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Magnesium in PDB 7s8w: Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine

Enzymatic activity of Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine

All present enzymatic activity of Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine:
4.2.1.113;

Protein crystallography data

The structure of Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine, PDB code: 7s8w was solved by D.P.Truong, S.Rousseau, J.C.Sacchettini, M.E.Glasner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.80 / 2.90
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 213.742, 213.742, 253.077, 90, 90, 120
R / Rfree (%) 17 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine (pdb code 7s8w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine, PDB code: 7s8w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7s8w

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Magnesium binding site 1 out of 4 in the Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:44.9
occ:1.00
 O10 A:8JI401 1.7 73.8 1.0
OD2 A:ASP239 2.1 57.4 1.0
OE2 A:GLU214 2.2 54.1 1.0
O A:HOH502 2.2 52.8 1.0
OD2 A:ASP189 2.2 59.9 1.0
C08 A:8JI401 2.6 79.4 1.0
O09 A:8JI401 2.7 82.1 1.0
CD A:GLU214 3.2 56.8 1.0
CG A:ASP189 3.2 61.0 1.0
CG A:ASP239 3.2 58.7 1.0
OD1 A:ASP189 3.6 56.0 1.0
O A:HOH501 3.6 67.6 1.0
NZ A:LYS161 3.6 58.5 1.0
CB A:ASP239 3.8 51.0 1.0
NZ A:LYS263 3.9 58.6 1.0
OE1 A:GLU214 3.9 58.5 1.0
ND2 A:ASN261 4.0 55.3 1.0
C07 A:8JI401 4.0 81.3 1.0
ND2 A:ASN191 4.0 69.0 1.0
CG A:GLU214 4.1 55.4 1.0
OD1 A:ASP239 4.3 49.6 1.0
CE A:LYS263 4.3 59.0 1.0
OE1 A:GLU240 4.3 50.9 1.0
NZ A:LYS163 4.6 74.5 1.0
CB A:ASP189 4.6 55.4 1.0
CE A:LYS161 4.7 57.0 1.0
N11 A:8JI401 4.7 73.2 1.0
CG A:ASN191 4.9 64.2 1.0
O13 A:8JI401 4.9 68.4 1.0
CB A:GLU214 5.0 54.5 1.0
OD1 A:ASN191 5.0 65.6 1.0
CD A:GLU240 5.0 63.4 1.0

Magnesium binding site 2 out of 4 in 7s8w

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Magnesium binding site 2 out of 4 in the Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:37.3
occ:1.00
 O B:HOH504 1.9 58.1 1.0
O09 B:8JI401 2.1 55.8 1.0
OE2 B:GLU214 2.1 54.1 1.0
OD2 B:ASP239 2.2 52.7 1.0
OD2 B:ASP189 2.2 57.7 1.0
O10 B:8JI401 2.3 69.2 1.0
C08 B:8JI401 2.5 66.0 1.0
CD B:GLU214 3.0 55.0 1.0
CG B:ASP189 3.1 55.2 1.0
CG B:ASP239 3.3 52.0 1.0
OD1 B:ASP189 3.3 58.5 1.0
CB B:ASP239 3.8 47.6 1.0
OE1 B:GLU214 3.8 58.3 1.0
NZ B:LYS161 3.8 56.2 1.0
CG B:GLU214 3.9 51.2 1.0
NZ B:LYS263 3.9 50.9 1.0
C07 B:8JI401 4.0 70.8 1.0
ND2 B:ASN191 4.0 61.7 1.0
OE1 B:GLU240 4.2 47.3 1.0
NZ B:LYS163 4.2 70.8 1.0
ND2 B:ASN261 4.3 49.1 1.0
OD1 B:ASP239 4.3 55.0 1.0
CB B:ASP189 4.5 52.9 1.0
O B:HOH508 4.6 53.5 1.0
CE B:LYS263 4.7 49.8 1.0
CD B:GLU240 4.7 56.7 1.0
OE2 B:GLU240 4.7 58.8 1.0
CE B:LYS161 4.8 51.1 1.0
N11 B:8JI401 4.8 70.1 1.0
CG B:ASN191 4.9 66.9 1.0
C04 B:8JI401 4.9 69.7 1.0
CB B:GLU214 5.0 55.4 1.0

Magnesium binding site 3 out of 4 in 7s8w

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Magnesium binding site 3 out of 4 in the Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:42.7
occ:1.00
 O10 C:8JI402 1.9 61.9 1.0
O C:HOH503 2.0 60.3 1.0
OD2 C:ASP239 2.1 55.0 1.0
OD2 C:ASP189 2.1 49.9 1.0
OE2 C:GLU214 2.3 54.1 1.0
C08 C:8JI402 2.6 71.0 1.0
O09 C:8JI402 2.6 77.3 1.0
CG C:ASP189 3.1 55.8 1.0
CG C:ASP239 3.2 56.2 1.0
CD C:GLU214 3.2 55.4 1.0
OD1 C:ASP189 3.5 52.9 1.0
ND2 C:ASN191 3.7 57.7 1.0
CB C:ASP239 3.7 49.9 1.0
NZ C:LYS263 3.8 59.2 1.0
NZ C:LYS161 3.9 48.7 1.0
OE1 C:GLU240 3.9 49.6 1.0
C07 C:8JI402 4.0 76.5 1.0
CG C:GLU214 4.0 51.5 1.0
OE1 C:GLU214 4.0 60.5 1.0
OD1 C:ASP239 4.2 43.6 1.0
ND2 C:ASN261 4.3 52.0 1.0
NZ C:LYS163 4.4 68.0 1.0
O C:HOH511 4.4 56.1 1.0
CB C:ASP189 4.5 55.1 1.0
CG C:ASN191 4.5 61.6 1.0
CD C:GLU240 4.7 60.4 1.0
OD1 C:ASN191 4.8 71.2 1.0
CE C:LYS263 4.8 52.6 1.0
N11 C:8JI402 4.8 78.6 1.0
CE C:LYS161 4.9 56.4 1.0

Magnesium binding site 4 out of 4 in 7s8w

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Magnesium binding site 4 out of 4 in the Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Amycolatopsis Sp. T-1-60 N-Succinylamino Acid Racemase/O- Succinylbenzoate Synthase R266Q Mutant in Complex with N- Succinylphenylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:63.1
occ:1.00
 OD2 D:ASP239 1.9 67.5 1.0
O D:HOH501 2.0 58.8 1.0
O09 D:8JI401 2.0 74.6 1.0
OD2 D:ASP189 2.1 73.9 1.0
OE2 D:GLU214 2.3 69.7 1.0
O10 D:8JI401 2.6 87.1 1.0
C08 D:8JI401 2.6 84.8 1.0
CD D:GLU214 3.0 70.9 1.0
CG D:ASP239 3.1 61.8 1.0
CG D:ASP189 3.1 75.7 1.0
OD1 D:ASP189 3.6 73.3 1.0
OE1 D:GLU214 3.7 71.7 1.0
CB D:ASP239 3.7 70.8 1.0
CG D:GLU214 3.7 63.7 1.0
ND2 D:ASN261 3.9 63.4 1.0
NZ D:LYS161 3.9 52.7 1.0
NZ D:LYS263 3.9 68.5 1.0
C07 D:8JI401 4.1 91.6 1.0
OD1 D:ASP239 4.1 55.9 1.0
ND2 D:ASN191 4.1 77.0 1.0
OE1 D:GLU240 4.2 62.2 1.0
O D:HOH513 4.3 65.9 1.0
NZ D:LYS163 4.4 74.6 1.0
CB D:ASP189 4.4 68.4 1.0
CE D:LYS263 4.5 64.3 1.0
OD1 D:ASN191 4.7 78.3 1.0
CG D:ASN191 4.7 79.7 1.0
CE D:LYS161 4.8 51.7 1.0
N11 D:8JI401 4.8 85.8 1.0
CB D:GLU214 4.9 64.9 1.0

Reference:

D.P.Truong, S.Rousseau, B.W.Machala, J.Huddleston, M.Zhu, K.G.Hull, D.Romo, F.Raushel, J.C.Sacchettini, M.E.Glasner. The Second-Shell Amino Acid R266 Helps Determine N-Succinylamino Acid Racemase Reaction Specificity in Promiscuous N-Succinylamino Acid Racemase/O-Succinylbenzoate Synthase Enzymes To Be Published.
Page generated: Thu Aug 14 15:35:24 2025

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