Atomistry » Sodium » PDB 3a07-3ahi » 3abr
Atomistry »
  Sodium »
    PDB 3a07-3ahi »
      3abr »

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

Go back to Sodium Binding Sites List in 3abr
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

Go back to Sodium Binding Sites List in 3abr
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

Go back to Sodium Binding Sites List in 3abr
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

Go back to Sodium Binding Sites List in 3abr
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

Go back to Sodium Binding Sites List in 3abr
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

Go back to Sodium Binding Sites List in 3abr
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

Go back to Sodium Binding Sites List in 3abr
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy