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Magnesium in PDB 3n6h: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate, PDB code: 3n6h was solved by V.N.Malashkevich, Y.Patskovsky, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.397, 85.884, 112.424, 90.00, 96.03, 90.00
R / Rfree (%) 21.9 / 27.8

Other elements in 3n6h:

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate (pdb code 3n6h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate, PDB code: 3n6h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3n6h

Go back to Magnesium Binding Sites List in 3n6h
Magnesium binding site 1 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate


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 Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:28.9
occ:1.00
OD1 A:ASN290 2.0 28.5 1.0
OD1 A:ASP236 2.4 22.6 1.0
O A:HOH576 2.4 11.7 1.0
OE2 A:GLU261 2.4 34.2 1.0
O A:HOH588 2.6 25.3 1.0
O A:HOH547 2.8 11.6 1.0
CG A:ASN290 3.0 43.8 1.0
CD A:GLU261 3.0 22.6 1.0
CG A:ASP236 3.1 25.2 1.0
OE1 A:GLU261 3.3 33.8 1.0
ND2 A:ASN290 3.3 28.7 1.0
OD2 A:ASP236 3.4 22.8 1.0
OD2 A:ASP262 3.8 24.9 1.0
CG A:GLU261 4.2 34.4 1.0
CB A:ASP236 4.3 22.1 1.0
OD1 A:ASN238 4.3 26.7 1.0
CB A:ASN290 4.3 27.9 1.0
N A:ASN290 4.6 27.9 1.0
CD1 A:LEU312 4.6 24.2 1.0
OH A:TYR151 4.7 34.9 1.0
NZ A:LYS208 4.7 21.2 1.0
ND1 A:HIS340 4.8 21.4 1.0
CG A:ASP262 4.9 30.6 1.0
CB A:GLU261 5.0 23.2 1.0

Magnesium binding site 2 out of 4 in 3n6h

Go back to Magnesium Binding Sites List in 3n6h
Magnesium binding site 2 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate


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 Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:45.5
occ:1.00
O B:HOH458 2.1 30.2 1.0
OD1 B:ASN290 2.4 32.8 1.0
OE2 B:GLU261 2.4 29.0 1.0
OD1 B:ASP236 2.7 28.5 1.0
OD2 B:ASP236 3.1 28.5 1.0
CG B:ASP236 3.2 34.9 1.0
OD2 B:ASP262 3.4 25.2 1.0
CD B:GLU261 3.4 29.6 1.0
CG B:ASN290 3.5 34.8 1.0
CG B:GLU261 3.9 29.4 1.0
OD1 B:ASN238 4.0 32.3 1.0
ND2 B:ASN290 4.1 32.8 1.0
CG B:ASN238 4.2 39.6 1.0
ND2 B:ASN238 4.3 31.7 1.0
CG B:MSE291 4.3 16.1 1.0
CG B:ASP262 4.3 22.8 1.0
SE B:MSE291 4.3 42.5 1.0
OE1 B:GLU261 4.5 29.6 1.0
CB B:ASP262 4.5 25.8 1.0
NZ B:LYS208 4.5 27.1 1.0
CA B:ASN238 4.7 30.6 1.0
CB B:ASP236 4.7 28.4 1.0
CB B:ASN290 4.7 32.2 1.0
N B:ASN290 4.9 31.8 1.0

Magnesium binding site 3 out of 4 in 3n6h

Go back to Magnesium Binding Sites List in 3n6h
Magnesium binding site 3 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate


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 Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:40.7
occ:1.00
O C:HOH478 2.4 20.1 1.0
OE2 C:GLU261 2.6 53.7 1.0
OD1 C:ASN290 2.6 34.1 1.0
OD1 C:ASP236 2.9 30.1 1.0
OD2 C:ASP262 2.9 32.3 1.0
OD2 C:ASP236 3.0 29.2 1.0
CG C:ASP236 3.2 28.7 1.0
CD C:GLU261 3.5 35.3 1.0
CB C:ASP262 3.6 31.9 1.0
CG C:ASN290 3.6 36.6 1.0
CG C:ASP262 3.7 31.2 1.0
ND2 C:ASN238 3.8 29.3 1.0
CG C:GLU261 3.9 52.8 1.0
SE C:MSE291 4.0 41.6 1.0
ND2 C:ASN290 4.0 35.0 1.0
CG C:MSE291 4.2 22.6 1.0
CA C:ASN238 4.4 27.8 1.0
O C:GLU261 4.5 33.9 1.0
CG C:ASN238 4.5 33.9 1.0
CB C:ASP236 4.5 29.6 1.0
OE1 C:GLU261 4.6 53.9 1.0
N C:ASN290 4.6 32.5 1.0
C C:GLU261 4.7 33.3 1.0
CB C:GLU261 4.8 34.3 1.0
N C:ASN238 4.8 28.1 1.0
CA C:ASP262 4.8 32.0 1.0
N C:ASP262 4.9 32.5 1.0
CB C:ASN290 4.9 34.6 1.0
OD1 C:ASP262 4.9 31.8 1.0

Magnesium binding site 4 out of 4 in 3n6h

Go back to Magnesium Binding Sites List in 3n6h
Magnesium binding site 4 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate


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 Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:49.2
occ:1.00
OD1 D:ASP236 2.4 59.2 1.0
OD1 D:ASN290 2.4 47.0 1.0
CG D:ASN290 3.2 45.0 1.0
NZ D:LYS208 3.4 56.6 1.0
OE2 D:GLU261 3.5 59.4 1.0
OH D:TYR151 3.6 69.0 1.0
ND2 D:ASN290 3.6 47.4 1.0
CG D:ASP236 3.7 61.6 1.0
OE1 D:GLU261 3.7 61.3 1.0
ND1 D:HIS340 3.8 64.0 1.0
CD D:GLU261 3.9 53.2 1.0
CE1 D:HIS340 4.2 64.9 1.0
CB D:ASN290 4.4 46.5 1.0
OD2 D:ASP236 4.4 57.9 1.0
ND2 D:ASN238 4.4 53.9 1.0
CB D:ASP236 4.7 59.5 1.0
CE D:LYS208 4.8 63.4 1.0
CG D:HIS340 4.9 64.0 1.0
CZ D:TYR151 4.9 63.0 1.0
OD2 D:ASP367 4.9 60.8 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 Actinobacillus Succinogenes 130Z Complexed with Magnesium/Sulfate To Be Published.
Page generated: Mon Dec 14 08:27:45 2020

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