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Magnesium in PDB 5fjp: N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine

Enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine

All present enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine:
4.2.1.113;

Protein crystallography data

The structure of N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine, PDB code: 5fjp 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) 76.44 / 2.58
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 217.290, 217.290, 262.220, 90.00, 90.00, 120.00
R / Rfree (%) 17.926 / 20.834

Magnesium Binding Sites:

The binding sites of Magnesium atom in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine (pdb code 5fjp). 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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine, PDB code: 5fjp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5fjp

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Magnesium binding site 1 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine


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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1370

b:34.2
occ:1.00
 O A:HOH2062 2.3 19.7 1.0
OD2 A:ASP239 2.3 33.0 1.0
OD2 A:ASP189 2.4 32.8 1.0
OE2 A:GLU214 2.4 31.8 1.0
OXT A:NPQ1369 2.5 35.3 1.0
O A:NPQ1369 2.7 30.8 1.0
C A:NPQ1369 3.0 39.2 1.0
CD A:GLU214 3.2 34.4 1.0
CG A:ASP189 3.3 31.0 1.0
CG A:ASP239 3.5 31.2 1.0
ND2 A:ASN191 3.6 37.9 1.0
NZ A:LYS161 3.6 32.2 1.0
OD1 A:ASP189 3.7 29.2 1.0
NZ A:LYS263 3.8 34.6 1.0
NZ A:LYS163 3.9 43.5 1.0
CB A:ASP239 3.9 28.2 1.0
OE1 A:GLU214 3.9 33.8 1.0
CG A:GLU214 4.0 32.5 1.0
ND2 A:ASN261 4.2 31.1 1.0
CG A:ASN191 4.4 42.5 1.0
OE1 A:GLU240 4.4 27.3 1.0
O A:HOH2055 4.4 26.1 1.0
OD1 A:ASN191 4.5 45.5 1.0
CE A:LYS263 4.5 31.9 1.0
CA A:NPQ1369 4.5 39.3 1.0
OD1 A:ASP239 4.5 31.5 1.0
CB A:ASP189 4.6 28.9 1.0
CE A:LYS161 4.7 30.6 1.0
N A:NPQ1369 4.7 39.9 1.0

Magnesium binding site 2 out of 4 in 5fjp

Go back to Magnesium Binding Sites List in 5fjp
Magnesium binding site 2 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine


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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1370

b:35.4
occ:1.00
 OD2 B:ASP239 2.2 34.0 1.0
OE2 B:GLU214 2.2 33.1 1.0
O B:HOH2056 2.2 26.3 1.0
OD2 B:ASP189 2.4 31.5 1.0
OXT B:NPQ1369 2.7 40.0 1.0
O B:NPQ1369 2.7 34.5 1.0
CD B:GLU214 3.1 34.6 1.0
C B:NPQ1369 3.1 42.6 1.0
CG B:ASP239 3.3 35.5 1.0
CG B:ASP189 3.3 29.1 1.0
OD1 B:ASP189 3.6 31.5 1.0
CB B:ASP239 3.7 30.9 1.0
ND2 B:ASN191 3.7 34.8 1.0
NZ B:LYS161 3.7 35.3 1.0
CG B:GLU214 3.8 33.6 1.0
OE1 B:GLU214 3.8 36.6 1.0
NZ B:LYS263 3.9 38.9 1.0
NZ B:LYS163 4.1 51.5 1.0
ND2 B:ASN261 4.1 40.0 1.0
OE1 B:GLU240 4.2 30.5 1.0
OD1 B:ASP239 4.4 35.6 1.0
O B:HOH2051 4.4 32.1 1.0
CG B:ASN191 4.5 33.5 1.0
CE B:LYS263 4.6 37.8 1.0
CB B:ASP189 4.6 28.4 1.0
OD1 B:ASN191 4.6 32.6 1.0
CA B:NPQ1369 4.7 43.7 1.0
CE B:LYS161 4.7 33.4 1.0
N B:NPQ1369 4.9 43.4 1.0
CD B:GLU240 5.0 31.1 1.0
CB B:GLU214 5.0 35.8 1.0

Magnesium binding site 3 out of 4 in 5fjp

Go back to Magnesium Binding Sites List in 5fjp
Magnesium binding site 3 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine


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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1369

b:40.2
occ:1.00
 O C:HOH2037 2.1 33.2 1.0
OD2 C:ASP239 2.2 31.0 1.0
OE2 C:GLU214 2.3 33.8 1.0
OD2 C:ASP189 2.4 35.1 1.0
O C:NPQ1368 2.6 45.0 1.0
OXT C:NPQ1368 3.0 56.8 1.0
CD C:GLU214 3.1 33.7 1.0
C C:NPQ1368 3.2 50.6 1.0
CG C:ASP239 3.3 34.0 1.0
CG C:ASP189 3.4 34.4 1.0
ND2 C:ASN191 3.6 48.4 1.0
OD1 C:ASP189 3.6 38.0 1.0
CB C:ASP239 3.7 31.9 1.0
CG C:GLU214 3.8 32.0 1.0
NZ C:LYS161 3.8 38.9 1.0
OE1 C:GLU214 3.9 32.0 1.0
NZ C:LYS263 3.9 46.0 1.0
NZ C:LYS163 4.1 48.5 1.0
OE1 C:GLU240 4.2 30.1 1.0
ND2 C:ASN261 4.2 34.9 1.0
CG C:ASN191 4.4 48.0 1.0
OD1 C:ASP239 4.4 27.1 1.0
OD1 C:ASN191 4.6 44.8 1.0
CB C:ASP189 4.6 30.9 1.0
CE C:LYS263 4.7 39.8 1.0
CA C:NPQ1368 4.7 52.4 1.0
CE C:LYS161 4.8 37.6 1.0
N C:NPQ1368 4.9 57.1 1.0
CD C:GLU240 4.9 30.9 1.0
OE2 C:GLU240 5.0 32.4 1.0
CB C:GLU214 5.0 30.1 1.0

Magnesium binding site 4 out of 4 in 5fjp

Go back to Magnesium Binding Sites List in 5fjp
Magnesium binding site 4 out of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine


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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1369

b:55.6
occ:1.00
 OE2 D:GLU214 2.0 39.1 1.0
O D:HOH2031 2.2 32.9 1.0
OD2 D:ASP239 2.3 35.0 1.0
OD2 D:ASP189 2.4 36.0 1.0
OXT D:NPQ1368 2.6 50.1 1.0
O D:NPQ1368 2.9 50.4 1.0
CD D:GLU214 3.0 38.2 1.0
C D:NPQ1368 3.1 52.1 1.0
CG D:ASP189 3.3 40.8 1.0
CG D:ASP239 3.4 38.6 1.0
OD1 D:ASP189 3.6 44.6 1.0
NZ D:LYS161 3.7 44.2 1.0
OE1 D:GLU214 3.7 32.1 1.0
CB D:ASP239 3.7 38.5 1.0
CG D:GLU214 3.8 35.8 1.0
ND2 D:ASN191 3.8 43.0 1.0
NZ D:LYS263 3.9 42.9 1.0
NZ D:LYS163 4.1 50.5 1.0
ND2 D:ASN261 4.1 46.2 1.0
OE1 D:GLU240 4.3 37.6 1.0
OD1 D:ASP239 4.5 36.5 1.0
CG D:ASN191 4.5 46.6 1.0
CB D:ASP189 4.5 40.5 1.0
O D:HOH2028 4.6 38.0 1.0
CE D:LYS263 4.6 38.6 1.0
CE D:LYS161 4.7 39.1 1.0
OD1 D:ASN191 4.7 46.2 1.0
CA D:NPQ1368 4.7 53.1 1.0
CB D:GLU214 4.8 32.9 1.0
N D:NPQ1368 4.9 49.3 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 20:18:52 2020

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