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Cobalt in PDB 6d5k: Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin

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

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

Protein crystallography data

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin, PDB code: 6d5k was solved by G.J.Dodge, G.Campanello, J.L.Smith, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.252, 112.252, 117.993, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.9

Other elements in 6d5k:

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

Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin (pdb code 6d5k). 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 Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and Adenosylcobalamin, PDB code: 6d5k:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 6d5k

Go back to Cobalt Binding Sites List in 6d5k
Cobalt binding site 1 out of 2 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and 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 Bound to Atp, and Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co302

b:78.9
occ:1.00
CO A:B12302 0.0 78.9 1.0
N21 A:B12302 1.9 80.9 1.0
N24 A:B12302 1.9 86.2 1.0
N23 A:B12302 1.9 76.9 1.0
N22 A:B12302 1.9 80.7 1.0
C5' A:5AD301 2.1 79.3 0.9
C9 A:B12302 2.8 75.2 1.0
C19 A:B12302 2.8 81.9 1.0
C11 A:B12302 2.9 67.8 1.0
C1 A:B12302 2.9 81.4 1.0
C4 A:B12302 2.9 84.7 1.0
C16 A:B12302 3.0 77.4 1.0
C6 A:B12302 3.0 80.1 1.0
C14 A:B12302 3.0 77.8 1.0
C10 A:B12302 3.2 76.3 1.0
C4' A:5AD301 3.3 77.6 0.9
C5 A:B12302 3.3 84.5 1.0
C15 A:B12302 3.4 75.0 1.0
C20 A:B12302 3.5 80.8 1.0
CE1 A:PHE170 3.7 72.2 1.0
CZ A:PHE170 4.0 78.1 1.0
C18 A:B12302 4.1 75.9 1.0
C2 A:B12302 4.1 82.2 1.0
O4' A:5AD301 4.1 81.9 0.9
C8 A:B12302 4.2 64.9 1.0
C12 A:B12302 4.2 66.5 1.0
C3 A:B12302 4.2 86.3 1.0
C7 A:B12302 4.2 71.6 1.0
C17 A:B12302 4.3 73.2 1.0
C13 A:B12302 4.3 68.9 1.0
C3' A:5AD301 4.5 80.2 0.9
C26 A:B12302 4.5 85.8 1.0
O3' A:5AD301 4.7 81.0 0.9
C37 A:B12302 4.7 76.8 1.0
C35 A:B12302 4.8 81.1 1.0
C41 A:B12302 4.8 59.8 1.0
C47 A:B12302 4.8 75.0 1.0
CD1 A:PHE170 4.9 71.7 1.0
C53 A:B12302 4.9 65.5 1.0

Cobalt binding site 2 out of 2 in 6d5k

Go back to Cobalt Binding Sites List in 6d5k
Cobalt binding site 2 out of 2 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, and 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 Bound to Atp, and Adenosylcobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co303

b:0.9
occ:0.88
CO A:B12303 0.0 0.9 0.9
N21 A:B12303 1.9 0.9 0.9
N24 A:B12303 1.9 0.8 0.9
N23 A:B12303 1.9 0.9 0.9
N22 A:B12303 1.9 0.7 0.9
C5' B:5AD301 2.0 0.1 1.0
C19 A:B12303 2.8 0.7 0.9
C4 A:B12303 2.9 0.2 0.9
C9 A:B12303 2.9 1.0 0.9
C1 A:B12303 2.9 0.7 0.9
C11 A:B12303 2.9 0.2 0.9
C6 A:B12303 3.0 0.3 0.9
C16 A:B12303 3.0 0.2 0.9
C14 A:B12303 3.0 0.9 0.9
C10 A:B12303 3.3 0.7 0.9
C5 A:B12303 3.3 0.2 0.9
C4' B:5AD301 3.4 0.8 1.0
C15 A:B12303 3.5 0.4 0.9
C20 A:B12303 3.6 0.9 0.9
C2 A:B12303 4.1 0.8 0.9
C18 A:B12303 4.1 0.2 0.9
CZ B:PHE170 4.2 0.7 1.0
C3 A:B12303 4.2 0.7 0.9
O4' B:5AD301 4.2 0.6 1.0
C8 A:B12303 4.2 0.9 0.9
C7 A:B12303 4.2 0.8 0.9
C12 A:B12303 4.3 0.7 0.9
C17 A:B12303 4.3 0.1 0.9
C13 A:B12303 4.3 0.6 0.9
C3' B:5AD301 4.4 0.6 1.0
C26 A:B12303 4.5 0.1 0.9
CE2 B:PHE170 4.7 0.1 1.0
C35 A:B12303 4.7 0.8 0.9
C37 A:B12303 4.7 0.8 0.9
O3' B:5AD301 4.8 0.2 1.0
C41 A:B12303 4.9 0.6 0.9
C53 A:B12303 5.0 0.4 0.9
NH2 B:ARG190 5.0 0.8 1.0
C47 A:B12303 5.0 0.6 0.9

Reference:

G.C.Campanello, M.Ruetz, G.J.Dodge, H.Gouda, A.Gupta, U.T.Twahir, M.M.Killian, D.Watkins, D.S.Rosenblatt, T.C.Brunold, K.Warncke, J.L.Smith, R.Banerjee. Sacrificial Cobalt-Carbon Bond Homolysis in Coenzyme B12AS A Cofactor Conservation Strategy. J. Am. Chem. Soc. V. 140 13205 2018.
ISSN: ESSN 1520-5126
PubMed: 30282455
DOI: 10.1021/JACS.8B08659
Page generated: Sun Dec 13 10:49:54 2020

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