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Sodium in PDB 1f6d: The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli.

Enzymatic activity of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli.

All present enzymatic activity of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli.:
5.1.3.14;

Protein crystallography data

The structure of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli., PDB code: 1f6d was solved by R.E.Campbell, S.C.Mosimann, M.E.Tanner, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.32 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.008, 94.541, 100.970, 90.00, 109.13, 90.00
R / Rfree (%) 19.8 / 27.1

Other elements in 1f6d:

The structure of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli. also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli. (pdb code 1f6d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli., PDB code: 1f6d:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1f6d

Go back to Sodium Binding Sites List in 1f6d
Sodium binding site 1 out of 4 in the The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1378

b:21.6
occ:1.00
 O A:HOH1389 2.2 12.9 1.0
O A:PRO298 2.4 14.4 1.0
O A:HOH1412 2.5 20.8 1.0
O A:ALA352 2.5 19.2 1.0
O A:SER350 2.9 15.8 1.0
C A:PRO298 3.6 14.9 1.0
C A:ALA352 3.6 18.6 1.0
CL A:CL1379 3.8 28.8 1.0
C A:SER350 4.0 17.2 1.0
CA A:GLY301 4.0 18.0 1.0
CA A:PRO298 4.2 14.6 1.0
N A:GLY301 4.3 18.2 1.0
N A:ALA352 4.3 18.8 1.0
N A:ASN354 4.4 14.4 1.0
C A:ARG351 4.4 19.0 1.0
O A:MSE349 4.4 18.5 1.0
CB A:PRO298 4.4 14.0 1.0
CA A:HIS353 4.5 16.6 1.0
N A:HIS353 4.5 16.9 1.0
O A:HOH1411 4.5 20.4 1.0
C A:HIS353 4.6 15.0 1.0
CA A:ALA352 4.6 18.6 1.0
N A:SER299 4.6 14.3 1.0
O A:ARG351 4.7 17.6 1.0
CG2 A:THR321 4.8 20.3 1.0
CA A:SER350 4.8 17.4 1.0
N A:ARG351 4.8 18.9 1.0
CA A:SER299 4.8 13.7 1.0
CA A:ARG351 4.8 19.5 1.0
C A:GLY301 4.9 20.7 1.0

Sodium binding site 2 out of 4 in 1f6d

Go back to Sodium Binding Sites List in 1f6d
Sodium binding site 2 out of 4 in the The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2378

b:25.2
occ:1.00
 O B:ALA352 2.2 18.3 1.0
O B:HOH2402 2.4 18.7 1.0
O B:PRO298 2.6 19.5 1.0
O B:HOH2487 2.6 31.8 1.0
O B:SER350 2.8 22.6 1.0
C B:ALA352 3.4 19.7 1.0
O B:HOH2458 3.5 27.5 1.0
C B:PRO298 3.6 19.2 1.0
C B:SER350 3.7 22.1 1.0
CA B:PRO298 3.9 19.5 1.0
N B:ALA352 3.9 21.7 1.0
CA B:GLY301 4.0 14.4 1.0
C B:ARG351 4.1 22.4 1.0
O B:HOH2548 4.1 41.4 1.0
CB B:PRO298 4.1 19.2 1.0
CA B:ALA352 4.2 19.9 1.0
O B:HOH2513 4.2 34.2 1.0
O B:MSE349 4.3 24.1 1.0
N B:GLY301 4.3 16.4 1.0
O B:ARG351 4.4 22.0 1.0
N B:HIS353 4.5 19.0 1.0
CA B:SER350 4.5 22.0 1.0
N B:ARG351 4.5 22.4 1.0
CA B:ARG351 4.5 23.1 1.0
CA B:HIS353 4.6 23.2 1.0
CG2 B:THR321 4.7 16.1 1.0
N B:ASN354 4.8 22.1 1.0
N B:SER299 4.8 19.3 1.0
CB B:ALA352 4.8 18.0 1.0
C B:HIS353 4.9 22.6 1.0
C B:GLY301 5.0 16.0 1.0

Sodium binding site 3 out of 4 in 1f6d

Go back to Sodium Binding Sites List in 1f6d
Sodium binding site 3 out of 4 in the The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3378

b:36.9
occ:1.00
 O C:ALA352 2.7 21.3 1.0
O C:SER350 2.9 23.6 1.0
O C:PRO298 3.0 23.8 1.0
O C:MSE349 3.3 22.4 1.0
O C:HOH3407 3.3 21.8 1.0
C C:SER350 3.4 22.3 1.0
CA C:PRO298 3.6 23.3 1.0
C C:ALA352 3.7 22.8 1.0
C C:PRO298 3.7 23.3 1.0
CB C:PRO298 3.8 22.3 1.0
N C:ALA352 3.9 23.9 1.0
CA C:GLY301 4.0 21.8 1.0
CA C:SER350 4.0 20.6 1.0
C C:ARG351 4.2 24.5 1.0
N C:ARG351 4.2 23.1 1.0
CA C:ALA352 4.2 22.9 1.0
C C:MSE349 4.3 20.9 1.0
CG2 C:THR321 4.4 20.8 1.0
CB C:ALA352 4.4 22.6 1.0
C C:GLY301 4.5 22.4 1.0
N C:GLY301 4.5 24.9 1.0
CA C:ARG351 4.5 24.7 1.0
N C:SER350 4.6 19.8 1.0
CB C:THR321 4.7 21.9 1.0
O C:ARG351 4.8 24.0 1.0
N C:LYS302 4.8 20.3 1.0
N C:HIS353 4.8 24.7 1.0
N C:PRO298 5.0 22.3 1.0

Sodium binding site 4 out of 4 in 1f6d

Go back to Sodium Binding Sites List in 1f6d
Sodium binding site 4 out of 4 in the The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Udp-N-Acetylglucosamine 2-Epimerase From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4378

b:17.1
occ:1.00
 O D:HOH4386 2.3 13.5 1.0
O D:HOH4418 2.5 23.9 1.0
O D:PRO298 2.6 14.8 1.0
O D:SER350 2.6 14.2 1.0
O D:ALA352 2.9 12.2 1.0
CA D:GLY301 3.5 17.7 1.0
C D:PRO298 3.5 17.1 1.0
C D:SER350 3.6 14.7 1.0
O D:MSE349 3.8 17.6 1.0
N D:GLY301 3.9 17.3 1.0
CA D:PRO298 3.9 18.5 1.0
CB D:PRO298 4.0 19.0 1.0
C D:GLY301 4.1 18.3 1.0
CA D:SER350 4.1 13.3 1.0
C D:ALA352 4.1 13.0 1.0
N D:ALA352 4.4 14.9 1.0
N D:LYS302 4.5 16.9 1.0
N D:ARG351 4.6 15.9 1.0
CG2 D:THR321 4.7 20.7 1.0
C D:ARG351 4.7 16.3 1.0
O D:GLY301 4.7 19.8 1.0
C D:MSE349 4.8 17.1 1.0
N D:SER299 4.8 16.3 1.0
CL D:CL4379 4.8 28.2 1.0
CA D:ALA352 4.8 12.8 1.0
CA D:ARG351 4.9 16.8 1.0
N D:SER350 4.9 14.3 1.0

Reference:

R.E.Campbell, S.C.Mosimann, M.E.Tanner, N.C.Strynadka. The Structure of Udp-N-Acetylglucosamine 2-Epimerase Reveals Homology to Phosphoglycosyl Transferases. Biochemistry V. 39 14993 2000.
ISSN: ISSN 0006-2960
PubMed: 11106477
DOI: 10.1021/BI001627X
Page generated: Sun Aug 17 05:00:02 2025

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