYR130 4.0 23.1 1.0
OE1 B:GLU234 4.1 17.9 1.0
O B:HOH2908 4.1 34.8 1.0
O B:HOH504 4.2 16.3 1.0
O B:THR209 4.2 17.6 1.0
O B:HOH466 4.4 7.5 1.0
CD2 B:HIS310 4.4 14.7 1.0
NE2 B:HIS310 4.5 14.9 1.0
NE2 B:HIS210 4.5 19.9 1.0
CE B:LYS165 4.5 14.5 1.0
CG B:GLU260 4.6 16.2 1.0
OE1 B:GLU235 4.6 19.4 1.0
CD2 B:HIS210 4.6 18.3 1.0
O B:GLY208 4.8 18.6 1.0

Magnesium binding site 3 out of 8 in 3rcy

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Magnesium binding site 3 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg500

b:18.0
occ:1.00
 OE1 C:GLU260 2.2 14.0 1.0
OE2 C:GLU234 2.2 16.5 1.0
O C:HOH999 2.3 16.6 1.0
O C:HOH842 2.3 14.5 1.0
O C:HOH474 2.3 15.2 1.0
O C:HOH687 2.6 25.7 1.0
CD C:GLU260 3.2 13.2 1.0
CD C:GLU234 3.2 15.1 1.0
OE2 C:GLU260 3.5 14.1 1.0
NZ C:LYS165 3.8 14.0 1.0
CG C:GLU234 3.9 15.1 1.0
OH C:TYR130 4.0 22.5 1.0
OE1 C:GLU234 4.1 15.4 1.0
O C:HOH524 4.1 12.1 1.0
O C:THR209 4.3 16.0 1.0
CD2 C:HIS310 4.3 13.6 1.0
O C:HOH434 4.3 10.4 1.0
NE2 C:HIS310 4.3 14.5 1.0
OE1 C:GLU235 4.5 15.1 1.0
CG C:GLU260 4.5 13.5 1.0
CE C:LYS165 4.5 13.7 1.0
NE2 C:HIS210 4.5 19.2 1.0
CD2 C:HIS210 4.6 18.8 1.0
O C:GLY208 4.9 15.9 1.0

Magnesium binding site 4 out of 8 in 3rcy

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Magnesium binding site 4 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg500

b:19.9
occ:1.00
 OE1 D:GLU260 2.2 17.4 1.0
OE2 D:GLU234 2.2 17.2 1.0
O D:HOH1930 2.3 21.3 1.0
O D:HOH727 2.3 14.8 1.0
O D:HOH475 2.4 18.3 1.0
O D:HOH1939 2.8 30.8 1.0
CD D:GLU234 3.2 15.4 1.0
CD D:GLU260 3.2 14.3 1.0
OE2 D:GLU260 3.5 17.4 1.0
NZ D:LYS165 3.8 14.2 1.0
CG D:GLU234 3.9 16.6 1.0
OH D:TYR130 4.0 21.8 1.0
OE1 D:GLU234 4.0 16.7 1.0
O D:HOH460 4.2 13.6 1.0
O D:HOH451 4.2 12.0 1.0
CD2 D:HIS310 4.3 14.5 1.0
O D:THR209 4.3 18.0 1.0
NE2 D:HIS310 4.3 14.7 1.0
OE1 D:GLU235 4.5 17.0 1.0
CG D:GLU260 4.5 16.9 1.0
NE2 D:HIS210 4.6 20.5 1.0
CE D:LYS165 4.6 12.9 1.0
CD2 D:HIS210 4.7 19.9 1.0
CE1 D:HIS210 5.0 20.8 1.0

Magnesium binding site 5 out of 8 in 3rcy

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Magnesium binding site 5 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg500

b:23.4
occ:1.00
 OE2 E:GLU234 2.1 17.9 1.0
OE1 E:GLU260 2.1 17.3 1.0
O E:HOH458 2.3 19.9 1.0
O E:HOH962 2.3 18.2 1.0
O E:HOH2792 2.4 33.3 1.0
O E:HOH1083 2.5 24.4 1.0
CD E:GLU234 3.1 14.6 1.0
CD E:GLU260 3.2 16.4 1.0
OE2 E:GLU260 3.5 17.5 1.0
NZ E:LYS165 3.8 13.6 1.0
CG E:GLU234 3.9 17.0 1.0
OH E:TYR130 4.0 24.4 1.0
OE1 E:GLU234 4.0 17.1 1.0
O E:HOH2694 4.0 36.3 1.0
O E:HOH512 4.1 21.2 1.0
O E:HOH465 4.2 14.9 1.0
CD2 E:HIS310 4.3 14.6 1.0
NE2 E:HIS310 4.3 15.1 1.0
O E:THR209 4.4 16.7 1.0
CG E:GLU260 4.5 16.9 1.0
OE1 E:GLU235 4.5 19.9 1.0
CE E:LYS165 4.6 14.5 1.0
NE2 E:HIS210 4.7 19.3 1.0
CD2 E:HIS210 4.8 19.1 1.0
O E:GLY208 4.9 17.8 1.0

Magnesium binding site 6 out of 8 in 3rcy

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Magnesium binding site 6 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg500

b:21.1
occ:1.00
 OE1 F:GLU260 2.1 20.5 1.0
O F:HOH1039 2.1 16.0 1.0
OE2 F:GLU234 2.2 20.9 1.0
O F:HOH690 2.3 15.0 1.0
O F:HOH1315 2.4 20.1 1.0
O F:HOH1031 2.4 21.9 1.0
CD F:GLU260 3.1 17.7 1.0
CD F:GLU234 3.2 15.9 1.0
OE2 F:GLU260 3.4 20.8 1.0
NZ F:LYS165 3.8 16.5 1.0
CG F:GLU234 3.9 20.3 1.0
OH F:TYR130 4.0 27.4 1.0
OE1 F:GLU234 4.1 20.2 1.0
O F:HOH2000 4.3 36.8 1.0
O F:HOH451 4.3 16.7 1.0
O F:HOH555 4.3 13.0 1.0
O F:THR209 4.3 19.2 1.0
OE1 F:GLU235 4.4 18.4 1.0
CD2 F:HIS310 4.4 18.1 1.0
CG F:GLU260 4.4 20.0 1.0
NE2 F:HIS310 4.5 19.1 1.0
NE2 F:HIS210 4.6 20.1 1.0
CE F:LYS165 4.7 16.4 1.0
CD2 F:HIS210 4.7 19.7 1.0
O F:HOH1565 4.8 40.5 1.0
O F:GLY208 4.9 20.0 1.0

Magnesium binding site 7 out of 8 in 3rcy

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Magnesium binding site 7 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg500

b:21.2
occ:1.00
 OE1 G:GLU260 2.1 20.4 1.0
OE2 G:GLU234 2.2 20.3 1.0
O G:HOH468 2.2 17.7 1.0
O G:HOH1053 2.3 13.9 1.0
O G:HOH975 2.3 26.8 1.0
O G:HOH1061 2.5 21.1 1.0
CD G:GLU260 3.1 17.6 1.0
CD G:GLU234 3.2 17.5 1.0
OE2 G:GLU260 3.5 20.3 1.0
CG G:GLU234 3.9 19.3 1.0
NZ G:LYS165 3.9 16.2 1.0
OH G:TYR130 4.0 28.5 1.0
O G:HOH532 4.0 20.1 1.0
OE1 G:GLU234 4.1 19.8 1.0
O G:HOH469 4.2 9.4 1.0
O G:THR209 4.4 18.2 1.0
CD2 G:HIS310 4.4 16.2 1.0
O G:HOH1288 4.4 34.6 1.0
OE1 G:GLU235 4.4 17.3 1.0
CG G:GLU260 4.5 20.2 1.0
NE2 G:HIS310 4.5 16.6 1.0
NE2 G:HIS210 4.5 20.1 1.0
CE G:LYS165 4.6 15.9 1.0
CD2 G:HIS210 4.6 19.6 1.0
O G:GLY208 4.9 19.8 1.0

Magnesium binding site 8 out of 8 in 3rcy

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Magnesium binding site 8 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme- Like Protein From Roseovarius Sp. TM1035


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- Like Protein From Roseovarius Sp. TM1035 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg500

b:25.4
occ:1.00
 OE2 H:GLU234 2.2 24.4 1.0
OE1 H:GLU260 2.2 20.1 1.0
O H:HOH595 2.2 15.1 1.0
O H:HOH506 2.3 16.2 1.0
O H:HOH529 2.3 20.0 1.0
O H:HOH459 2.6 21.6 1.0
CD H:GLU234 3.2 19.2 1.0
CD H:GLU260 3.2 19.9 1.0
OE2 H:GLU260 3.5 20.6 1.0
NZ H:LYS165 3.7 18.3 1.0
OH H:TYR130 3.9 28.1 1.0
CG H:GLU234 3.9 23.5 1.0
OE1 H:GLU234 4.1 23.8 1.0
O H:HOH914 4.2 14.3 1.0
O H:HOH2660 4.3 34.6 1.0
O H:HOH443 4.3 12.1 1.0
O H:THR209 4.3 21.3 1.0
CD2 H:HIS310 4.3 18.7 1.0
NE2 H:HIS310 4.4 18.8 1.0
OE1 H:GLU235 4.5 20.3 1.0
CG H:GLU260 4.6 20.0 1.0
NE2 H:HIS210 4.6 24.4 1.0
CE H:LYS165 4.6 20.5 1.0
CD2 H:HIS210 4.7 23.1 1.0
O H:GLY208 4.8 21.7 1.0

Reference:

V.N.Malashkevich, R.Toro, R.Seidel, S.Garrett, R.Foti, S.C.Almo. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme-Like Protein From Roseovarius Sp. TM1035 To Be Published.
Page generated: Mon Aug 11 02:40:47 2025

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