Atomistry » Magnesium » PDB 4c2z-4cfv » 4c5a
Atomistry »
  Magnesium »
    PDB 4c2z-4cfv »
      4c5a »

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

Go back to Magnesium Binding Sites List in 4c5a
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: Thu Aug 15 16:42:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy