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Cobalt in PDB 7ruv: Structure of Human Atp:Cobalamin Adenosyltransferase E193K Bound to Adenosylcobalamin

Enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase E193K Bound to Adenosylcobalamin

All present enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase E193K Bound to Adenosylcobalamin:
2.5.1.17;

Protein crystallography data

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase E193K Bound to Adenosylcobalamin, PDB code: 7ruv 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) 33.00 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 121.181, 121.181, 169.77, 90, 90, 120
R / Rfree (%) 18.5 / 21.7

Other elements in 7ruv:

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase E193K Bound to Adenosylcobalamin also contains other interesting chemical elements:

Potassium (K) 1 atom
Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Human Atp:Cobalamin Adenosyltransferase E193K Bound to Adenosylcobalamin (pdb code 7ruv). 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 E193K Bound to Adenosylcobalamin, PDB code: 7ruv:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 7ruv

Go back to Cobalt Binding Sites List in 7ruv
Cobalt binding site 1 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase E193K 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 E193K Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co303

b:38.5
occ:1.00
 CO A:B12303 0.0 38.5 1.0
N23 A:B12303 1.9 39.9 1.0
N21 A:B12303 1.9 41.1 1.0
N24 A:B12303 1.9 44.5 1.0
N22 A:B12303 1.9 42.0 1.0
C5' A:5AD304 2.0 39.1 1.0
C1 A:B12303 2.8 37.8 1.0
C11 A:B12303 2.8 37.5 1.0
C9 A:B12303 2.9 39.8 1.0
C19 A:B12303 2.9 39.3 1.0
C4 A:B12303 2.9 43.4 1.0
C16 A:B12303 2.9 41.8 1.0
C14 A:B12303 2.9 39.9 1.0
C6 A:B12303 3.0 42.9 1.0
C4' A:5AD304 3.1 44.7 1.0
C10 A:B12303 3.2 35.5 1.0
C5 A:B12303 3.4 44.2 1.0
C15 A:B12303 3.4 41.3 1.0
C20 A:B12303 3.5 39.0 1.0
CE1 A:PHE170 3.6 41.0 1.0
CZ A:PHE170 3.9 38.8 1.0
O4' A:5AD304 4.0 43.6 1.0
C18 A:B12303 4.1 39.3 1.0
C2 A:B12303 4.1 42.1 1.0
C17 A:B12303 4.2 42.6 1.0
C12 A:B12303 4.2 39.7 1.0
C8 A:B12303 4.2 38.6 1.0
C3 A:B12303 4.2 37.8 1.0
C13 A:B12303 4.2 41.6 1.0
C7 A:B12303 4.3 36.4 1.0
C3' A:5AD304 4.3 43.0 1.0
C26 A:B12303 4.5 39.8 1.0
O3' A:5AD304 4.5 49.4 1.0
CD1 A:PHE170 4.8 41.3 1.0
C49 A:B12303 4.8 37.4 1.0
C41 A:B12303 4.8 37.8 1.0
C37 A:B12303 4.8 38.5 1.0
C35 A:B12303 4.9 39.3 1.0
C46 A:B12303 4.9 37.3 1.0
C54 A:B12303 4.9 42.3 1.0
C53 A:B12303 4.9 40.5 1.0

Cobalt binding site 2 out of 4 in 7ruv

Go back to Cobalt Binding Sites List in 7ruv
Cobalt binding site 2 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase E193K 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 E193K Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co301

b:35.6
occ:1.00
 CO B:B12301 0.0 35.6 1.0
N23 B:B12301 1.9 40.1 1.0
N21 B:B12301 1.9 41.7 1.0
N24 B:B12301 1.9 40.2 1.0
N22 B:B12301 1.9 39.0 1.0
C5' B:5AD302 2.1 32.1 1.0
C19 B:B12301 2.8 37.6 1.0
C11 B:B12301 2.9 35.5 1.0
C9 B:B12301 2.9 37.9 1.0
C1 B:B12301 2.9 36.9 1.0
C16 B:B12301 2.9 41.7 1.0
C4 B:B12301 2.9 38.3 1.0
C14 B:B12301 2.9 40.5 1.0
C6 B:B12301 3.0 37.5 1.0
C4' B:5AD302 3.1 42.5 1.0
C10 B:B12301 3.2 33.2 1.0
C15 B:B12301 3.4 40.3 1.0
C5 B:B12301 3.4 38.9 1.0
C20 B:B12301 3.5 35.0 1.0
CE1 B:PHE170 3.8 38.8 1.0
O4' B:5AD302 3.9 40.7 1.0
C18 B:B12301 4.1 38.4 1.0
C2 B:B12301 4.1 39.5 1.0
C17 B:B12301 4.2 40.8 1.0
C12 B:B12301 4.2 38.6 1.0
C3 B:B12301 4.2 39.5 1.0
C8 B:B12301 4.2 35.1 1.0
C13 B:B12301 4.2 37.3 1.0
CZ B:PHE170 4.3 41.0 1.0
C7 B:B12301 4.3 38.1 1.0
C3' B:5AD302 4.3 40.3 1.0
C26 B:B12301 4.5 39.2 1.0
O3' B:5AD302 4.5 44.4 1.0
C49 B:B12301 4.7 41.5 1.0
C37 B:B12301 4.8 33.1 1.0
C35 B:B12301 4.9 38.1 1.0
C54 B:B12301 4.9 36.6 1.0
C46 B:B12301 4.9 35.7 1.0
C53 B:B12301 4.9 35.7 1.0
C41 B:B12301 4.9 37.9 1.0
CD1 B:PHE170 5.0 40.1 1.0

Cobalt binding site 3 out of 4 in 7ruv

Go back to Cobalt Binding Sites List in 7ruv
Cobalt binding site 3 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase E193K 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 E193K Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co503

b:37.3
occ:1.00
 CO C:B12503 0.0 37.3 1.0
N23 C:B12503 1.8 36.5 1.0
N21 C:B12503 1.8 36.8 1.0
N24 C:B12503 1.9 38.2 1.0
N22 C:B12503 1.9 36.4 1.0
C5' C:5AD504 2.1 35.7 1.0
C1 C:B12503 2.8 39.5 1.0
C11 C:B12503 2.8 36.7 1.0
C9 C:B12503 2.9 34.4 1.0
C19 C:B12503 2.9 35.4 1.0
C4 C:B12503 2.9 36.4 1.0
C14 C:B12503 2.9 37.5 1.0
C16 C:B12503 2.9 38.5 1.0
C6 C:B12503 3.0 36.5 1.0
C4' C:5AD504 3.2 41.0 1.0
C10 C:B12503 3.2 35.4 1.0
C5 C:B12503 3.4 36.0 1.0
C15 C:B12503 3.4 39.4 1.0
C20 C:B12503 3.5 37.9 1.0
CE1 C:PHE170 3.5 40.9 1.0
CZ C:PHE170 3.7 41.6 1.0
O4' C:5AD504 4.0 38.7 1.0
C2 C:B12503 4.1 39.1 1.0
C18 C:B12503 4.1 39.0 1.0
C3 C:B12503 4.2 35.1 1.0
C17 C:B12503 4.2 38.8 1.0
C12 C:B12503 4.2 37.4 1.0
C13 C:B12503 4.2 37.6 1.0
C8 C:B12503 4.2 32.7 1.0
C7 C:B12503 4.3 38.7 1.0
C3' C:5AD504 4.4 42.1 1.0
C26 C:B12503 4.4 36.1 1.0
O3' C:5AD504 4.6 42.0 1.0
C37 C:B12503 4.8 37.1 1.0
C49 C:B12503 4.8 38.3 1.0
CD1 C:PHE170 4.8 36.6 1.0
C35 C:B12503 4.9 32.3 1.0
C46 C:B12503 4.9 39.4 1.0
C41 C:B12503 4.9 37.3 1.0
O C:HOH622 4.9 45.3 1.0
C53 C:B12503 4.9 38.7 1.0
C54 C:B12503 5.0 35.7 1.0

Cobalt binding site 4 out of 4 in 7ruv

Go back to Cobalt Binding Sites List in 7ruv
Cobalt binding site 4 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase E193K 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 E193K Bound to Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co301

b:53.3
occ:1.00
 CO D:B12301 0.0 53.3 1.0
N23 D:B12301 1.8 52.1 1.0
N21 D:B12301 1.9 54.9 1.0
N24 D:B12301 1.9 57.2 1.0
N22 D:B12301 1.9 55.5 1.0
C5' D:5AD302 2.2 57.1 1.0
C11 D:B12301 2.8 55.8 1.0
C9 D:B12301 2.9 52.3 1.0
C1 D:B12301 2.9 58.2 1.0
C14 D:B12301 2.9 59.1 1.0
C19 D:B12301 2.9 57.9 1.0
C4 D:B12301 2.9 57.4 1.0
C16 D:B12301 2.9 55.6 1.0
C6 D:B12301 3.0 51.2 1.0
C4' D:5AD302 3.2 60.4 1.0
C10 D:B12301 3.2 44.1 1.0
C5 D:B12301 3.4 56.3 1.0
C15 D:B12301 3.4 56.7 1.0
C20 D:B12301 3.5 60.1 1.0
CE1 D:PHE170 3.5 54.6 1.0
CZ D:PHE170 3.8 54.6 1.0
O4' D:5AD302 3.9 63.0 1.0
C18 D:B12301 4.1 59.9 1.0
C2 D:B12301 4.1 60.8 1.0
C12 D:B12301 4.2 52.3 1.0
C17 D:B12301 4.2 58.7 1.0
C13 D:B12301 4.2 53.0 1.0
C3 D:B12301 4.2 57.1 1.0
C8 D:B12301 4.2 47.9 1.0
C7 D:B12301 4.3 46.8 1.0
C3' D:5AD302 4.5 60.8 1.0
C26 D:B12301 4.5 61.5 1.0
C37 D:B12301 4.8 49.4 1.0
C35 D:B12301 4.8 52.4 1.0
CD1 D:PHE170 4.8 50.5 1.0
C49 D:B12301 4.8 52.8 1.0
O3' D:5AD302 4.8 62.7 1.0
C46 D:B12301 4.8 54.6 1.0
C41 D:B12301 4.9 44.2 1.0
C53 D:B12301 4.9 57.1 1.0
C54 D:B12301 4.9 58.2 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: Sun Jul 13 21:37:04 2025

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