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Magnesium in PDB 4c5b: The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala

Enzymatic activity of The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala

All present enzymatic activity of The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala:
6.3.2.4;

Protein crystallography data

The structure of The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala, PDB code: 4c5b 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) 47.99 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.000, 97.620, 109.490, 90.00, 90.00, 90.00
R / Rfree (%) 17.015 / 20.013

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala (pdb code 4c5b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala, PDB code: 4c5b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4c5b

Go back to Magnesium Binding Sites List in 4c5b
Magnesium binding site 1 out of 6 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala


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 Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1313

b:6.2
occ:1.00
 O2 A:CO3313 2.0 7.1 1.0
O A:HOH2254 2.1 3.1 1.0
O1B A:ADP310 2.1 5.8 1.0
OD1 A:ASN272 2.2 6.4 1.0
OE2 A:GLU270 2.2 6.5 1.0
OE1 A:GLU270 2.2 6.1 1.0
CD A:GLU270 2.5 5.0 1.0
C A:CO3313 3.0 6.0 1.0
CG A:ASN272 3.1 7.8 1.0
PB A:ADP310 3.2 6.1 1.0
O3 A:CO3313 3.3 7.1 1.0
O2B A:ADP310 3.4 6.0 1.0
ND2 A:ASN272 3.5 9.4 1.0
MG A:MG1314 3.6 7.0 1.0
O A:HOH2185 3.7 2.0 1.0
CA A:GLY149 3.9 7.3 1.0
CG A:GLU270 4.0 7.1 1.0
NZ A:LYS97 4.0 7.5 1.0
O1 A:CO3313 4.1 7.1 1.0
O A:GLU148 4.1 7.8 1.0
O3A A:ADP310 4.2 5.9 1.0
O A:HOH2038 4.2 6.9 1.0
O3B A:ADP310 4.3 6.7 1.0
N A:DAL311 4.3 7.9 1.0
CB A:ASN272 4.5 7.7 1.0
O A:HOH2187 4.6 6.1 1.0
O1A A:ADP310 4.7 7.3 1.0
N A:SER150 4.7 5.9 1.0
OD2 A:ASP257 4.7 7.2 1.0
CE A:LYS97 4.8 9.1 1.0
C A:GLY149 4.9 6.4 1.0
N A:GLY149 4.9 6.1 1.0
CB A:GLU270 4.9 7.0 1.0
C A:GLU148 5.0 7.6 1.0

Magnesium binding site 2 out of 6 in 4c5b

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Magnesium binding site 2 out of 6 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala


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 Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1314

b:7.0
occ:1.00
 O2B A:ADP310 2.0 6.0 1.0
O1A A:ADP310 2.1 7.3 1.0
OD2 A:ASP257 2.1 7.2 1.0
O3 A:CO3313 2.1 7.1 1.0
O A:HOH2326 2.1 4.7 1.0
OE2 A:GLU270 2.1 6.5 1.0
C A:CO3313 3.0 6.0 1.0
PB A:ADP310 3.2 6.1 1.0
CD A:GLU270 3.3 5.0 1.0
CG A:ASP257 3.3 8.2 1.0
PA A:ADP310 3.3 6.9 1.0
O3A A:ADP310 3.5 5.9 1.0
O2 A:CO3313 3.5 7.1 1.0
MG A:MG1313 3.6 6.2 1.0
O1B A:ADP310 3.7 5.8 1.0
NZ A:LYS215 3.8 7.4 1.0
CG A:GLU270 3.8 7.1 1.0
O1 A:CO3313 3.9 7.1 1.0
ND2 A:ASN272 4.0 9.4 1.0
NH2 A:ARG255 4.1 8.8 1.0
O A:HOH2367 4.1 8.1 1.0
CB A:ASP257 4.1 7.4 1.0
OD1 A:ASP257 4.1 8.2 1.0
C5' A:ADP310 4.2 6.6 1.0
O5' A:ADP310 4.2 6.8 1.0
OE1 A:GLU270 4.3 6.1 1.0
O3' A:ADP310 4.4 7.4 1.0
O2A A:ADP310 4.5 6.7 1.0
O3B A:ADP310 4.5 6.7 1.0
OD1 A:ASN272 4.7 6.4 1.0
CE A:LYS215 4.8 6.1 1.0
CG A:ASN272 4.8 7.8 1.0
C3' A:ADP310 4.9 7.6 1.0

Magnesium binding site 3 out of 6 in 4c5b

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Magnesium binding site 3 out of 6 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala


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 Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1307

b:9.3
occ:1.00
 O2 B:CO3313 1.9 9.0 1.0
O3B B:ADP310 2.0 9.9 1.0
O B:HOH2198 2.1 5.0 1.0
OD1 B:ASN272 2.1 10.1 1.0
OE2 B:GLU270 2.2 9.1 1.0
OE1 B:GLU270 2.3 9.5 1.0
CD B:GLU270 2.5 8.1 1.0
C B:CO3313 3.0 9.0 1.0
CG B:ASN272 3.1 10.4 1.0
PB B:ADP310 3.2 9.0 1.0
O3 B:CO3313 3.3 8.7 1.0
O1B B:ADP310 3.4 9.1 1.0
ND2 B:ASN272 3.5 13.0 1.0
MG B:MG1308 3.6 9.5 1.0
O B:HOH2139 3.6 2.0 1.0
CA B:GLY149 3.9 8.3 1.0
NZ B:LYS97 4.0 10.3 1.0
O1 B:CO3313 4.0 8.6 1.0
CG B:GLU270 4.1 9.8 1.0
O3A B:ADP310 4.1 9.8 1.0
O B:HOH2032 4.2 9.3 1.0
O B:GLU148 4.2 10.3 1.0
N B:DAL311 4.2 9.0 1.0
O2B B:ADP310 4.3 10.3 1.0
CB B:ASN272 4.5 9.4 1.0
O B:HOH2141 4.6 8.1 1.0
N B:SER150 4.7 9.2 1.0
O1A B:ADP310 4.7 10.3 1.0
OD2 B:ASP257 4.7 11.1 1.0
CE B:LYS97 4.8 10.2 1.0
C B:GLY149 4.8 9.3 1.0
N B:GLY149 5.0 8.2 1.0
CB B:GLU270 5.0 9.1 1.0
O B:ALA271 5.0 10.0 1.0

Magnesium binding site 4 out of 6 in 4c5b

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Magnesium binding site 4 out of 6 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala


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 Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1308

b:9.5
occ:1.00
 O1A B:ADP310 2.0 10.3 1.0
OD2 B:ASP257 2.0 11.1 1.0
OE2 B:GLU270 2.1 9.1 1.0
O B:HOH2278 2.1 5.2 1.0
O1B B:ADP310 2.1 9.1 1.0
O3 B:CO3313 2.1 8.7 1.0
C B:CO3313 3.0 9.0 1.0
PB B:ADP310 3.2 9.0 1.0
CG B:ASP257 3.2 10.7 1.0
PA B:ADP310 3.2 10.1 1.0
CD B:GLU270 3.2 8.1 1.0
O3A B:ADP310 3.5 9.8 1.0
O2 B:CO3313 3.6 9.0 1.0
MG B:MG1307 3.6 9.3 1.0
O3B B:ADP310 3.7 9.9 1.0
CG B:GLU270 3.8 9.8 1.0
NZ B:LYS215 3.8 8.9 1.0
O1 B:CO3313 3.9 8.6 1.0
ND2 B:ASN272 3.9 13.0 1.0
CB B:ASP257 4.1 10.3 1.0
O B:HOH2320 4.1 8.0 1.0
NH2 B:ARG255 4.1 11.5 1.0
C5' B:ADP310 4.1 11.1 1.0
OD1 B:ASP257 4.1 13.7 1.0
O5' B:ADP310 4.2 11.5 1.0
OE1 B:GLU270 4.3 9.5 1.0
O3' B:ADP310 4.4 11.1 1.0
O2A B:ADP310 4.5 10.1 1.0
O2B B:ADP310 4.5 10.3 1.0
OD1 B:ASN272 4.6 10.1 1.0
CG B:ASN272 4.7 10.4 1.0
CE B:LYS215 4.8 10.1 1.0
C3' B:ADP310 4.8 10.2 1.0

Magnesium binding site 5 out of 6 in 4c5b

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Magnesium binding site 5 out of 6 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1309

b:16.0
occ:1.00
 O B:HOH2357 2.0 14.8 1.0
O B:HOH2336 2.0 12.2 1.0
O B:HOH2334 2.1 10.2 1.0
O B:HOH2285 2.2 12.7 1.0
O B:HOH2281 2.2 12.2 1.0
NE2 B:HIS280 2.3 14.8 1.0
CE1 B:HIS280 3.2 14.8 1.0
CD2 B:HIS280 3.3 14.3 1.0
O B:HOH2335 4.0 15.8 1.0
O B:HOH2120 4.2 18.6 1.0
O B:HOH2015 4.3 17.2 1.0
ND1 B:HIS280 4.3 13.3 1.0
O B:TYR216 4.3 12.6 1.0
CG B:HIS280 4.4 13.1 1.0
OD1 B:ASP219 4.5 33.2 1.0
OG B:SER279 4.9 12.6 1.0

Magnesium binding site 6 out of 6 in 4c5b

Go back to Magnesium Binding Sites List in 4c5b
Magnesium binding site 6 out of 6 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Atp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1310

b:30.1
occ:1.00
 O B:HOH2225 2.0 20.5 1.0
O B:HOH2358 2.0 26.2 1.0
O B:HOH2359 2.1 22.6 1.0
O B:HOH2224 2.1 22.9 1.0
O B:HOH2360 2.2 16.5 1.0
O B:HOH2361 2.3 28.3 1.0
OD2 B:ASP165 4.1 28.9 1.0
OD1 B:ASP165 4.4 29.4 1.0
CG B:ASP165 4.7 24.4 1.0
O B:HOH2217 5.0 15.6 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 16:42:35 2024

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