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Magnesium in PDB 4c5c: The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp and D-Ala-D-Ala

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

All present enzymatic activity of The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 Adp and D-Ala-D-Ala, PDB code: 4c5c 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) 48.90 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.230, 97.800, 110.120, 90.00, 90.00, 90.00
R / Rfree (%) 17.975 / 20.341

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 Adp and D-Ala-D-Ala (pdb code 4c5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp and D-Ala-D-Ala, PDB code: 4c5c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4c5c

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Magnesium binding site 1 out of 7 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 Adp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1313

b:7.7
occ:1.00
 O3G A:ATP310 2.0 8.5 1.0
O1B A:ATP310 2.0 7.2 1.0
O A:HOH2194 2.1 5.2 1.0
OE2 A:GLU270 2.1 6.5 1.0
OD1 A:ASN272 2.2 9.2 1.0
OE1 A:GLU270 2.2 7.5 1.0
CD A:GLU270 2.5 7.0 1.0
PG A:ATP310 2.9 19.9 1.0
CG A:ASN272 3.2 10.0 1.0
PB A:ATP310 3.2 8.1 1.0
O3B A:ATP310 3.3 9.7 1.0
O2G A:ATP310 3.4 8.6 1.0
ND2 A:ASN272 3.6 11.6 1.0
MG A:MG1314 3.6 9.2 1.0
O A:HOH2122 3.6 2.0 1.0
NZ A:LYS97 4.0 7.0 1.0
CG A:GLU270 4.0 7.4 1.0
CA A:GLY149 4.0 8.7 1.0
O1G A:ATP310 4.1 9.2 1.0
O3A A:ATP310 4.1 8.5 1.0
O A:GLU148 4.2 9.4 1.0
O A:HOH2024 4.2 9.9 1.0
N A:DAL311 4.3 9.8 1.0
O2B A:ATP310 4.3 8.3 1.0
CB A:ASN272 4.5 9.1 1.0
O A:HOH2124 4.6 7.8 1.0
O1A A:ATP310 4.6 8.3 1.0
CE A:LYS97 4.7 7.5 1.0
N A:SER150 4.7 7.6 1.0
OD2 A:ASP257 4.8 9.3 1.0
C A:GLY149 4.9 8.6 1.0
CB A:GLU270 4.9 7.1 1.0
O A:ALA271 5.0 9.3 1.0
C A:GLU148 5.0 8.2 1.0

Magnesium binding site 2 out of 7 in 4c5c

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Magnesium binding site 2 out of 7 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 Adp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1314

b:9.2
occ:1.00
 O1A A:ATP310 2.0 8.3 1.0
O2G A:ATP310 2.0 8.6 1.0
OD2 A:ASP257 2.0 9.3 1.0
O A:HOH2272 2.1 7.1 1.0
OE2 A:GLU270 2.1 6.5 1.0
O3B A:ATP310 2.2 9.7 1.0
PG A:ATP310 2.7 19.9 1.0
CD A:GLU270 3.3 7.0 1.0
CG A:ASP257 3.3 9.3 1.0
PA A:ATP310 3.3 8.2 1.0
PB A:ATP310 3.3 8.1 1.0
O3A A:ATP310 3.6 8.5 1.0
O3G A:ATP310 3.6 8.5 1.0
MG A:MG1313 3.6 7.7 1.0
O1B A:ATP310 3.8 7.2 1.0
CG A:GLU270 3.8 7.4 1.0
NZ A:LYS215 3.9 10.1 1.0
O1G A:ATP310 4.0 9.2 1.0
ND2 A:ASN272 4.0 11.6 1.0
O A:HOH2309 4.0 11.1 1.0
CB A:ASP257 4.1 9.6 1.0
NH2 A:ARG255 4.1 10.3 1.0
OD1 A:ASP257 4.2 10.5 1.0
C5' A:ATP310 4.2 10.2 1.0
O5' A:ATP310 4.2 8.4 1.0
OE1 A:GLU270 4.3 7.5 1.0
O3' A:ATP310 4.4 9.4 1.0
O2A A:ATP310 4.4 9.1 1.0
O2B A:ATP310 4.6 8.3 1.0
OD1 A:ASN272 4.7 9.2 1.0
CG A:ASN272 4.8 10.0 1.0
C3' A:ATP310 4.9 9.6 1.0
CE A:LYS215 4.9 9.3 1.0

Magnesium binding site 3 out of 7 in 4c5c

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Magnesium binding site 3 out of 7 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 Adp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1315

b:27.4
occ:1.00
 O A:HOH2273 1.9 26.5 1.0
O A:HOH2322 2.0 20.4 1.0
O A:HOH2323 2.0 23.5 1.0
NE2 A:HIS280 2.2 17.8 1.0
O A:HOH2343 2.2 34.7 1.0
O A:HOH2278 2.3 26.5 1.0
CE1 A:HIS280 3.0 15.1 1.0
CD2 A:HIS280 3.3 16.9 1.0
O A:TYR216 4.1 11.9 1.0
ND1 A:HIS280 4.2 14.2 1.0
CG A:HIS280 4.3 12.8 1.0
OD1 A:ASP219 4.5 32.0 1.0
CA A:LEU217 4.9 13.8 1.0

