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Magnesium in PDB 3n4f: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10, PDB code: 3n4f was solved by V.N.Malashkevich, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.88
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.387, 66.100, 151.536, 90.00, 94.33, 90.00
R / Rfree (%) 18.5 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 (pdb code 3n4f). 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 Protein From Geobacillus Sp. Y412MC10, PDB code: 3n4f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3n4f

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Magnesium binding site 1 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:8.3
occ:1.00
 OD1 A:ASP261 2.0 7.4 1.0
O A:HOH399 2.1 4.0 1.0
OE2 A:GLU238 2.1 8.8 1.0
OE2 A:GLU234 2.1 12.2 1.0
O A:HOH397 2.1 4.5 1.0
O A:HOH395 2.1 2.5 1.0
CG A:ASP261 3.0 11.2 1.0
CD A:GLU234 3.1 7.8 1.0
CD A:GLU238 3.1 9.5 1.0
OD2 A:ASP261 3.4 8.6 1.0
CG A:GLU234 3.4 12.3 1.0
OE1 A:GLU238 3.5 9.1 1.0
O A:HOH419 3.9 9.0 1.0
N A:GLY262 4.1 8.6 1.0
OD1 A:ASN210 4.2 9.3 1.0
OE1 A:GLU234 4.2 13.0 1.0
ND1 A:HIS237 4.3 8.4 1.0
N A:GLU238 4.3 8.5 1.0
CB A:ASP261 4.3 7.2 1.0
O A:GLU263 4.4 12.5 1.0
ND2 A:ASN210 4.4 9.1 1.0
CB A:GLU234 4.4 8.2 1.0
CG A:GLU238 4.5 9.2 1.0
CG A:ASN210 4.7 14.2 1.0
CA A:HIS237 4.8 8.4 1.0
CE1 A:HIS237 4.8 10.1 1.0
CB A:GLU238 4.8 9.0 1.0
CA A:ASP261 4.8 6.9 1.0
CA A:GLY262 4.9 9.9 1.0
N A:GLU263 4.9 11.1 1.0
CA A:GLU234 5.0 7.4 1.0
C A:ASP261 5.0 8.1 1.0

Magnesium binding site 2 out of 8 in 3n4f

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Magnesium binding site 2 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:10.7
occ:1.00
 OE2 A:GLU233 2.0 11.4 1.0
O A:HOH402 2.0 11.7 1.0
O A:HOH405 2.1 6.8 1.0
O A:HOH404 2.1 6.5 1.0
OD2 A:ASP207 2.1 7.2 1.0
OE2 A:GLU263 2.2 17.1 1.0
CD A:GLU233 3.1 8.7 1.0
CG A:ASP207 3.1 13.2 1.0
CD A:GLU263 3.2 15.2 1.0
OD1 A:ASP207 3.5 7.1 1.0
OE1 A:GLU263 3.5 17.3 1.0
CG A:GLU233 3.8 10.5 1.0
NZ A:LYS170 3.9 13.1 1.0
OE1 A:GLU233 4.0 10.9 1.0
NZ A:LYS168 4.1 15.4 1.0
ND2 A:ASN209 4.2 9.0 1.0
O A:HOH523 4.2 11.0 1.0
CB A:ASP207 4.4 7.5 1.0
OE1 A:GLU234 4.4 13.0 1.0
O A:HOH524 4.4 5.8 1.0
CG A:GLU263 4.4 17.4 1.0
CD2 A:HIS311 4.8 12.1 1.0
OD1 A:ASN209 4.8 8.6 1.0
CG A:ASN209 4.9 9.1 1.0

Magnesium binding site 3 out of 8 in 3n4f

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Magnesium binding site 3 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:13.3
occ:1.00
 OD1 B:ASP261 2.0 11.8 1.0
O B:HOH393 2.1 6.7 1.0
OE2 B:GLU238 2.1 9.4 1.0
O B:HOH395 2.2 6.3 1.0
OE2 B:GLU234 2.2 14.3 1.0
O B:HOH394 2.3 6.4 1.0
CG B:ASP261 3.0 12.3 1.0
CD B:GLU238 3.1 12.5 1.0
CD B:GLU234 3.2 13.4 1.0
OD2 B:ASP261 3.4 12.3 1.0
OE1 B:GLU238 3.5 9.8 1.0
CG B:GLU234 3.5 13.5 1.0
O B:HOH932 3.8 19.1 1.0
N B:GLY262 4.1 12.3 1.0
OD1 B:ASN210 4.2 10.1 1.0
O B:GLU263 4.3 12.4 1.0
ND1 B:HIS237 4.3 12.4 1.0
OE1 B:GLU234 4.3 13.9 1.0
N B:GLU238 4.3 12.0 1.0
ND2 B:ASN210 4.3 9.1 1.0
CB B:ASP261 4.4 11.9 1.0
CG B:GLU238 4.5 9.8 1.0
CB B:GLU234 4.5 12.4 1.0
CG B:ASN210 4.7 11.8 1.0
CB B:GLU238 4.8 12.2 1.0
CA B:HIS237 4.8 11.8 1.0
CA B:ASP261 4.8 11.8 1.0
CA B:GLY262 4.8 12.2 1.0
CE1 B:HIS237 4.8 12.6 1.0
N B:GLU263 4.9 13.0 1.0
C B:ASP261 5.0 12.3 1.0

