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Cobalt in PDB 7ruu: Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin

Enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin

All present enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin:
2.5.1.17;

Protein crystallography data

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin, PDB code: 7ruu was solved by R.Mascarenhas, H.Gouda, M.Koutmos, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.16 / 1.85
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 121.807, 121.807, 171.629, 90, 90, 120
R / Rfree (%) 17.7 / 20.2

Other elements in 7ruu:

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin also contains other interesting chemical elements:

Potassium (K) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin (pdb code 7ruu). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin, PDB code: 7ruu:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 7ruu

Go back to Cobalt Binding Sites List in 7ruu
Cobalt binding site 1 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co305

b:29.4
occ:1.00
 CO A:B12305 0.0 29.4 1.0
N21 A:B12305 1.9 31.0 1.0
N23 A:B12305 1.9 27.5 1.0
N24 A:B12305 1.9 32.0 1.0
N22 A:B12305 1.9 26.2 1.0
C5' A:5AD304 2.0 30.6 1.0
C9 A:B12305 2.9 25.3 1.0
C19 A:B12305 2.9 29.9 1.0
C1 A:B12305 2.9 28.6 1.0
C11 A:B12305 2.9 30.3 1.0
C4 A:B12305 2.9 30.4 1.0
C16 A:B12305 2.9 24.7 1.0
C14 A:B12305 2.9 26.9 1.0
C6 A:B12305 3.0 28.8 1.0
C4' A:5AD304 3.1 32.8 1.0
C10 A:B12305 3.2 28.1 1.0
C5 A:B12305 3.4 26.7 1.0
C15 A:B12305 3.4 29.2 1.0
C20 A:B12305 3.6 29.2 1.0
CE1 A:PHE170 3.7 31.9 1.0
O4' A:5AD304 3.9 33.3 1.0
CZ A:PHE170 4.1 29.8 1.0
C18 A:B12305 4.1 27.1 1.0
C2 A:B12305 4.1 29.5 1.0
C17 A:B12305 4.2 31.4 1.0
C3 A:B12305 4.2 31.2 1.0
C8 A:B12305 4.2 24.9 1.0
C12 A:B12305 4.2 30.4 1.0
C13 A:B12305 4.2 26.3 1.0
C7 A:B12305 4.3 24.4 1.0
C3' A:5AD304 4.3 33.2 1.0
C26 A:B12305 4.5 31.7 1.0
O3' A:5AD304 4.5 36.5 1.0
C37 A:B12305 4.8 28.6 1.0
C49 A:B12305 4.8 25.1 1.0
C54 A:B12305 4.8 34.7 1.0
CD1 A:PHE170 4.8 28.0 1.0
C35 A:B12305 4.8 29.8 1.0
C46 A:B12305 4.9 30.7 1.0
C41 A:B12305 4.9 26.6 1.0
O A:HOH449 4.9 36.8 1.0
C53 A:B12305 4.9 30.4 1.0

Cobalt binding site 2 out of 4 in 7ruu

Go back to Cobalt Binding Sites List in 7ruu
Cobalt binding site 2 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co303

b:30.2
occ:1.00
 CO B:B12303 0.0 30.2 1.0
N23 B:B12303 1.8 33.0 1.0
N21 B:B12303 1.9 30.0 1.0
N24 B:B12303 1.9 30.1 1.0
N22 B:B12303 1.9 28.6 1.0
C5' B:5AD302 2.1 31.5 1.0
C11 B:B12303 2.8 28.7 1.0
C9 B:B12303 2.9 29.4 1.0
C19 B:B12303 2.9 27.1 1.0
C1 B:B12303 2.9 28.0 1.0
C4 B:B12303 2.9 30.6 1.0
C16 B:B12303 2.9 28.5 1.0
C14 B:B12303 2.9 30.4 1.0
C6 B:B12303 3.0 28.4 1.0
C4' B:5AD302 3.1 32.5 1.0
C10 B:B12303 3.2 29.5 1.0
C5 B:B12303 3.4 30.8 1.0
C15 B:B12303 3.4 32.4 1.0
C20 B:B12303 3.6 27.5 1.0
CE1 B:PHE170 3.7 33.4 1.0
O4' B:5AD302 3.9 35.1 1.0
CZ B:PHE170 4.1 35.2 1.0
C18 B:B12303 4.1 30.3 1.0
C2 B:B12303 4.1 32.5 1.0
C12 B:B12303 4.2 34.9 1.0
C3 B:B12303 4.2 31.0 1.0
C17 B:B12303 4.2 28.6 1.0
C8 B:B12303 4.2 28.3 1.0
C13 B:B12303 4.2 34.4 1.0
C7 B:B12303 4.3 25.6 1.0
C3' B:5AD302 4.3 37.0 1.0
C26 B:B12303 4.5 28.3 1.0
O3' B:5AD302 4.5 35.6 1.0
C37 B:B12303 4.7 28.5 1.0
C46 B:B12303 4.8 31.9 1.0
C49 B:B12303 4.8 32.6 1.0
CD1 B:PHE170 4.9 32.8 1.0
C35 B:B12303 4.9 28.1 1.0
C54 B:B12303 4.9 32.9 1.0
C41 B:B12303 4.9 32.1 1.0
C53 B:B12303 4.9 31.8 1.0

