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Cobalt in PDB 4hut: Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp

Enzymatic activity of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp

All present enzymatic activity of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp:
2.5.1.17;

Protein crystallography data

The structure of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp, PDB code: 4hut was solved by T.C.Moore, S.A.Newmister, I.Rayment, J.C.Escalante-Semerena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.862, 74.223, 92.396, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.2

Other elements in 4hut:

The structure of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp (pdb code 4hut). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp, PDB code: 4hut:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 4hut

Go back to Cobalt Binding Sites List in 4hut
Cobalt binding site 1 out of 2 in the Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co203

b:34.8
occ:1.00
 CO A:B12203 0.0 34.8 1.0
N21 A:B12203 1.9 34.6 1.0
N24 A:B12203 1.9 32.4 1.0
N22 A:B12203 1.9 35.4 1.0
N23 A:B12203 1.9 32.6 1.0
N3B A:B12203 2.3 51.9 1.0
C19 A:B12203 2.8 35.5 1.0
C1 A:B12203 2.9 34.2 1.0
C9 A:B12203 2.9 38.7 1.0
C11 A:B12203 2.9 32.6 1.0
C4 A:B12203 2.9 37.8 1.0
C6 A:B12203 2.9 39.0 1.0
C14 A:B12203 3.0 34.1 1.0
C16 A:B12203 3.0 34.1 1.0
C2B A:B12203 3.1 50.9 1.0
C10 A:B12203 3.3 39.3 1.0
C5 A:B12203 3.3 32.8 1.0
C20 A:B12203 3.4 39.9 1.0
C5' A:ATP202 3.4 28.1 1.0
C15 A:B12203 3.4 34.2 1.0
C4' A:ATP202 3.5 26.6 1.0
C9B A:B12203 3.5 52.5 1.0
O4' A:ATP202 3.9 30.0 1.0
C4B A:B12203 4.1 48.7 1.0
C18 A:B12203 4.1 35.5 1.0
C2 A:B12203 4.2 32.5 1.0
C7 A:B12203 4.2 42.7 1.0
C3 A:B12203 4.2 33.1 1.0
C8 A:B12203 4.2 37.6 1.0
C12 A:B12203 4.3 33.5 1.0
C17 A:B12203 4.3 35.1 1.0
C13 A:B12203 4.3 33.5 1.0
N1B A:B12203 4.4 56.1 1.0
C8B A:B12203 4.6 56.0 1.0
C26 A:B12203 4.7 29.2 1.0
C37 A:B12203 4.7 37.0 1.0
C41 A:B12203 4.8 49.3 1.0
C3' A:ATP202 4.8 27.9 1.0
O5' A:ATP202 4.8 29.7 1.0
C35 A:B12203 4.8 34.6 1.0
C47 A:B12203 4.9 31.0 1.0
C53 A:B12203 4.9 35.1 1.0
C30 A:B12203 5.0 37.0 1.0

Cobalt binding site 2 out of 2 in 4hut

Go back to Cobalt Binding Sites List in 4hut
Cobalt binding site 2 out of 2 in the Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co203

b:29.1
occ:1.00
 CO B:B12203 0.0 29.1 1.0
N21 B:B12203 1.9 26.5 1.0
N24 B:B12203 1.9 27.0 1.0
N22 B:B12203 1.9 26.8 1.0
N23 B:B12203 1.9 23.9 1.0
C1 B:B12203 2.8 27.4 1.0
C19 B:B12203 2.8 25.2 1.0
C11 B:B12203 2.8 25.5 1.0
C4 B:B12203 2.9 27.6 1.0
C9 B:B12203 2.9 23.8 1.0
C6 B:B12203 2.9 24.9 1.0
C16 B:B12203 2.9 25.8 1.0
C14 B:B12203 2.9 27.0 1.0
C5' B:ATP202 3.0 38.8 1.0
C4' B:ATP202 3.1 32.4 1.0
C10 B:B12203 3.2 22.6 1.0
C5 B:B12203 3.3 28.6 1.0
C20 B:B12203 3.3 27.5 1.0
C15 B:B12203 3.4 24.9 1.0
CE2 B:PHE91 3.5 28.4 1.0
CZ B:PHE91 3.7 28.6 1.0
O4' B:ATP202 3.8 31.9 1.0
C18 B:B12203 4.1 28.2 1.0
C2 B:B12203 4.1 26.4 1.0
C3 B:B12203 4.2 25.3 1.0
C12 B:B12203 4.2 27.9 1.0
C17 B:B12203 4.2 26.6 1.0
C8 B:B12203 4.2 25.1 1.0
C7 B:B12203 4.2 27.9 1.0
C13 B:B12203 4.3 23.4 1.0
C3' B:ATP202 4.5 34.4 1.0
O5' B:ATP202 4.5 35.9 1.0
C26 B:B12203 4.6 23.3 1.0
C47 B:B12203 4.6 27.1 1.0
C37 B:B12203 4.6 24.5 1.0
CD2 B:PHE91 4.7 30.3 1.0
C35 B:B12203 4.7 30.9 1.0
C48 B:B12203 4.8 27.6 1.0
C54 B:B12203 4.8 28.2 1.0
C53 B:B12203 4.9 26.1 1.0
C30 B:B12203 4.9 28.8 1.0
C41 B:B12203 4.9 25.6 1.0
O3' B:ATP202 4.9 34.5 1.0

Reference:

T.C.Moore, S.A.Newmister, I.Rayment, J.C.Escalante-Semerena. Structural Insights Into the Mechanism of Four-Coordinate Cob(II)Alamin Formation in the Active Site of the Salmonella Enterica Atp:Co(I)Rrinoid Adenosyltransferase Enzyme: Critical Role of Residues PHE91 and TRP93. Biochemistry V. 51 9647 2012.
ISSN: ISSN 0006-2960
PubMed: 23148601
DOI: 10.1021/BI301378D
Page generated: Sun Dec 13 10:44:31 2020

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