Magnesium binding site 4 out of 8 in 3n4f

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Magnesium binding site 4 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:15.3
occ:1.00
 OE2 B:GLU233 2.0 15.2 1.0
OE2 B:GLU263 2.1 20.0 1.0
O B:HOH1403 2.1 10.6 1.0
O B:HOH1416 2.2 7.5 1.0
OD2 B:ASP207 2.2 12.3 1.0
O B:HOH496 2.3 15.2 1.0
CD B:GLU263 3.0 14.3 1.0
CD B:GLU233 3.1 11.1 1.0
CG B:ASP207 3.1 15.8 1.0
OE1 B:GLU263 3.4 19.8 1.0
OD1 B:ASP207 3.4 11.8 1.0
CG B:GLU233 3.8 15.6 1.0
NZ B:LYS168 3.9 17.7 1.0
O B:HOH1573 4.0 31.1 1.0
NZ B:LYS170 4.0 16.1 1.0
OE1 B:GLU233 4.0 15.8 1.0
O B:HOH1095 4.2 16.0 1.0
O B:HOH474 4.2 6.1 1.0
OE1 B:GLU234 4.3 13.9 1.0
ND2 B:ASN209 4.3 10.6 1.0
CG B:GLU263 4.4 20.1 1.0
CB B:ASP207 4.4 12.4 1.0
CD2 B:HIS311 4.6 12.3 1.0
O B:HOH1134 4.8 28.0 1.0
CE B:LYS168 4.9 13.8 1.0
CG B:ASN209 4.9 12.1 1.0
OD1 B:ASN209 5.0 10.7 1.0
CD B:GLU234 5.0 13.4 1.0

Magnesium binding site 5 out of 8 in 3n4f

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Magnesium binding site 5 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:9.7
occ:1.00
 OE2 C:GLU238 2.1 9.7 1.0
OD1 C:ASP261 2.1 6.4 1.0
O C:HOH396 2.1 2.0 1.0
O C:HOH393 2.2 2.0 1.0
O C:HOH394 2.2 2.0 1.0
OE2 C:GLU234 2.2 10.4 1.0
CD C:GLU238 3.1 7.4 1.0
CG C:ASP261 3.1 8.4 1.0
CD C:GLU234 3.2 9.6 1.0
OE1 C:GLU238 3.4 8.7 1.0
OD2 C:ASP261 3.5 7.1 1.0
CG C:GLU234 3.6 9.4 1.0
O C:HOH713 3.8 12.1 1.0
ND1 C:HIS237 4.2 8.3 1.0
N C:GLY262 4.2 5.7 1.0
O C:GLU263 4.2 7.4 1.0
OD1 C:ASN210 4.2 6.6 1.0
N C:GLU238 4.3 7.3 1.0
OE1 C:GLU234 4.3 9.6 1.0
ND2 C:ASN210 4.4 7.3 1.0
CB C:ASP261 4.4 6.0 1.0
CG C:GLU238 4.4 8.8 1.0
CB C:GLU234 4.6 8.0 1.0
CE1 C:HIS237 4.7 8.4 1.0
CB C:GLU238 4.7 7.0 1.0
CG C:ASN210 4.8 6.4 1.0
CA C:HIS237 4.8 8.0 1.0
CA C:ASP261 4.8 5.5 1.0
CA C:GLY262 4.9 7.6 1.0
N C:GLU263 5.0 9.2 1.0

