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Sodium in PDB 3abr: Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)

Enzymatic activity of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)

All present enzymatic activity of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form):
4.3.1.7;

Protein crystallography data

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

Resolution Low / High (Å) 42.29 / 2.10
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 244.120, 244.120, 77.150, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 28.5

Other elements in 3abr:

The structure of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form) 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 (Substrate-Free Form) (pdb code 3abr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form), PDB code: 3abr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3abr

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Sodium binding site 1 out of 7 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)


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 (Substrate-Free Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3001

b:20.7
occ:1.00
 OH A:TYR334 2.2 35.9 1.0
CZ A:TYR334 3.3 34.6 1.0
CG B:PRO137 3.5 37.5 1.0
CA A:SER295 3.6 34.8 1.0
CE2 A:TYR334 3.7 34.4 1.0
CB B:PRO137 3.9 38.0 1.0
O A:LEU294 4.0 35.5 1.0
N A:SER295 4.0 33.4 1.0
NH1 B:ARG141 4.1 36.1 1.0
C A:LEU294 4.2 34.0 1.0
CD2 A:LEU33 4.2 39.6 1.0
NH2 B:ARG141 4.3 35.1 1.0
O A:HOH518 4.3 4.6 1.0
CZ B:ARG141 4.3 36.3 1.0
CB A:SER295 4.4 33.9 1.0
CG A:LEU294 4.4 34.2 1.0
O A:SER295 4.5 37.2 1.0
CE1 A:TYR334 4.5 33.6 1.0
C A:SER295 4.5 35.7 1.0
O A:HOH834 4.6 17.0 1.0
CD1 A:LEU294 4.7 35.6 1.0
OG A:SER295 4.7 35.2 1.0
CD B:PRO137 4.9 38.5 1.0
N B:ASP138 4.9 40.7 1.0

Sodium binding site 2 out of 7 in 3abr

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Sodium binding site 2 out of 7 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)


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 (Substrate-Free Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3004

b:19.8
occ:1.00
 O A:ALA239 2.4 32.4 1.0
O A:ILE235 2.7 34.2 1.0
O A:HOH736 3.1 14.9 1.0
C A:ALA239 3.4 33.2 1.0
C A:GLY238 3.6 36.5 1.0
C A:ILE235 3.6 33.7 1.0
CG2 A:ILE235 3.7 30.7 1.0
N A:ALA239 3.7 35.7 1.0
O A:GLY238 3.8 36.7 1.0
CA A:ILE235 3.8 32.8 1.0
CA A:GLY238 3.9 37.4 1.0
CD1 A:PHE275 4.1 32.1 1.0
CA A:ALA239 4.2 34.8 1.0
O A:HOH484 4.2 11.8 1.0
N A:GLY241 4.3 29.4 1.0
CB A:PHE275 4.3 29.6 1.0
CB A:ILE235 4.3 31.1 1.0
N A:GLY238 4.3 37.5 1.0
N A:PRO240 4.3 32.9 1.0
CA A:PRO240 4.4 31.6 1.0
CG A:PHE275 4.5 30.8 1.0
O A:PHE275 4.5 29.2 1.0
C A:PRO240 4.7 30.2 1.0
CG1 A:ILE235 4.7 30.3 1.0
N A:ARG236 4.9 34.1 1.0

Sodium binding site 3 out of 7 in 3abr

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Sodium binding site 3 out of 7 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3005

b:22.3
occ:1.00
 O B:HOH348 2.4 21.4 1.0
O B:VAL75 2.5 38.6 1.0
O A:HOH984 3.1 6.7 1.0
OD1 A:ASP398 3.4 38.6 1.0
CG1 B:VAL75 3.6 41.0 1.0
C B:VAL75 3.6 39.0 1.0
CG2 A:ILE400 3.8 39.4 1.0
NE B:ARG77 3.9 35.2 1.0
CG B:ARG77 3.9 35.1 1.0
CZ B:ARG77 4.3 36.4 1.0
NH2 B:ARG77 4.3 37.0 1.0
CA B:ALA76 4.3 35.9 1.0
N B:ALA76 4.4 37.6 1.0
O A:HOH460 4.5 8.3 1.0
CG A:ASP398 4.5 37.1 1.0
CD B:ARG77 4.5 34.4 1.0
C B:ALA76 4.5 36.0 1.0
N B:ARG77 4.5 34.8 1.0
CA B:VAL75 4.7 41.0 1.0
CB B:VAL75 4.7 41.9 1.0
NH2 B:ARG94 4.9 38.3 1.0

