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Magnesium in PDB 5fjr: N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine

Enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine

All present enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine:
4.2.1.113;

Protein crystallography data

The structure of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine, PDB code: 5fjr was solved by G.Sanchez Carron, D.Campopiano, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.89 / 2.44
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 217.670, 217.670, 263.150, 90.00, 90.00, 120.00
R / Rfree (%) 17.222 / 22.052

Magnesium Binding Sites:

The binding sites of Magnesium atom in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine (pdb code 5fjr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine, PDB code: 5fjr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5fjr

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Magnesium binding site 1 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1370

b:42.3
occ:1.00
 OD2 A:ASP239 2.2 43.9 1.0
OE2 A:GLU214 2.3 38.8 1.0
OD2 A:ASP189 2.5 40.3 1.0
OXT A:NPQ1369 2.7 38.4 1.0
O A:NPQ1369 2.8 42.1 1.0
CD A:GLU214 3.1 38.1 1.0
C A:NPQ1369 3.1 44.5 1.0
CG A:ASP189 3.2 36.4 1.0
CG A:ASP239 3.3 35.5 1.0
OD1 A:ASP189 3.4 40.2 1.0
ND2 A:ASN191 3.6 41.6 1.0
CB A:ASP239 3.8 33.0 1.0
CG A:GLU214 3.8 31.4 1.0
OE1 A:GLU214 3.8 43.0 1.0
NZ A:LYS161 3.9 35.1 1.0
NZ A:LYS263 3.9 42.6 1.0
NZ A:LYS163 4.1 38.1 1.0
OE1 A:GLU240 4.2 44.9 1.0
OD1 A:ASP239 4.4 37.4 1.0
CG A:ASN191 4.4 44.7 1.0
ND2 A:ASN261 4.6 42.2 1.0
CB A:ASP189 4.6 29.6 1.0
CA A:NPQ1369 4.7 42.2 1.0
OD1 A:ASN191 4.7 41.7 1.0
CE A:LYS263 4.7 32.7 1.0
CB A:GLU214 4.8 31.9 1.0
O A:HOH2137 4.8 44.2 1.0
OE2 A:GLU240 4.9 38.9 1.0
CE1 A:TYR55 4.9 36.6 1.0
CE A:LYS161 4.9 33.5 1.0
CD A:GLU240 4.9 45.0 1.0

Magnesium binding site 2 out of 4 in 5fjr

Go back to Magnesium Binding Sites List in 5fjr
Magnesium binding site 2 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1369

b:58.6
occ:1.00
 OD2 B:ASP239 2.3 50.5 1.0
O B:HOH2080 2.3 46.7 1.0
OE2 B:GLU214 2.4 54.2 1.0
OD2 B:ASP189 2.5 51.2 1.0
O B:NPQ1368 2.7 50.0 1.0
OXT B:NPQ1368 2.9 57.6 1.0
CD B:GLU214 3.1 53.7 1.0
C B:NPQ1368 3.2 61.4 1.0
CG B:ASP189 3.2 41.1 1.0
OD1 B:ASP189 3.3 45.9 1.0
CG B:ASP239 3.4 48.1 1.0
CG B:GLU214 3.6 44.6 1.0
ND2 B:ASN191 3.7 44.5 1.0
NZ B:LYS161 3.8 47.5 1.0
CB B:ASP239 3.8 41.3 1.0
OE1 B:GLU214 3.9 60.0 1.0
NZ B:LYS263 4.0 52.8 1.0
NZ B:LYS163 4.1 52.9 1.0
OE1 B:GLU240 4.2 46.9 1.0
CG B:ASN191 4.4 43.5 1.0
OD1 B:ASP239 4.4 45.2 1.0
OD1 B:ASN191 4.4 42.6 1.0
ND2 B:ASN261 4.6 62.4 1.0
CB B:ASP189 4.6 39.8 1.0
CE B:LYS263 4.7 46.9 1.0
CA B:NPQ1368 4.8 52.3 1.0
CE B:LYS161 4.8 39.5 1.0
CE2 B:TYR55 4.8 46.2 1.0
CB B:GLU214 4.9 44.6 1.0
CD B:GLU240 4.9 44.7 1.0
OE2 B:GLU240 5.0 44.1 1.0

Magnesium binding site 3 out of 4 in 5fjr

Go back to Magnesium Binding Sites List in 5fjr
Magnesium binding site 3 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1369

b:52.5
occ:1.00
 O C:HOH2066 2.2 41.1 1.0
OE2 C:GLU214 2.2 48.9 1.0
OD2 C:ASP239 2.2 50.9 1.0
OD2 C:ASP189 2.6 46.8 1.0
O C:NPQ1368 2.8 53.3 1.0
OXT C:NPQ1368 2.9 64.6 1.0
CD C:GLU214 3.0 46.0 1.0
C C:NPQ1368 3.2 59.9 1.0
CG C:ASP239 3.3 46.3 1.0
CG C:ASP189 3.3 52.1 1.0
OD1 C:ASP189 3.4 47.8 1.0
CB C:ASP239 3.6 37.7 1.0
ND2 C:ASN191 3.7 46.4 1.0
CG C:GLU214 3.7 39.5 1.0
OE1 C:GLU214 3.7 49.2 1.0
NZ C:LYS161 4.0 41.3 1.0
NZ C:LYS263 4.1 48.2 1.0
OE1 C:GLU240 4.2 47.5 1.0
NZ C:LYS163 4.3 49.5 1.0
ND2 C:ASN261 4.4 41.8 1.0
OD1 C:ASP239 4.4 40.5 1.0
CG C:ASN191 4.5 51.2 1.0
OD1 C:ASN191 4.6 52.4 1.0
CB C:ASP189 4.7 41.7 1.0
CA C:NPQ1368 4.7 59.2 1.0
CE C:LYS263 4.8 39.4 1.0
CB C:GLU214 4.8 36.5 1.0
CE C:LYS161 4.9 37.9 1.0
OE2 C:GLU240 4.9 48.5 1.0
CD C:GLU240 4.9 48.7 1.0

Magnesium binding site 4 out of 4 in 5fjr

Go back to Magnesium Binding Sites List in 5fjr
Magnesium binding site 4 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1369

b:54.1
occ:1.00
 OE2 D:GLU214 2.1 52.7 1.0
OD2 D:ASP239 2.3 46.2 1.0
O D:HOH2059 2.4 36.7 1.0
OD2 D:ASP189 2.5 46.1 1.0
O D:NPQ1368 2.8 53.4 1.0
CD D:GLU214 2.9 52.1 1.0
OXT D:NPQ1368 2.9 48.8 1.0
C D:NPQ1368 3.2 55.8 1.0
CG D:ASP189 3.2 50.3 1.0
CG D:ASP239 3.3 49.9 1.0
OD1 D:ASP189 3.4 51.8 1.0
CG D:GLU214 3.6 45.4 1.0
OE1 D:GLU214 3.7 42.2 1.0
CB D:ASP239 3.7 37.3 1.0
NZ D:LYS161 3.7 39.4 1.0
ND2 D:ASN191 3.9 48.4 1.0
NZ D:LYS263 4.1 53.0 1.0
OE1 D:GLU240 4.3 52.2 1.0
NZ D:LYS163 4.3 50.7 1.0
OD1 D:ASP239 4.4 42.5 1.0
ND2 D:ASN261 4.5 57.6 1.0
CB D:ASP189 4.5 42.2 1.0
CG D:ASN191 4.6 48.1 1.0
O D:HOH2051 4.7 46.6 1.0
CE D:LYS161 4.7 33.4 1.0
OD1 D:ASN191 4.7 44.0 1.0
CE D:LYS263 4.7 45.8 1.0
CB D:GLU214 4.8 42.3 1.0
CA D:NPQ1368 4.9 53.5 1.0
OE2 D:GLU240 5.0 39.5 1.0

Reference:

G.Sanchez-Carron, D.Campopiano, G.Grogan. Structure of N-Acylamino Acid Racemase Mutants in Complex with Substrates To Be Published.
Page generated: Mon Dec 14 20:18:54 2020

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