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Magnesium in PDB 4c5a: The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate

Enzymatic activity of The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate

All present enzymatic activity of The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate:
6.3.2.4;

Protein crystallography data

The structure of The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate, PDB code: 4c5a was solved by S.Batson, V.Majce, A.J.Lloyd, D.Rea, C.W.G.Fishwick, K.J.Simmons, V.Fulop, D.I.Roper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.76 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.790, 97.510, 109.990, 90.00, 90.00, 90.00
R / Rfree (%) 20.504 / 23.726

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate (pdb code 4c5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate, PDB code: 4c5a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4c5a

Go back to Magnesium Binding Sites List in 4c5a
Magnesium binding site 1 out of 4 in the The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg330

b:13.6
occ:1.00
 O10 A:DS0311 2.0 14.5 1.0
O1B A:ADP310 2.0 13.6 1.0
O A:HOH2135 2.1 2.0 1.0
OE2 A:GLU270 2.1 13.6 1.0
OD1 A:ASN272 2.2 13.6 1.0
OE1 A:GLU270 2.3 13.6 1.0
CD A:GLU270 2.5 13.7 1.0
P8 A:DS0311 3.1 15.6 1.0
PB A:ADP310 3.1 15.1 1.0
CG A:ASN272 3.2 13.6 1.0
O2B A:ADP310 3.3 14.2 1.0
O9 A:DS0311 3.4 14.8 1.0
ND2 A:ASN272 3.6 13.6 1.0
MG A:MG331 3.6 14.0 1.0
O A:HOH2100 3.7 2.0 1.0
CA A:GLY149 3.9 14.7 1.0
NZ A:LYS97 4.0 14.3 1.0
CG A:GLU270 4.0 13.7 1.0
O7 A:DS0311 4.0 16.4 1.0
O3A A:ADP310 4.1 15.0 1.0
O A:GLU148 4.2 14.6 1.0
O3B A:ADP310 4.2 13.4 1.0
N6 A:DS0311 4.3 18.8 1.0
O A:HOH2028 4.3 2.5 1.0
O11 A:DS0311 4.3 17.1 1.0
CB A:ASN272 4.5 13.6 1.0
O A:HOH2103 4.6 2.0 1.0
N A:SER150 4.6 14.9 1.0
O1A A:ADP310 4.7 14.1 1.0
CE A:LYS97 4.7 14.4 1.0
OD2 A:ASP257 4.7 14.4 1.0
C A:GLY149 4.8 14.8 1.0
C3 A:DS0311 4.9 17.3 1.0
CB A:GLU270 4.9 13.8 1.0
N A:GLY149 4.9 14.6 1.0
O A:ALA271 5.0 13.7 1.0
C A:GLU148 5.0 14.5 1.0
C4 A:DS0311 5.0 19.6 1.0

Magnesium binding site 2 out of 4 in 4c5a

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Magnesium binding site 2 out of 4 in the The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg331

b:14.0
occ:1.00
 O1A A:ADP310 2.0 14.1 1.0
OD2 A:ASP257 2.0 14.4 1.0
O9 A:DS0311 2.0 14.8 1.0
OE2 A:GLU270 2.1 13.6 1.0
O2B A:ADP310 2.1 14.2 1.0
CD A:GLU270 3.2 13.7 1.0
P8 A:DS0311 3.2 15.6 1.0
PB A:ADP310 3.2 15.1 1.0
CG A:ASP257 3.2 15.8 1.0
PA A:ADP310 3.3 15.0 1.0
O3A A:ADP310 3.5 15.0 1.0
MG A:MG330 3.6 13.6 1.0
O10 A:DS0311 3.7 14.5 1.0
CG A:GLU270 3.7 13.7 1.0
O1B A:ADP310 3.7 13.6 1.0
NZ A:LYS215 3.9 14.4 1.0
ND2 A:ASN272 4.0 13.6 1.0
O11 A:DS0311 4.0 17.1 1.0
NH2 A:ARG255 4.1 15.8 1.0
CB A:ASP257 4.1 14.0 1.0
O A:HOH2211 4.1 3.6 1.0
OD1 A:ASP257 4.1 14.7 1.0
C5' A:ADP310 4.2 14.3 1.0
O5' A:ADP310 4.2 15.6 1.0
OE1 A:GLU270 4.3 13.6 1.0
O3' A:ADP310 4.4 16.6 1.0
O2A A:ADP310 4.4 14.0 1.0
O7 A:DS0311 4.4 16.4 1.0
O3B A:ADP310 4.6 13.4 1.0
OD1 A:ASN272 4.6 13.6 1.0
CG A:ASN272 4.7 13.6 1.0
C3' A:ADP310 4.9 15.0 1.0
CE A:LYS215 4.9 14.2 1.0

