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Cobalt 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:

Sodium (Na) 7 atoms

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt 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 Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 3abr

Go back to Cobalt Binding Sites List in 3abr
Cobalt binding site 1 out of 2 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 Cobalt with other atoms in the Co 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
B:Co601

b:18.2
occ:1.00
CO B:B12601 0.0 18.2 1.0
N21 B:B12601 1.9 18.0 1.0
N23 B:B12601 1.9 17.9 1.0
N22 B:B12601 1.9 17.9 1.0
N24 B:B12601 1.9 18.1 1.0
N3B B:B12601 2.3 17.8 1.0
C19 B:B12601 2.8 18.2 1.0
C1 B:B12601 2.9 18.2 1.0
C14 B:B12601 2.9 18.0 1.0
C9 B:B12601 2.9 17.9 1.0
C4 B:B12601 3.0 18.1 1.0
C11 B:B12601 3.0 18.0 1.0
C6 B:B12601 3.0 17.9 1.0
C16 B:B12601 3.0 18.1 1.0
C9B B:B12601 3.2 17.9 1.0
C2B B:B12601 3.3 18.0 1.0
C10 B:B12601 3.4 17.9 1.0
C5 B:B12601 3.4 17.9 1.0
C15 B:B12601 3.4 18.1 1.0
C20 B:B12601 3.6 18.3 1.0
C4B B:B12601 3.7 18.0 1.0
C18 B:B12601 4.1 18.2 1.0
C2 B:B12601 4.1 18.3 1.0
C13 B:B12601 4.2 17.9 1.0
C3 B:B12601 4.2 18.3 1.0
C17 B:B12601 4.2 18.2 1.0
C8 B:B12601 4.2 17.8 1.0
C12 B:B12601 4.2 17.9 1.0
C7 B:B12601 4.2 18.0 1.0
N1B B:B12601 4.5 17.9 1.0
C42 B:B12601 4.5 17.6 1.0
C8B B:B12601 4.5 18.0 1.0
C26 B:B12601 4.5 18.2 1.0
O39 B:B12601 4.7 18.5 1.0
C38 B:B12601 4.7 18.4 1.0
C35 B:B12601 4.9 17.8 1.0
C53 B:B12601 4.9 18.1 1.0
C46 B:B12601 4.9 18.0 1.0
C48 B:B12601 4.9 18.1 1.0
C30 B:B12601 5.0 18.7 1.0
C54 B:B12601 5.0 18.2 1.0

Cobalt binding site 2 out of 2 in 3abr

Go back to Cobalt Binding Sites List in 3abr
Cobalt binding site 2 out of 2 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 Cobalt with other atoms in the Co 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
D:Co601

b:18.5
occ:1.00
CO D:B12601 0.0 18.5 1.0
N21 D:B12601 1.9 18.3 1.0
N24 D:B12601 1.9 18.3 1.0
N23 D:B12601 1.9 18.4 1.0
N22 D:B12601 1.9 18.5 1.0
N3B D:B12601 2.2 19.0 1.0
C19 D:B12601 2.8 18.4 1.0
C1 D:B12601 2.9 18.5 1.0
C9 D:B12601 2.9 18.5 1.0
C14 D:B12601 2.9 18.5 1.0
C11 D:B12601 2.9 18.5 1.0
C4 D:B12601 3.0 18.5 1.0
C16 D:B12601 3.0 18.3 1.0
C6 D:B12601 3.0 18.4 1.0
C2B D:B12601 3.2 19.1 1.0
C9B D:B12601 3.3 19.2 1.0
C10 D:B12601 3.3 18.5 1.0
C15 D:B12601 3.4 18.4 1.0
C5 D:B12601 3.4 18.4 1.0
C20 D:B12601 3.5 18.5 1.0
C4B D:B12601 3.8 19.2 1.0
C18 D:B12601 4.1 18.5 1.0
C2 D:B12601 4.1 18.6 1.0
C13 D:B12601 4.2 18.6 1.0
C3 D:B12601 4.2 18.6 1.0
C8 D:B12601 4.2 18.5 1.0
C17 D:B12601 4.2 18.4 1.0
C12 D:B12601 4.2 18.5 1.0
C7 D:B12601 4.3 18.5 1.0
N1B D:B12601 4.4 19.0 1.0
C42 D:B12601 4.4 18.4 1.0
C8B D:B12601 4.5 19.1 1.0
C26 D:B12601 4.7 18.5 1.0
O39 D:B12601 4.7 19.1 1.0
C48 D:B12601 4.7 18.7 1.0
C53 D:B12601 4.9 18.4 1.0
C35 D:B12601 4.9 18.5 1.0
C41 D:B12601 4.9 18.4 1.0
C54 D:B12601 4.9 18.3 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: Sun Dec 13 10:39:47 2020

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