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Sodium in PDB 3abo: Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine

Enzymatic activity of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine

All present enzymatic activity of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine:
4.3.1.7;

Protein crystallography data

The structure of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine, PDB code: 3abo was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.51 / 2.10
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 242.760, 242.760, 76.460, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 26.6

Other elements in 3abo:

The structure of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine (pdb code 3abo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine, PDB code: 3abo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3abo

Go back to Sodium Binding Sites List in 3abo
Sodium binding site 1 out of 2 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1001

b:45.0
occ:1.00
 OD1 C:ASP338 2.5 36.8 1.0
O A:HOH684 2.6 16.7 1.0
OD1 C:ASP372 2.8 31.1 1.0
O A:HOH571 3.5 11.9 1.0
CG C:ASP372 3.6 34.1 1.0
CG C:ASP338 3.7 36.4 1.0
OD2 C:ASP372 3.8 32.2 1.0
N C:LEU375 3.9 28.6 1.0
CB C:ASN374 3.9 28.3 1.0
CG A:ARG339 3.9 43.6 1.0
O A:HOH640 4.0 13.1 1.0
NE A:ARG339 4.1 52.1 1.0
OD2 C:ASP338 4.2 41.8 1.0
CD A:ARG339 4.2 51.4 1.0
O C:HOH567 4.3 16.5 1.0
C C:ASN374 4.3 27.4 1.0
CB C:LEU375 4.5 30.9 1.0
CA C:LEU375 4.5 29.4 1.0
CB A:ARG339 4.6 35.6 1.0
CA C:ASN374 4.6 28.2 1.0
CB C:ASP338 4.8 31.6 1.0
N C:ASP372 4.9 36.2 1.0
O C:ASN374 5.0 25.3 1.0

Sodium binding site 2 out of 2 in 3abo

Go back to Sodium Binding Sites List in 3abo
Sodium binding site 2 out of 2 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl and Ethanolamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1002

b:94.5
occ:1.00
 OE2 C:GLU179 2.7 44.9 1.0
O D:ARG77 2.8 39.0 1.0
OG1 D:THR80 3.0 37.5 1.0
O C:HOH487 3.8 15.5 1.0
CE1 C:HIS410 3.9 26.1 1.0
CD C:GLU179 3.9 38.7 1.0
C D:ARG77 4.0 39.9 1.0
N D:THR80 4.1 36.7 1.0
CB D:THR80 4.1 36.3 1.0
CA D:VAL78 4.1 37.8 1.0
CG C:LEU396 4.1 29.9 1.0
C D:VAL78 4.2 38.2 1.0
N D:CYS79 4.2 38.5 1.0
CD2 C:LEU396 4.2 32.2 1.0
N C:LEU396 4.3 30.0 1.0
CG2 D:THR80 4.4 44.0 1.0
CA C:PRO395 4.4 30.6 1.0
CB C:PRO395 4.5 32.5 1.0
N D:VAL78 4.5 39.8 1.0
O C:HOH523 4.6 9.3 1.0
C C:PRO395 4.6 31.5 1.0
CA D:THR80 4.6 37.2 1.0
CG C:GLU179 4.6 38.2 1.0
ND1 C:HIS410 4.7 27.5 1.0
OE1 C:GLU179 4.7 46.2 1.0
O D:VAL78 4.7 37.2 1.0
O D:HOH296 4.8 10.2 1.0
NE2 C:HIS410 4.9 25.2 1.0
O D:GLY81 4.9 26.4 1.0
N D:GLY81 4.9 31.5 1.0
CD1 C:LEU396 4.9 33.6 1.0

Reference:

N.Shibata, H.Tamagaki, N.Hieda, K.Akita, H.Komori, Y.Shomura, S.Terawaki, K.Mori, N.Yasuoka, Y.Higuchi, T.Toraya. Crystal Structures of Ethanolamine Ammonia-Lyase Complexed with Coenzyme B12 Analogs and Substrates. J.Biol.Chem. V. 285 26484 2010.
ISSN: ISSN 0021-9258
PubMed: 20519496
DOI: 10.1074/JBC.M110.125112
Page generated: Mon Oct 7 05:46:24 2024

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