Magnesium binding site 4 out of 7 in 4c5c

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Magnesium binding site 4 out of 7 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 Adp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1307

b:8.3
occ:1.00
 O3G B:ATP310 2.0 9.6 1.0
O1B B:ATP310 2.0 8.6 1.0
O B:HOH2165 2.1 4.8 1.0
OD1 B:ASN272 2.2 8.6 1.0
OE2 B:GLU270 2.2 6.7 1.0
OE1 B:GLU270 2.2 9.3 1.0
CD B:GLU270 2.5 6.5 1.0
PG B:ATP310 2.9 23.6 1.0
CG B:ASN272 3.2 9.6 1.0
PB B:ATP310 3.2 8.6 1.0
O3B B:ATP310 3.3 10.0 1.0
O2G B:ATP310 3.4 9.5 1.0
ND2 B:ASN272 3.6 11.7 1.0
MG B:MG1308 3.6 9.3 1.0
O B:HOH2105 3.6 2.0 1.0
CA B:GLY149 4.0 9.3 1.0
CG B:GLU270 4.0 8.3 1.0
NZ B:LYS97 4.0 7.2 1.0
O1G B:ATP310 4.1 10.4 1.0
O3A B:ATP310 4.2 8.1 1.0
O B:GLU148 4.2 8.8 1.0
O B:HOH2018 4.2 10.3 1.0
N B:DAL311 4.3 10.1 1.0
O2B B:ATP310 4.3 8.3 1.0
CB B:ASN272 4.5 9.5 1.0
O B:HOH2106 4.6 7.6 1.0
O1A B:ATP310 4.6 7.8 1.0
N B:SER150 4.7 7.8 1.0
CE B:LYS97 4.7 7.9 1.0
OD2 B:ASP257 4.8 9.2 1.0
C B:GLY149 4.9 8.4 1.0
CB B:GLU270 4.9 8.2 1.0
O B:ALA271 5.0 10.8 1.0
C B:GLU148 5.0 8.7 1.0
N B:GLY149 5.0 9.1 1.0

Magnesium binding site 5 out of 7 in 4c5c

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Magnesium binding site 5 out of 7 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 Adp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1308

b:9.3
occ:1.00
 O1A B:ATP310 1.9 7.8 1.0
OE2 B:GLU270 2.1 6.7 1.0
OD2 B:ASP257 2.1 9.2 1.0
O3B B:ATP310 2.1 10.0 1.0
O B:HOH2236 2.1 7.9 1.0
O2G B:ATP310 2.1 9.5 1.0
PG B:ATP310 2.7 23.6 1.0
PA B:ATP310 3.2 9.3 1.0
CD B:GLU270 3.2 6.5 1.0
PB B:ATP310 3.2 8.6 1.0
CG B:ASP257 3.3 9.8 1.0
O3A B:ATP310 3.5 8.1 1.0
MG B:MG1307 3.6 8.3 1.0
O3G B:ATP310 3.6 9.6 1.0
O1B B:ATP310 3.7 8.6 1.0
CG B:GLU270 3.8 8.3 1.0
NZ B:LYS215 3.9 10.9 1.0
O1G B:ATP310 3.9 10.4 1.0
ND2 B:ASN272 4.0 11.7 1.0
O B:HOH2275 4.1 10.9 1.0
CB B:ASP257 4.1 10.8 1.0
NH2 B:ARG255 4.1 11.1 1.0
C5' B:ATP310 4.2 10.2 1.0
O5' B:ATP310 4.2 8.3 1.0
OD1 B:ASP257 4.2 12.1 1.0
OE1 B:GLU270 4.2 9.3 1.0
O3' B:ATP310 4.4 10.1 1.0
O2A B:ATP310 4.4 10.1 1.0
O2B B:ATP310 4.6 8.3 1.0
OD1 B:ASN272 4.6 8.6 1.0
CG B:ASN272 4.8 9.6 1.0
CE B:LYS215 4.9 10.1 1.0
C3' B:ATP310 4.9 10.0 1.0

Magnesium binding site 6 out of 7 in 4c5c

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Magnesium binding site 6 out of 7 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 Adp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1309

b:24.3
occ:1.00
 O B:HOH2241 1.8 22.9 1.0
O B:HOH2286 1.9 17.0 1.0
O B:HOH2238 2.0 23.6 1.0
NE2 B:HIS280 2.1 21.5 1.0
O B:HOH2240 2.3 24.8 1.0
O B:HOH2306 2.3 34.9 1.0
CE1 B:HIS280 3.0 20.8 1.0
CD2 B:HIS280 3.3 20.0 1.0
O B:HOH2287 3.8 25.9 1.0
O B:TYR216 4.1 13.9 1.0
ND1 B:HIS280 4.2 19.6 1.0
OD1 B:ASP219 4.3 32.9 1.0
CG B:HIS280 4.3 15.5 1.0
CA B:LEU217 4.8 17.3 1.0
OG B:SER279 4.9 17.0 1.0
C B:TYR216 5.0 12.8 1.0

Magnesium binding site 7 out of 7 in 4c5c

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Magnesium binding site 7 out of 7 in the The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp 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 7 of The X-Ray Crystal Structure of D-Alanyl-D-Alanine Ligase in Complex with Adp and D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1310

b:38.7
occ:1.00
 O B:HOH2308 2.0 26.7 1.0
O B:HOH2307 2.0 20.0 1.0
O B:HOH2182 2.1 20.3 1.0
O B:HOH2187 2.3 15.2 1.0
O B:HOH2181 2.5 25.6 1.0
O B:HOH2186 2.6 32.6 1.0
OD2 B:ASP165 3.9 19.9 1.0
O B:ASN161 4.4 21.1 1.0
OD1 B:ASP165 4.5 18.7 1.0
CG B:ASP165 4.6 17.6 1.0
CB B:ASN161 4.8 22.4 1.0
C B:ASN161 5.0 19.5 1.0
ND2 B:ASN161 5.0 33.9 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 07:11:38 2025

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