Magnesium binding site 3 out of 4 in 4c5a

Go back to Magnesium Binding Sites List in 4c5a
Magnesium binding site 3 out of 4 in the The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg330

b:28.9
occ:1.00
 O10 B:DS0311 2.0 33.2 1.0
O3B B:ADP310 2.1 28.4 1.0
OE2 B:GLU270 2.1 25.9 1.0
OE1 B:GLU270 2.2 24.7 1.0
OD1 B:ASN272 2.3 26.8 1.0
CD B:GLU270 2.5 23.5 1.0
PB B:ADP310 3.1 29.3 1.0
P8 B:DS0311 3.2 36.3 1.0
O1B B:ADP310 3.2 31.6 1.0
CG B:ASN272 3.3 25.3 1.0
O9 B:DS0311 3.4 31.8 1.0
MG B:MG331 3.7 28.5 1.0
O B:HOH2038 3.8 2.0 1.0
ND2 B:ASN272 3.8 23.6 1.0
CA B:GLY149 4.0 28.2 1.0
NZ B:LYS97 4.0 25.4 1.0
O7 B:DS0311 4.0 33.1 1.0
CG B:GLU270 4.0 22.0 1.0
N6 B:DS0311 4.1 36.2 1.0
O3A B:ADP310 4.1 28.0 1.0
O B:GLU148 4.2 28.0 1.0
O B:HOH2006 4.2 16.6 1.0
O2B B:ADP310 4.3 28.2 1.0
O11 B:DS0311 4.3 34.5 1.0
O1A B:ADP310 4.6 28.6 1.0
O B:HOH2039 4.6 15.4 1.0
CE B:LYS97 4.6 25.2 1.0
N B:SER150 4.6 30.6 1.0
CB B:ASN272 4.7 23.7 1.0
OD2 B:ASP257 4.7 28.4 1.0
C B:GLY149 4.8 30.2 1.0
C3 B:DS0311 4.9 36.5 1.0
C4 B:DS0311 4.9 37.7 1.0
CB B:GLU270 4.9 21.1 1.0
PA B:ADP310 4.9 28.4 1.0
N B:GLY149 5.0 28.1 1.0
C B:GLU148 5.0 28.5 1.0

Magnesium binding site 4 out of 4 in 4c5a

Go back to Magnesium Binding Sites List in 4c5a
Magnesium binding site 4 out of 4 in the The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The X-Ray Crystal Structures of D-Alanyl-D-Alanine Ligase in Complex Adp and D-Cycloserine Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg331

b:28.5
occ:1.00
 O1A B:ADP310 1.9 28.6 1.0
OD2 B:ASP257 2.0 28.4 1.0
OE2 B:GLU270 2.1 25.9 1.0
O B:HOH2077 2.1 12.9 1.0
O9 B:DS0311 2.2 31.8 1.0
O1B B:ADP310 2.2 31.6 1.0
CD B:GLU270 3.2 23.5 1.0
PA B:ADP310 3.2 28.4 1.0
CG B:ASP257 3.2 27.2 1.0
P8 B:DS0311 3.3 36.3 1.0
PB B:ADP310 3.4 29.3 1.0
O3A B:ADP310 3.6 28.0 1.0
CG B:GLU270 3.7 22.0 1.0
MG B:MG330 3.7 28.9 1.0
O10 B:DS0311 3.8 33.2 1.0
O3B B:ADP310 4.0 28.4 1.0
NZ B:LYS215 4.0 32.0 1.0
ND2 B:ASN272 4.1 23.6 1.0
O11 B:DS0311 4.1 34.5 1.0
CB B:ASP257 4.1 27.0 1.0
OD1 B:ASP257 4.1 28.6 1.0
C5' B:ADP310 4.1 29.9 1.0
NH2 B:ARG255 4.1 29.2 1.0
O5' B:ADP310 4.1 31.6 1.0
O B:HOH2092 4.2 19.1 1.0
OE1 B:GLU270 4.2 24.7 1.0
O3' B:ADP310 4.2 30.6 1.0
O2A B:ADP310 4.4 30.6 1.0
O7 B:DS0311 4.5 33.1 1.0
O2B B:ADP310 4.7 28.2 1.0
OD1 B:ASN272 4.7 26.8 1.0
C3' B:ADP310 4.7 29.4 1.0
CG B:ASN272 4.8 25.3 1.0
CE B:LYS215 5.0 34.2 1.0

Reference:

S.Batson, V.Majce, A.J.Lloyd, D.Rea, C.W.G.Fishwick, K.J.Simmons, V.Fulop, D.I.Roper. D-Cycloserine Inhibition Occurs By A Novel Phosphoryl Intermediate: Prospects For Novel Antimicrobials Without Psychotic Side Effects. To Be Published.
Page generated: Mon Aug 11 07:11:30 2025

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