Cobalt binding site 3 out of 4 in 7ruu

Go back to Cobalt Binding Sites List in 7ruu
Cobalt binding site 3 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co304

b:56.3
occ:1.00
 CO C:B12304 0.0 56.3 1.0
N23 C:B12304 1.8 59.8 1.0
N21 C:B12304 1.9 56.8 1.0
N24 C:B12304 1.9 64.1 1.0
N22 C:B12304 1.9 58.6 1.0
C5' C:5AD303 2.2 64.3 1.0
C11 C:B12304 2.8 57.5 1.0
C9 C:B12304 2.8 50.9 1.0
C1 C:B12304 2.9 63.9 1.0
C19 C:B12304 2.9 60.0 1.0
C14 C:B12304 2.9 59.9 1.0
C4 C:B12304 2.9 64.1 1.0
C16 C:B12304 2.9 61.9 1.0
C6 C:B12304 3.0 52.8 1.0
C4' C:5AD303 3.0 68.2 1.0
C10 C:B12304 3.2 48.6 1.0
C5 C:B12304 3.4 61.8 1.0
C15 C:B12304 3.4 64.6 1.0
C20 C:B12304 3.6 60.4 1.0
O4' C:5AD303 3.7 71.8 1.0
CE1 C:PHE170 3.7 63.3 1.0
CZ C:PHE170 4.0 57.7 1.0
C18 C:B12304 4.1 62.6 1.0
C2 C:B12304 4.2 64.2 1.0
C17 C:B12304 4.2 65.0 1.0
C12 C:B12304 4.2 57.3 1.0
C13 C:B12304 4.2 58.2 1.0
C3 C:B12304 4.2 64.6 1.0
C8 C:B12304 4.2 49.5 1.0
C7 C:B12304 4.3 55.1 1.0
C3' C:5AD303 4.4 72.2 1.0
C26 C:B12304 4.5 71.2 1.0
C37 C:B12304 4.7 49.4 1.0
O3' C:5AD303 4.7 77.0 1.0
C49 C:B12304 4.8 59.4 1.0
C35 C:B12304 4.8 56.3 1.0
C46 C:B12304 4.8 48.9 1.0
C53 C:B12304 4.9 61.5 1.0
CD1 C:PHE170 4.9 60.3 1.0
C54 C:B12304 4.9 58.8 1.0
C41 C:B12304 4.9 41.8 1.0
O C:HOH439 4.9 61.6 1.0

Cobalt binding site 4 out of 4 in 7ruu

Go back to Cobalt Binding Sites List in 7ruu
Cobalt binding site 4 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co303

b:31.9
occ:1.00
 CO D:B12303 0.0 31.9 1.0
N23 D:B12303 1.9 29.6 1.0
C5' D:5AD302 1.9 26.3 1.0
N21 D:B12303 1.9 32.0 1.0
N24 D:B12303 1.9 32.3 1.0
N22 D:B12303 1.9 29.7 1.0
C9 D:B12303 2.9 31.7 1.0
C11 D:B12303 2.9 31.3 1.0
C19 D:B12303 2.9 30.3 1.0
C1 D:B12303 2.9 27.5 1.0
C16 D:B12303 2.9 33.9 1.0
C14 D:B12303 2.9 32.6 1.0
C4 D:B12303 2.9 31.2 1.0
C4' D:5AD302 3.0 40.9 1.0
C6 D:B12303 3.0 32.1 1.0
C10 D:B12303 3.2 29.5 1.0
C5 D:B12303 3.4 32.7 1.0
C15 D:B12303 3.4 31.1 1.0
C20 D:B12303 3.6 31.6 1.0
O4' D:5AD302 3.8 41.2 1.0
CE1 D:PHE170 3.9 32.4 1.0
C18 D:B12303 4.1 31.7 1.0
C2 D:B12303 4.2 33.1 1.0
C17 D:B12303 4.2 32.1 1.0
C12 D:B12303 4.2 31.9 1.0
C3 D:B12303 4.2 31.2 1.0
C13 D:B12303 4.2 31.3 1.0
C3' D:5AD302 4.2 41.9 1.0
C8 D:B12303 4.2 27.5 1.0
C7 D:B12303 4.3 31.0 1.0
CZ D:PHE170 4.4 35.9 1.0
O3' D:5AD302 4.5 44.1 1.0
C26 D:B12303 4.6 32.2 1.0
C49 D:B12303 4.6 35.3 1.0
C37 D:B12303 4.7 33.1 1.0
O D:HOH438 4.8 44.3 1.0
C54 D:B12303 4.8 31.6 1.0
C35 D:B12303 4.8 32.1 1.0
C46 D:B12303 4.9 32.3 1.0
C41 D:B12303 4.9 32.6 1.0
C53 D:B12303 4.9 32.7 1.0
CD1 D:PHE170 5.0 32.6 1.0

Reference:

H.Gouda, R.Mascarenhas, S.Pillay, M.Ruetz, M.Koutmos, R.Banerjee. Patient Mutations in Human Atp:Cob(I)Alamin Adenosyltransferase Differentially Affect Its Catalytic Versus Chaperone Functions. J.Biol.Chem. 01373 2021.
ISSN: ESSN 1083-351X
PubMed: 34757128
DOI: 10.1016/J.JBC.2021.101373
Page generated: Tue Jul 30 19:27:51 2024

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