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Sodium in PDB 4r7u: Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin

Enzymatic activity of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin

All present enzymatic activity of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin:
2.5.1.7;

Protein crystallography data

The structure of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin, PDB code: 4r7u was solved by B.Nocek, N.Maltseva, W.Anderson, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.64 / 2.45
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 204.283, 204.283, 118.878, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 23.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin (pdb code 4r7u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin, PDB code: 4r7u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4r7u

Go back to Sodium Binding Sites List in 4r7u
Sodium binding site 1 out of 5 in the Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:28.0
occ:1.00
 O A:ASN315 2.2 24.7 1.0
O A:ALA318 2.2 26.7 1.0
OD1 A:ASP357 2.3 34.6 1.0
O A:GLY356 2.4 28.0 1.0
O A:GLY321 2.5 27.6 1.0
C A:GLY356 3.2 29.8 1.0
CG A:ASP357 3.4 35.5 1.0
C A:ASN315 3.4 24.6 1.0
C A:ALA318 3.4 27.2 1.0
C A:GLY321 3.5 28.8 1.0
CA A:ASP357 3.5 31.6 1.0
N A:ASP357 3.7 31.3 1.0
N A:GLY321 3.9 29.7 1.0
CA A:GLY321 3.9 29.5 1.0
CB A:ASP357 3.9 33.1 1.0
O A:CYS355 4.0 27.4 1.0
N A:ALA318 4.1 27.7 1.0
O A:MET316 4.1 25.8 1.0
C A:MET316 4.1 26.5 1.0
CA A:MET316 4.1 26.2 1.0
CB A:CYS355 4.2 29.6 1.0
N A:MET316 4.2 25.2 1.0
CA A:ALA318 4.2 27.0 1.0
C A:CYS355 4.2 28.7 1.0
CA A:GLY356 4.3 29.6 1.0
CA A:ASN315 4.4 23.3 1.0
OD2 A:ASP357 4.4 36.4 1.0
N A:LYS319 4.4 37.0 1.0
N A:GLY356 4.5 29.2 1.0
CB A:ALA292 4.5 28.0 1.0
CB A:ALA318 4.6 26.5 1.0
CA A:LYS319 4.6 38.1 1.0
N A:MET317 4.6 27.0 1.0
N A:GLY322 4.7 28.8 1.0
CB A:ASN315 4.8 22.6 1.0
C A:LYS319 4.8 34.6 1.0
N A:GLY320 4.8 33.4 1.0
C A:MET317 4.9 27.7 1.0
C A:ASP357 4.9 31.1 1.0
CA A:CYS355 4.9 28.6 1.0
C A:GLY320 5.0 30.4 1.0

Sodium binding site 2 out of 5 in 4r7u

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Sodium binding site 2 out of 5 in the Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:29.2
occ:1.00
 O B:GLY356 2.2 30.7 1.0
O B:ASN315 2.2 24.8 1.0
O B:GLY321 2.4 26.9 1.0
O B:ALA318 2.4 31.2 1.0
OD1 B:ASP357 2.6 37.3 1.0
C B:GLY356 3.1 31.9 1.0
C B:ASN315 3.3 24.7 1.0
C B:GLY321 3.4 30.1 1.0
CG B:ASP357 3.6 38.1 1.0
C B:ALA318 3.6 33.0 1.0
CA B:ASP357 3.7 35.1 1.0
N B:ASP357 3.7 33.8 1.0
CA B:GLY321 3.8 31.1 1.0
N B:GLY321 3.9 32.5 1.0
O B:MET316 4.0 27.1 1.0
C B:MET316 4.0 26.3 1.0
CA B:MET316 4.0 25.2 1.0
N B:MET316 4.1 23.7 1.0
CB B:ASP357 4.1 36.4 1.0
O B:CYS355 4.1 27.8 1.0
CA B:GLY356 4.2 31.9 1.0
C B:CYS355 4.3 28.6 1.0
N B:ALA318 4.3 32.4 1.0
CB B:CYS355 4.3 30.3 1.0
CA B:ASN315 4.3 25.1 1.0
CA B:ALA318 4.4 32.0 1.0
N B:GLY356 4.4 30.5 1.0
CB B:ALA292 4.5 34.1 1.0
N B:LYS319 4.5 36.2 1.0
OD2 B:ASP357 4.5 41.1 1.0
N B:GLY322 4.6 29.4 1.0
CB B:ALA318 4.7 31.0 1.0
CB B:ASN315 4.7 25.5 1.0
N B:MET317 4.7 27.4 1.0
CA B:LYS319 4.7 39.0 1.0
N B:GLY320 4.9 33.9 1.0
C B:LYS319 4.9 36.8 1.0
C B:MET317 4.9 30.9 1.0
C B:GLY320 4.9 33.4 1.0
C B:ASP357 5.0 36.0 1.0

Sodium binding site 3 out of 5 in 4r7u

Go back to Sodium Binding Sites List in 4r7u
Sodium binding site 3 out of 5 in the Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:19.0
occ:1.00
 O C:GLY321 2.2 24.9 1.0
O C:ASN315 2.3 25.4 1.0
OD1 C:ASP357 2.4 29.2 1.0
O C:GLY356 2.5 27.3 1.0
O C:ALA318 2.5 36.7 1.0
C C:GLY321 3.2 27.3 1.0
C C:GLY356 3.3 27.9 1.0
CG C:ASP357 3.4 29.8 1.0
N C:GLY321 3.5 30.8 1.0
C C:ALA318 3.5 34.7 1.0
C C:ASN315 3.5 24.8 1.0
CA C:GLY321 3.5 29.1 1.0
CA C:ASP357 3.7 28.9 1.0
N C:ASP357 3.8 28.5 1.0
CB C:ASP357 4.0 29.2 1.0
N C:ALA318 4.2 31.8 1.0
O C:CYS355 4.2 27.9 1.0
CB C:ALA292 4.2 32.3 1.0
CA C:ALA318 4.3 32.6 1.0
O C:MET316 4.3 30.7 1.0
CA C:GLY356 4.4 28.1 1.0
OD2 C:ASP357 4.4 30.0 1.0
N C:LYS319 4.4 38.0 1.0
CA C:MET316 4.4 27.7 1.0
C C:MET316 4.4 28.4 1.0
CB C:CYS355 4.4 29.5 1.0
N C:GLY322 4.4 26.9 1.0
N C:MET316 4.4 25.6 1.0
CA C:ASN315 4.4 24.8 1.0
CB C:ALA318 4.5 30.9 1.0
C C:CYS355 4.5 27.6 1.0
CA C:LYS319 4.5 42.8 1.0
N C:GLY320 4.5 37.0 1.0
C C:LYS319 4.6 41.4 1.0
C C:GLY320 4.6 33.2 1.0
N C:GLY356 4.6 27.4 1.0
CB C:ASN315 4.8 24.9 1.0
CA C:GLY322 5.0 26.5 1.0

Sodium binding site 4 out of 5 in 4r7u

Go back to Sodium Binding Sites List in 4r7u
Sodium binding site 4 out of 5 in the Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:54.2
occ:1.00
 O D:GLU330 2.6 36.5 1.0
O D:HOH669 2.6 21.4 1.0
O C:GLU330 2.9 31.2 1.0
O D:HOH668 3.0 30.8 1.0
O C:HOH658 3.1 24.9 1.0
O D:HOH670 3.4 37.6 1.0
C D:GLU330 3.7 34.9 1.0
O D:HOH683 3.8 24.2 1.0
C C:GLU330 3.8 33.6 1.0
CB C:GLU330 4.1 38.5 1.0
CB D:GLU330 4.4 36.2 1.0
CA C:GLU330 4.4 35.5 1.0
CA D:GLU330 4.5 34.3 1.0
N D:ASN331 4.6 34.9 1.0
CA D:ASN331 4.7 35.5 1.0
N C:ASN331 4.7 33.7 1.0
CG D:GLU330 4.9 37.8 1.0
CA C:ASN331 4.9 34.8 1.0
OD1 D:ASN331 4.9 38.1 1.0
CB C:ASN331 5.0 36.7 1.0
CB D:ASN331 5.0 38.1 1.0

Sodium binding site 5 out of 5 in 4r7u

Go back to Sodium Binding Sites List in 4r7u
Sodium binding site 5 out of 5 in the Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:24.2
occ:1.00
 O D:ASN315 2.3 27.1 1.0
O D:GLY356 2.3 25.4 1.0
O D:GLY321 2.3 23.2 1.0
OD1 D:ASP357 2.6 30.3 1.0
O D:ALA318 2.6 29.6 1.0
C D:GLY356 3.2 26.6 1.0
C D:GLY321 3.2 24.2 1.0
CA D:GLY321 3.4 25.1 1.0
C D:ASN315 3.4 26.7 1.0
CG D:ASP357 3.5 30.4 1.0
N D:GLY321 3.5 25.1 1.0
C D:ALA318 3.7 30.0 1.0
CA D:ASP357 3.7 29.2 1.0
N D:ASP357 3.8 28.4 1.0
O D:CYS355 4.0 26.9 1.0
N D:ALA318 4.1 29.8 1.0
CB D:ASP357 4.1 30.7 1.0
C D:MET316 4.2 27.2 1.0
CA D:MET316 4.2 27.2 1.0
O D:MET316 4.2 26.7 1.0
CB D:CYS355 4.2 26.8 1.0
C D:CYS355 4.2 26.2 1.0
CA D:GLY356 4.2 26.2 1.0
N D:MET316 4.3 26.2 1.0
CA D:ALA318 4.4 30.1 1.0
CA D:ASN315 4.4 27.2 1.0
CB D:ALA292 4.4 29.0 1.0
OD2 D:ASP357 4.4 31.7 1.0
N D:GLY322 4.5 24.4 1.0
N D:GLY356 4.5 26.1 1.0
CB D:ALA318 4.6 30.0 1.0
CB D:ASN315 4.7 27.8 1.0
N D:MET317 4.7 27.8 1.0
N D:LYS319 4.7 30.6 1.0
C D:GLY320 4.7 26.0 1.0
N D:GLY320 4.9 27.3 1.0
CA D:CYS355 4.9 26.4 1.0
C D:LYS319 4.9 29.0 1.0
CA D:LYS319 5.0 31.7 1.0
C D:MET317 5.0 30.0 1.0

Reference:

B.Nocek, N.Maltseva, W.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Vibrio Cholerae in Complex with Substrate Udp-N-Acetylglucosamine and the Drug Fosfomycin To Be Published.
Page generated: Mon Oct 7 18:13:46 2024

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