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Magnesium in PDB 3u4f: Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens

Protein crystallography data

The structure of Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens, PDB code: 3u4f was solved by S.Eswaramoorthy, D.Kumaran, S.Chamala, B.Evans, R.Foti, A.Gizzi, B.Hillerich, A.Kar, J.Lafleur, R.Seidel, G.Villigas, W.Zencheck, S.C.Almo, S.Swaminathan, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.63 / 1.90
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 125.871, 125.871, 98.017, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens (pdb code 3u4f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens, PDB code: 3u4f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3u4f

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Magnesium binding site 1 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg371

b:9.5
occ:1.00
 O A:HOH373 2.0 9.9 1.0
OE1 A:GLU235 2.0 6.9 1.0
OE2 A:GLU209 2.1 7.4 1.0
OD2 A:ASP183 2.1 9.8 1.0
N3 A:GAI372 2.2 7.2 1.0
N2 A:GAI372 2.2 7.8 1.0
C A:GAI372 2.6 9.6 1.0
CD A:GLU235 2.9 11.9 1.0
CD A:GLU209 3.0 9.7 1.0
CG A:ASP183 3.2 10.5 1.0
OE2 A:GLU235 3.3 11.0 1.0
OD1 A:ASP183 3.5 11.4 1.0
CG A:GLU209 3.7 6.9 1.0
O A:HOH484 3.8 19.3 1.0
N1 A:GAI372 3.9 7.0 1.0
O A:HOH388 3.9 11.0 1.0
OE1 A:GLU209 3.9 8.1 1.0
NZ A:LYS145 4.1 10.3 1.0
OD1 A:ASN185 4.1 11.8 1.0
CD2 A:HIS285 4.2 9.0 1.0
CG A:GLU235 4.3 9.1 1.0
NH1 A:ARG147 4.3 6.8 1.0
OE1 A:GLU210 4.5 10.6 1.0
CB A:ASP183 4.5 8.3 1.0
CB A:GLU209 4.8 5.8 1.0
CG A:ASN185 4.9 9.3 1.0
CB A:GLU235 4.9 8.0 1.0
NE2 A:HIS285 4.9 9.2 1.0
CE A:LYS145 5.0 8.8 1.0

Magnesium binding site 2 out of 9 in 3u4f

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Magnesium binding site 2 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg374

b:14.6
occ:1.00
 O A:SER224 2.1 11.2 1.0
O A:LEU227 2.1 12.8 1.0
O A:HOH378 2.1 13.2 1.0
O A:HOH376 2.1 12.0 1.0
O A:HOH375 2.2 13.4 1.0
O A:HOH377 2.2 11.0 1.0
C A:SER224 3.2 11.5 1.0
C A:LEU227 3.3 12.2 1.0
CA A:SER224 3.9 12.2 1.0
OD2 A:ASP253 4.1 7.8 1.0
N A:LEU227 4.1 13.1 1.0
CA A:LEU227 4.2 12.6 1.0
OD1 A:ASP253 4.2 9.1 1.0
N A:ASP228 4.2 13.3 1.0
O A:ILE229 4.3 10.5 1.0
N A:GLU225 4.3 12.6 1.0
CA A:ASP228 4.3 14.0 1.0
CB A:SER224 4.5 12.4 1.0
CA A:GLU225 4.5 14.6 1.0
CG A:ASP253 4.5 8.0 1.0
C A:GLU225 4.6 14.7 1.0
C A:ASP228 4.6 13.4 1.0
CB A:LEU227 4.6 12.2 1.0
O A:ASP228 4.6 14.1 1.0
O A:GLU225 4.7 15.5 1.0
O A:VAL223 5.0 10.2 1.0

Magnesium binding site 3 out of 9 in 3u4f

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Magnesium binding site 3 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg371

b:12.1
occ:1.00
 OE2 B:GLU209 2.0 11.9 1.0
OE1 B:GLU235 2.0 8.3 1.0
O B:HOH373 2.0 7.1 1.0
OD2 B:ASP183 2.0 7.6 1.0
N2 B:GAI372 2.1 9.6 1.0
N3 B:GAI372 2.3 13.2 1.0
C B:GAI372 2.6 12.6 1.0
CD B:GLU235 2.9 12.7 1.0
CD B:GLU209 3.0 11.5 1.0
CG B:ASP183 3.1 9.4 1.0
OE2 B:GLU235 3.2 12.7 1.0
OD1 B:ASP183 3.5 9.2 1.0
CG B:GLU209 3.7 11.5 1.0
O B:HOH420 3.7 16.2 1.0
O B:HOH409 3.9 14.4 1.0
OE1 B:GLU209 3.9 12.2 1.0
N1 B:GAI372 3.9 9.5 1.0
OD1 B:ASN185 4.0 11.9 1.0
NZ B:LYS145 4.1 7.7 1.0
CD2 B:HIS285 4.2 8.2 1.0
NH1 B:ARG147 4.3 11.3 1.0
CG B:GLU235 4.3 10.1 1.0
CB B:ASP183 4.4 10.4 1.0
OE1 B:GLU210 4.6 12.3 1.0
CB B:GLU209 4.8 10.8 1.0
CG B:ASN185 4.9 11.2 1.0
NE2 B:HIS285 4.9 9.5 1.0
CE B:LYS145 4.9 7.6 1.0
CB B:GLU235 4.9 9.1 1.0