Magnesium binding site 6 out of 8 in 3n4f

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Magnesium binding site 6 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:8.4
occ:1.00
 OE2 C:GLU233 1.9 8.2 1.0
O C:HOH398 2.1 2.5 1.0
OE2 C:GLU263 2.1 12.7 1.0
O C:HOH399 2.1 5.4 1.0
O C:HOH400 2.2 9.2 1.0
OD2 C:ASP207 2.2 8.9 1.0
CD C:GLU233 3.0 7.6 1.0
CD C:GLU263 3.1 12.2 1.0
CG C:ASP207 3.2 11.1 1.0
OE1 C:GLU263 3.5 12.8 1.0
OD1 C:ASP207 3.5 7.5 1.0
CG C:GLU233 3.7 7.4 1.0
OE1 C:GLU233 4.0 7.3 1.0
NZ C:LYS168 4.0 12.4 1.0
NZ C:LYS170 4.0 16.3 1.0
O C:HOH564 4.1 12.4 1.0
O C:HOH535 4.3 3.5 1.0
ND2 C:ASN209 4.3 9.5 1.0
OE1 C:GLU234 4.4 9.6 1.0
CG C:GLU263 4.4 12.7 1.0
CB C:ASP207 4.4 7.2 1.0
CD2 C:HIS311 4.5 8.9 1.0
CG C:ASN209 5.0 8.3 1.0
CE C:LYS168 5.0 20.4 1.0
OD1 C:ASN209 5.0 9.7 1.0

Magnesium binding site 7 out of 8 in 3n4f

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Magnesium binding site 7 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:13.4
occ:1.00
 O D:HOH393 2.1 5.0 1.0
OE2 D:GLU238 2.1 11.0 1.0
OD1 D:ASP261 2.1 13.3 1.0
O D:HOH395 2.1 5.9 1.0
OE2 D:GLU234 2.2 13.7 1.0
O D:HOH394 2.3 5.8 1.0
CG D:ASP261 3.1 6.9 1.0
CD D:GLU238 3.1 9.9 1.0
CD D:GLU234 3.2 15.4 1.0
OD2 D:ASP261 3.4 14.0 1.0
OE1 D:GLU238 3.5 11.1 1.0
CG D:GLU234 3.6 14.1 1.0
O D:HOH397 3.7 19.5 1.0
OD1 D:ASN210 4.2 13.2 1.0
N D:GLY262 4.2 12.1 1.0
ND2 D:ASN210 4.2 12.8 1.0
ND1 D:HIS237 4.3 14.3 1.0
O D:GLU263 4.3 18.1 1.0
N D:GLU238 4.3 9.1 1.0
OE1 D:GLU234 4.3 14.3 1.0
CB D:ASP261 4.4 13.0 1.0
CG D:GLU238 4.5 11.2 1.0
CB D:GLU234 4.5 14.4 1.0
CG D:ASN210 4.7 14.4 1.0
CA D:HIS237 4.7 12.6 1.0
CB D:GLU238 4.8 9.9 1.0
CE1 D:HIS237 4.8 13.6 1.0
N D:GLU263 4.9 15.6 1.0
CA D:ASP261 4.9 12.3 1.0
O D:PHE236 4.9 14.0 1.0
CA D:GLY262 5.0 13.8 1.0
CA D:GLU234 5.0 13.8 1.0

Magnesium binding site 8 out of 8 in 3n4f

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Magnesium binding site 8 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10


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 Protein From Geobacillus Sp. Y412MC10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:14.4
occ:1.00
 O D:HOH973 1.9 18.6 1.0
O D:HOH437 2.0 9.1 1.0
OE2 D:GLU263 2.0 19.6 1.0
O D:HOH405 2.1 8.2 1.0
OE2 D:GLU233 2.1 18.0 1.0
OD2 D:ASP207 2.1 13.3 1.0
CD D:GLU263 2.9 18.4 1.0
CD D:GLU233 3.1 16.0 1.0
CG D:ASP207 3.2 18.9 1.0
OE1 D:GLU263 3.2 19.5 1.0
OD1 D:ASP207 3.6 12.7 1.0
CG D:GLU233 3.8 17.2 1.0
NZ D:LYS170 4.0 15.8 1.0
O D:HOH813 4.1 26.5 1.0
OE1 D:GLU233 4.1 18.0 1.0
OE1 D:GLU234 4.1 14.3 1.0
CG D:GLU263 4.2 19.1 1.0
ND2 D:ASN209 4.2 13.9 1.0
O D:HOH968 4.2 11.8 1.0
NZ D:LYS168 4.3 20.9 1.0
CB D:ASP207 4.4 12.9 1.0
CD2 D:HIS311 4.6 17.3 1.0
CD D:GLU234 4.9 15.4 1.0
CG D:ASN209 4.9 7.8 1.0
OD1 D:ASN209 4.9 14.4 1.0
CG D:GLU234 4.9 14.1 1.0

Reference:

V.N.Malashkevich, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Geobacillus Sp. Y412MC10 To Be Published.
Page generated: Mon Aug 11 00:47:57 2025

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