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Magnesium in PDB 6d5x: Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate

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

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

Protein crystallography data

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate, PDB code: 6d5x 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) 48.79 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.685, 112.685, 117.939, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 21.2

Other elements in 6d5x:

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

Cobalt (Co) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate (pdb code 6d5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate, PDB code: 6d5x:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6d5x

Go back to Magnesium Binding Sites List in 6d5x
Magnesium binding site 1 out of 3 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:100.0
occ:1.00
 O3G A:3PO305 1.8 0.9 0.8
OD1 A:ASN214 2.0 84.4 1.0
O1A A:3PO305 2.1 0.1 0.8
O A:HOH406 2.2 77.1 1.0
O A:HOH410 2.3 83.2 1.0
O2B A:3PO305 2.6 88.0 0.8
CG A:ASN214 3.2 73.9 1.0
PG A:3PO305 3.2 87.2 0.8
PA A:3PO305 3.5 0.3 0.8
PB A:3PO305 3.6 98.8 0.8
O1G A:3PO305 3.7 83.4 0.8
ND2 A:ASN214 3.7 71.9 1.0
O3B A:3PO305 3.8 93.9 0.8
NH1 A:ARG190 3.9 68.9 1.0
O3A A:3PO305 4.0 0.3 0.8
NZ C:LYS78 4.1 79.6 1.0
O2G A:3PO305 4.2 89.4 0.8
OD1 A:ASP218 4.3 98.7 1.0
O5' A:3PO305 4.3 0.7 0.8
O2A A:3PO305 4.4 0.2 0.8
O A:ASN214 4.4 69.6 1.0
CB A:ASN214 4.4 70.6 1.0
OE1 A:GLU193 4.5 70.8 1.0
N7 A:5AD301 4.5 57.0 0.9
CA A:ASN214 4.5 57.4 1.0
OE2 A:GLU193 4.7 79.0 1.0
C A:ASN214 4.8 64.0 1.0
OD2 A:ASP218 4.8 82.8 1.0
C8 A:5AD301 4.9 59.3 0.9
CG A:ASP218 4.9 88.7 1.0
CZ A:ARG190 4.9 68.4 1.0

Magnesium binding site 2 out of 3 in 6d5x

Go back to Magnesium Binding Sites List in 6d5x
Magnesium binding site 2 out of 3 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:66.5
occ:1.00
 O C:HOH412 2.0 64.4 1.0
O B:HOH418 2.1 77.6 1.0
O C:HOH410 2.1 60.3 1.0
O1A C:ATP301 2.1 56.9 1.0
O C:HOH416 2.1 53.7 1.0
O C:HOH422 2.2 64.4 1.0
PA C:ATP301 3.5 45.6 1.0
O B:ILE58 4.0 75.8 1.0
O2A C:ATP301 4.1 49.2 1.0
OD1 C:ASP218 4.2 75.1 1.0
O2G C:ATP301 4.2 53.5 1.0
O3A C:ATP301 4.4 51.9 1.0
O3G C:ATP301 4.5 44.0 1.0
O5' C:ATP301 4.5 49.9 1.0
C5' C:ATP301 4.6 43.7 1.0
O C:HOH409 4.7 61.1 1.0
PG C:ATP301 4.8 53.0 1.0
O3B C:ATP301 5.0 44.6 1.0

Magnesium binding site 3 out of 3 in 6d5x

Go back to Magnesium Binding Sites List in 6d5x
Magnesium binding site 3 out of 3 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp, Adenosylcobalamin, and Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg306

b:48.7
occ:1.00
 O2A C:ATP301 1.9 49.2 1.0
O2B C:ATP301 2.0 42.3 1.0
OD1 C:ASN214 2.0 53.0 1.0
O3G C:ATP301 2.1 44.0 1.0
O C:HOH403 2.2 51.6 1.0
O C:HOH411 2.2 52.3 1.0
CG C:ASN214 3.2 54.0 1.0
PB C:ATP301 3.3 44.2 1.0
PA C:ATP301 3.3 45.6 1.0
PG C:ATP301 3.5 53.0 1.0
O3A C:ATP301 3.7 51.9 1.0
ND2 C:ASN214 3.8 49.3 1.0
O3B C:ATP301 3.8 44.6 1.0
O C:HOH416 3.9 53.7 1.0
NZ B:LYS78 4.0 48.0 1.0
O C:ASN214 4.0 49.7 1.0
NH1 C:ARG190 4.0 46.3 1.0
O C:HOH407 4.0 61.5 1.0
O1G C:ATP301 4.2 51.7 1.0
O1A C:ATP301 4.2 56.9 1.0
O5' C:ATP301 4.4 49.9 1.0
CB C:ASN214 4.4 49.6 1.0
OD2 C:ASP218 4.5 70.2 1.0
O C:HOH409 4.5 61.1 1.0
N7 C:ATP301 4.5 47.9 1.0
O1B C:ATP301 4.6 46.6 1.0
CA C:ASN214 4.6 51.4 1.0
OE1 C:GLU193 4.6 65.8 1.0
O2G C:ATP301 4.6 53.5 1.0
C C:ASN214 4.7 51.6 1.0
C8 C:ATP301 4.8 49.8 1.0
OE2 C:GLU193 4.9 69.4 1.0

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: Wed Aug 13 04:57:52 2025

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