Magnesium binding site 4 out of 9 in 3u4f

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Magnesium binding site 4 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg374

b:15.3
occ:1.00
 O B:SER224 2.0 16.4 1.0
O B:HOH375 2.0 12.6 1.0
O B:HOH377 2.0 16.9 1.0
O B:HOH378 2.1 12.5 1.0
O B:LEU227 2.1 19.1 1.0
O B:HOH376 2.2 12.8 1.0
C B:SER224 3.1 17.1 1.0
C B:LEU227 3.3 18.7 1.0
CA B:SER224 3.9 17.2 1.0
OD2 B:ASP253 4.0 12.8 1.0
N B:LEU227 4.1 18.4 1.0
OD1 B:ASP253 4.1 15.7 1.0
CA B:LEU227 4.2 18.7 1.0
N B:GLU225 4.2 18.4 1.0
N B:ASP228 4.3 19.2 1.0
CA B:ASP228 4.4 18.9 1.0
O B:ILE229 4.4 15.0 1.0
CA B:GLU225 4.5 19.6 1.0
CG B:ASP253 4.5 12.4 1.0
CB B:SER224 4.5 17.1 1.0
C B:GLU225 4.6 20.2 1.0
CB B:LEU227 4.6 18.3 1.0
C B:ASP228 4.7 18.1 1.0
O B:GLU225 4.8 20.8 1.0
O B:ASP228 4.8 18.0 1.0
O B:VAL223 5.0 15.9 1.0

Magnesium binding site 5 out of 9 in 3u4f

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Magnesium binding site 5 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg371

b:12.1
occ:1.00
 O C:HOH373 2.0 9.2 1.0
OE1 C:GLU235 2.0 9.1 1.0
OE2 C:GLU209 2.0 11.7 1.0
OD2 C:ASP183 2.0 9.7 1.0
N2 C:GAI372 2.2 10.7 1.0
N3 C:GAI372 2.3 11.5 1.0
C C:GAI372 2.7 12.8 1.0
CD C:GLU235 3.0 13.5 1.0
CD C:GLU209 3.0 11.3 1.0
CG C:ASP183 3.1 11.5 1.0
OE2 C:GLU235 3.3 12.6 1.0
OD1 C:ASP183 3.5 11.4 1.0
CG C:GLU209 3.7 9.5 1.0
O C:HOH410 3.9 12.5 1.0
O C:HOH412 3.9 16.3 1.0
OE1 C:GLU209 3.9 12.5 1.0
N1 C:GAI372 4.0 11.1 1.0
NZ C:LYS145 4.1 12.0 1.0
OD1 C:ASN185 4.1 14.6 1.0
CD2 C:HIS285 4.2 11.4 1.0
NH1 C:ARG147 4.2 8.2 1.0
CG C:GLU235 4.3 10.0 1.0
CB C:ASP183 4.4 9.7 1.0
OE1 C:GLU210 4.5 12.4 1.0
CB C:GLU209 4.8 7.2 1.0
NE2 C:HIS285 4.9 11.7 1.0
CG C:ASN185 5.0 9.9 1.0
CB C:GLU235 5.0 8.0 1.0
CE C:LYS145 5.0 10.6 1.0

Magnesium binding site 6 out of 9 in 3u4f

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Magnesium binding site 6 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg374

b:14.3
occ:1.00
 O C:LEU227 2.0 14.7 1.0
O C:HOH375 2.0 12.1 1.0
O C:SER224 2.0 11.4 1.0
O C:HOH376 2.1 8.3 1.0
O C:HOH378 2.2 12.2 1.0
O C:HOH377 2.2 10.9 1.0
C C:SER224 3.2 11.7 1.0
C C:LEU227 3.2 14.2 1.0
CA C:SER224 3.9 11.3 1.0
N C:LEU227 4.0 13.8 1.0
CA C:LEU227 4.1 14.1 1.0
OD2 C:ASP253 4.1 12.3 1.0
N C:ASP228 4.2 15.2 1.0
N C:GLU225 4.2 12.5 1.0
OD1 C:ASP253 4.3 10.2 1.0
CA C:ASP228 4.3 16.0 1.0
O C:ILE229 4.4 9.6 1.0
CB C:SER224 4.4 11.2 1.0
CA C:GLU225 4.5 14.8 1.0
C C:GLU225 4.6 15.0 1.0
CG C:ASP253 4.6 10.8 1.0
C C:ASP228 4.6 15.0 1.0
CB C:LEU227 4.6 13.3 1.0
O C:ASP228 4.7 14.6 1.0
O C:GLU225 4.7 14.8 1.0
O C:VAL223 5.0 9.4 1.0

Magnesium binding site 7 out of 9 in 3u4f

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Magnesium binding site 7 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg371

b:11.4
occ:1.00
 OE2 D:GLU209 1.9 12.2 1.0
OE1 D:GLU235 2.1 7.6 1.0
O D:HOH373 2.1 9.0 1.0
OD2 D:ASP183 2.1 8.4 1.0
N2 D:GAI372 2.1 8.1 1.0
N3 D:GAI372 2.3 9.4 1.0
C D:GAI372 2.6 10.6 1.0
CD D:GLU209 2.9 11.8 1.0
CD D:GLU235 3.0 11.6 1.0
CG D:ASP183 3.1 10.5 1.0
OE2 D:GLU235 3.3 10.4 1.0
OD1 D:ASP183 3.5 6.5 1.0
CG D:GLU209 3.6 6.9 1.0
O D:HOH404 3.8 9.7 1.0
O D:HOH451 3.8 16.1 1.0
N1 D:GAI372 3.8 9.5 1.0
OE1 D:GLU209 3.9 11.2 1.0
NZ D:LYS145 4.1 10.2 1.0
OD1 D:ASN185 4.1 10.6 1.0
CD2 D:HIS285 4.2 11.0 1.0
NH1 D:ARG147 4.3 6.6 1.0
CG D:GLU235 4.3 9.0 1.0
CB D:ASP183 4.4 8.9 1.0
OE1 D:GLU210 4.5 10.3 1.0
CB D:GLU209 4.8 7.0 1.0
NE2 D:HIS285 4.9 10.2 1.0
CE D:LYS145 4.9 10.9 1.0
CG D:ASN185 4.9 9.6 1.0
CB D:GLU235 5.0 8.1 1.0

Magnesium binding site 8 out of 9 in 3u4f

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Magnesium binding site 8 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


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 Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg374

b:11.7
occ:1.00
 O D:LEU227 2.0 13.0 1.0
O D:HOH375 2.0 11.2 1.0
O D:SER224 2.1 13.2 1.0
O D:HOH377 2.1 10.4 1.0
O D:HOH376 2.2 12.0 1.0
O D:HOH378 2.2 14.3 1.0
C D:SER224 3.2 13.3 1.0
C D:LEU227 3.2 12.9 1.0
CA D:SER224 3.9 13.2 1.0
OD2 D:ASP253 4.1 11.1 1.0
N D:LEU227 4.1 11.7 1.0
CA D:LEU227 4.2 12.8 1.0
N D:ASP228 4.2 14.0 1.0
OD1 D:ASP253 4.2 12.7 1.0
O D:HOH432 4.2 21.6 1.0
N D:GLU225 4.2 14.0 1.0
CA D:ASP228 4.3 14.5 1.0
O D:ILE229 4.4 11.6 1.0
CA D:GLU225 4.5 14.8 1.0
C D:GLU225 4.5 14.1 1.0
O D:HOH504 4.5 20.4 1.0
CB D:SER224 4.5 12.3 1.0
CG D:ASP253 4.6 11.4 1.0
O D:GLU225 4.6 14.1 1.0
C D:ASP228 4.7 14.2 1.0
CB D:LEU227 4.7 11.5 1.0
O D:ASP228 4.8 13.8 1.0
N D:ALA226 5.0 13.2 1.0

Magnesium binding site 9 out of 9 in 3u4f

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Magnesium binding site 9 out of 9 in the Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg379

b:25.1
occ:1.00
 O D:HOH380 2.1 22.9 1.0
O D:HOH384 2.1 18.8 1.0
O D:HOH385 2.1 21.7 1.0
O D:HOH381 2.2 21.1 1.0
O D:HOH382 2.2 23.8 1.0
O D:HOH383 2.3 26.5 1.0
O D:GLY98 3.9 16.5 1.0
OE1 D:GLU103 4.2 17.2 1.0
OE2 D:GLU103 4.3 23.9 1.0
O D:GLU343 4.6 15.0 1.0
CD D:GLU103 4.7 18.8 1.0
CB D:GLU343 4.8 18.4 1.0

Reference:

S.Eswaramoorthy, D.Kumaran, S.C.Almo, S.Swaminathan. Crystal Structure of A Mandelate Racemase (Muconate Lactonizing Enzyme Family Protein) From Roseovarius Nubinhibens To Be Published 2011.
Page generated: Thu Aug 15 12:20:35 2024

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