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Magnesium in PDB 2idx: Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp.

Enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp.

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

Protein crystallography data

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp., PDB code: 2idx was solved by H.L.Schubert, C.P.Hill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.238, 111.238, 115.526, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 25.1

Other elements in 2idx:

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

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 2idx

Go back to Magnesium Binding Sites List in 2idx
Magnesium binding site 1 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:33.5
occ:1.00
 OD1 A:ASN214 2.0 35.5 1.0
O2A A:ATP607 2.0 25.5 1.0
O A:HOH633 2.1 24.4 1.0
O3G A:ATP607 2.1 34.1 1.0
O2B A:ATP607 2.2 28.5 1.0
O A:HOH634 2.3 32.9 1.0
CG A:ASN214 3.1 32.3 1.0
PA A:ATP607 3.3 27.7 1.0
PB A:ATP607 3.3 29.8 1.0
PG A:ATP607 3.4 30.9 1.0
O A:HOH608 3.5 23.1 1.0
O3B A:ATP607 3.7 30.4 1.0
O3A A:ATP607 3.7 29.0 1.0
ND2 A:ASN214 3.8 33.1 1.0
O A:ASN214 3.8 28.7 1.0
NZ C:LYS78 3.9 25.8 1.0
O1G A:ATP607 4.0 26.6 1.0
O A:HOH628 4.0 27.6 1.0
NH1 A:ARG190 4.2 28.2 1.0
O1A A:ATP607 4.2 28.8 1.0
CB A:ASN214 4.4 29.8 1.0
O5' A:ATP607 4.4 28.3 1.0
OG A:SER217 4.4 32.7 1.0
C A:ASN214 4.4 28.8 1.0
CA A:ASN214 4.4 29.2 1.0
OE2 A:GLU193 4.5 27.4 1.0
OD1 A:ASP218 4.5 35.6 1.0
O2G A:ATP607 4.6 28.4 1.0
N7 A:ATP607 4.7 30.2 1.0
O1B A:ATP607 4.7 30.8 1.0
OE1 A:GLU193 4.7 29.7 1.0
OD2 A:ASP218 4.9 32.9 1.0
C8 A:ATP607 4.9 29.9 1.0
CE C:LYS78 5.0 26.8 1.0

Magnesium binding site 2 out of 4 in 2idx

Go back to Magnesium Binding Sites List in 2idx
Magnesium binding site 2 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:43.7
occ:1.00
 O A:HOH639 2.0 51.9 1.0
O A:HOH632 2.0 34.2 1.0
O A:HOH608 2.1 23.1 1.0
O1A A:ATP607 2.1 28.8 1.0
O A:HOH631 2.3 24.0 1.0
PA A:ATP607 3.4 27.7 1.0
O2A A:ATP607 3.8 25.5 1.0
OD1 A:ASP218 4.0 35.6 1.0
O2G A:ATP607 4.1 28.4 1.0
O3G A:ATP607 4.2 34.1 1.0
O A:HOH617 4.2 44.4 1.0
O5' A:ATP607 4.3 28.3 1.0
C5' A:ATP607 4.6 28.6 1.0
O3A A:ATP607 4.6 29.0 1.0
PG A:ATP607 4.7 30.9 1.0
O3B A:ATP607 4.8 30.4 1.0
CG A:ASP218 4.9 33.6 1.0

Magnesium binding site 3 out of 4 in 2idx

Go back to Magnesium Binding Sites List in 2idx
Magnesium binding site 3 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:46.1
occ:1.00
 O B:HOH669 1.8 37.6 1.0
O C:HOH665 1.9 44.2 1.0
O B:HOH670 2.0 37.1 1.0
O1A B:ATP606 2.2 22.9 1.0
O B:HOH659 2.3 28.2 1.0
O B:ILE58 3.5 41.4 1.0
PA B:ATP606 3.5 24.6 1.0
OD1 C:ASP218 3.8 29.3 1.0
O2A B:ATP606 4.0 20.5 1.0
O B:HOH675 4.2 41.3 1.0
O2G B:ATP606 4.3 24.4 1.0
O3G B:ATP606 4.3 23.2 1.0
O5' B:ATP606 4.5 24.2 1.0
OD2 C:ASP218 4.5 30.1 1.0
O C:HOH666 4.5 42.1 1.0
C B:ILE58 4.6 40.5 1.0
CG C:ASP218 4.6 27.5 1.0
O3A B:ATP606 4.7 22.4 1.0
C5' B:ATP606 4.7 21.5 1.0
O B:HOH628 4.8 31.9 1.0
PG B:ATP606 4.8 24.0 1.0

Magnesium binding site 4 out of 4 in 2idx

Go back to Magnesium Binding Sites List in 2idx
Magnesium binding site 4 out of 4 in the Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Atp:Cobalamin Adenosyltransferase Bound to Atp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:19.9
occ:1.00
 O3G B:ATP606 1.8 23.2 1.0
O2B B:ATP606 1.9 20.2 1.0
O2A B:ATP606 2.0 20.5 1.0
O C:HOH672 2.0 20.3 1.0
ND2 C:ASN214 2.2 24.1 1.0
O C:HOH652 2.3 17.6 1.0
PB B:ATP606 2.9 22.0 1.0
PA B:ATP606 3.0 24.6 1.0
PG B:ATP606 3.1 24.0 1.0
CG C:ASN214 3.2 24.5 1.0
O3A B:ATP606 3.3 22.4 1.0
O3B B:ATP606 3.4 19.3 1.0
OD1 C:ASN214 3.4 25.3 1.0
O B:HOH659 3.5 28.2 1.0
O1G B:ATP606 3.8 22.6 1.0
NZ B:LYS78 3.8 21.7 1.0
O1A B:ATP606 3.9 22.9 1.0
O C:HOH610 4.0 20.1 1.0
NH1 C:ARG190 4.2 20.4 1.0
O2G B:ATP606 4.3 24.4 1.0
O C:ASN214 4.3 25.8 1.0
O5' B:ATP606 4.3 24.2 1.0
O1B B:ATP606 4.3 19.2 1.0
N7 B:ATP606 4.5 22.8 1.0
CB C:ASN214 4.5 24.6 1.0
OE1 C:GLU193 4.7 24.6 1.0
OD2 C:ASP218 4.7 30.1 1.0
CA C:ASN214 4.7 24.8 1.0
C8 B:ATP606 4.8 21.8 1.0
CE B:LYS78 4.8 20.8 1.0
C C:ASN214 4.8 24.7 1.0
OG C:SER217 5.0 22.8 1.0

Reference:

H.L.Schubert, C.P.Hill. Structure of Atp-Bound Human Atp:Cobalamin Adenosyltransferase. Biochemistry V. 45 15188 2006.
ISSN: ISSN 0006-2960
PubMed: 17176040
DOI: 10.1021/BI061396F
Page generated: Wed Aug 14 00:07:57 2024

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