Sodium binding site 4 out of 7 in 3abr

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Sodium binding site 4 out of 7 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3002

b:20.7
occ:1.00
 O B:LEU96 2.3 36.7 1.0
O B:HOH913 2.8 16.3 1.0
O C:HOH466 3.1 26.3 1.0
C B:LEU96 3.2 36.4 1.0
N B:SER100 3.5 39.2 1.0
CA B:LEU96 3.6 34.7 1.0
CG2 C:VAL45 3.6 40.1 1.0
CB B:SER100 3.8 41.8 1.0
CB B:HIS99 3.9 35.3 1.0
CB B:LEU96 3.9 34.7 1.0
CA B:SER100 3.9 40.8 1.0
OG C:SER41 4.1 41.7 1.0
C B:HIS99 4.2 38.1 1.0
CG B:LEU96 4.2 33.6 1.0
ND1 B:HIS99 4.3 34.3 1.0
N B:ALA97 4.4 37.5 1.0
OG B:SER100 4.4 42.6 1.0
CA B:HIS99 4.4 36.8 1.0
O A:HOH567 4.5 11.1 1.0
CG B:HIS99 4.6 34.7 1.0
CD1 B:LEU96 4.7 32.1 1.0
N B:HIS99 4.7 37.3 1.0
O C:SER41 4.9 42.3 1.0
CA B:ALA97 4.9 39.4 1.0
CB C:SER41 4.9 43.6 1.0
O B:ALA97 4.9 40.2 1.0

Sodium binding site 5 out of 7 in 3abr

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Sodium binding site 5 out of 7 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3007

b:24.0
occ:1.00
 OD1 C:ASP69 2.2 45.9 1.0
CG C:ASP69 3.5 45.1 1.0
O C:GLU68 4.1 42.2 1.0
OD2 C:ASP69 4.2 46.1 1.0
C C:GLU68 4.3 41.9 1.0
CB C:GLU68 4.4 44.0 1.0
CA C:ASP69 4.4 41.9 1.0
CB C:ASP69 4.5 43.1 1.0
N C:ASP69 4.6 41.6 1.0
O C:HOH626 4.9 16.8 1.0

Sodium binding site 6 out of 7 in 3abr

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Sodium binding site 6 out of 7 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3003

b:21.5
occ:1.00
 O D:GLU228 2.2 44.5 1.0
O D:SER237 2.9 49.0 1.0
CB D:SER170 3.1 50.5 1.0
C D:GLU228 3.2 43.8 1.0
OG D:SER170 3.5 50.9 1.0
N D:GLU228 3.5 47.6 1.0
O D:SER235 3.6 51.5 1.0
CG D:GLU228 3.6 44.1 1.0
N D:SER237 3.8 49.3 1.0
O D:ARG229 3.8 39.1 1.0
C D:SER237 3.8 49.7 1.0
CA D:GLU228 3.8 45.1 1.0
C D:SER235 4.0 50.1 1.0
C D:ARG229 4.0 39.9 1.0
OE1 D:GLN234 4.0 45.9 1.0
CA D:SER237 4.0 48.5 1.0
CB D:SER237 4.1 45.8 1.0
CB D:ALA173 4.1 54.6 1.0
CA D:PRO230 4.2 40.2 1.0
N D:PRO230 4.2 40.3 1.0
CB D:GLU228 4.3 44.0 1.0
C D:GLY227 4.3 49.6 1.0
N D:ARG229 4.3 41.9 1.0
CA D:SER235 4.3 48.1 1.0
ND2 C:ASN403 4.4 37.7 1.0
C D:GLU236 4.6 51.8 1.0
CA D:GLY227 4.6 52.2 1.0
CA D:SER170 4.6 52.6 1.0
CA D:ARG229 4.6 40.6 1.0
N D:GLU236 4.7 50.3 1.0
CD D:GLU228 4.9 44.1 1.0
N D:SER170 5.0 52.1 1.0
CB D:PRO230 5.0 41.1 1.0

Sodium binding site 7 out of 7 in 3abr

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Sodium binding site 7 out of 7 in the Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Ethanolamine Ammonia-Lyase From Escherichia Coli Complexed with Cn-Cbl (Substrate-Free Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3006

b:20.8
occ:1.00
 O D:SER260 2.1 48.5 1.0
C D:SER260 3.3 47.4 1.0
O D:ASN261 3.4 49.5 1.0
O C:HOH549 3.4 12.5 1.0
C D:ASN261 3.6 49.1 1.0
CB D:ASN261 3.6 44.9 1.0
CB D:THR267 3.7 56.6 1.0
CG2 D:THR267 3.9 58.0 1.0
CA D:ASN261 3.9 46.5 1.0
CG1 C:VAL195 4.0 39.8 1.0
N D:ASN261 4.0 46.5 1.0
O D:HOH298 4.0 14.6 1.0
N D:SER260 4.2 48.6 1.0
N D:ILE262 4.2 50.9 1.0
CA D:SER260 4.3 47.4 1.0
N D:THR267 4.4 53.9 1.0
CG1 D:ILE259 4.5 54.6 1.0
OG1 D:THR267 4.6 58.3 1.0
CG D:ASN261 4.7 42.5 1.0
CA D:THR267 4.7 56.6 1.0
OD1 D:ASN261 4.7 42.0 1.0
OG D:SER260 4.7 43.7 1.0
C D:ILE259 4.8 50.9 1.0
CG1 D:ILE262 4.8 55.7 1.0
CA D:ILE262 4.8 53.6 1.0
O D:HOH799 4.9 21.0 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 05:46:23 2024

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