Atomistry » Cobalt » PDB 7nqf-7vo8 » 7ruv
Atomistry »
  Cobalt »
    PDB 7nqf-7vo8 »
      7ruv »

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: Tue Jul 30 19:27:57 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy