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Magnesium in PDB 4erm: Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution, PDB code: 4erm was solved by C.M.Zimanyi, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 280.471, 155.744, 166.919, 90.00, 119.07, 90.00
R / Rfree (%) 25.9 / 28.4

Other elements in 4erm:

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution (pdb code 4erm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution, PDB code: 4erm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4erm

Go back to Magnesium Binding Sites List in 4erm
Magnesium binding site 1 out of 4 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:94.5
occ:1.00
 O1G A:DTP803 1.7 94.5 1.0
PG A:DTP803 2.8 94.5 1.0
O1A A:DTP803 2.8 94.5 1.0
O3G A:DTP803 3.0 94.5 1.0
O1B A:DTP803 3.0 94.5 1.0
O3B A:DTP803 3.5 94.5 1.0
PB A:DTP803 3.6 94.5 1.0
O3A A:DTP803 3.9 94.5 1.0
PA A:DTP803 3.9 94.5 1.0
O2G A:DTP803 4.1 94.5 1.0
O A:ASP232 4.3 82.4 1.0
NH2 A:ARG262 4.8 77.6 1.0
O2A A:DTP803 4.8 94.5 1.0

Magnesium binding site 2 out of 4 in 4erm

Go back to Magnesium Binding Sites List in 4erm
Magnesium binding site 2 out of 4 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:94.1
occ:1.00
 O1G B:DTP803 1.7 94.1 1.0
PG B:DTP803 2.8 94.1 1.0
O3G B:DTP803 2.9 94.1 1.0
O1A B:DTP803 2.9 94.1 1.0
O1B B:DTP803 3.0 94.1 1.0
O3B B:DTP803 3.8 94.1 1.0
PA B:DTP803 3.9 94.1 1.0
PB B:DTP803 3.9 94.1 1.0
O2G B:DTP803 3.9 94.1 1.0
O5' B:DTP803 4.0 94.1 1.0
O B:ASP232 4.2 89.6 1.0
O3A B:DTP803 4.4 94.1 1.0
NH2 B:ARG262 4.5 91.1 1.0

Magnesium binding site 3 out of 4 in 4erm

Go back to Magnesium Binding Sites List in 4erm
Magnesium binding site 3 out of 4 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg804

b:0.3
occ:1.00
 O1G C:DTP803 1.7 0.3 1.0
PG C:DTP803 2.8 0.3 1.0
O3A C:DTP803 2.9 0.3 1.0
O3B C:DTP803 3.0 0.3 1.0
PB C:DTP803 3.4 0.3 1.0
O2G C:DTP803 3.5 0.3 1.0
O1B C:DTP803 3.8 0.3 1.0
O3G C:DTP803 4.0 0.3 1.0
PA C:DTP803 4.2 0.3 1.0
O C:ASP232 4.3 0.1 1.0
O1A C:DTP803 4.4 0.3 1.0
O5' C:DTP803 4.8 0.3 1.0
O2B C:DTP803 4.8 0.3 1.0
NH2 C:ARG262 4.9 0.4 1.0

Magnesium binding site 4 out of 4 in 4erm

Go back to Magnesium Binding Sites List in 4erm
Magnesium binding site 4 out of 4 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:0.6
occ:1.00
 O1G D:DTP803 1.7 0.6 1.0
PG D:DTP803 2.8 0.6 1.0
O2G D:DTP803 2.9 0.6 1.0
O1B D:DTP803 3.0 0.6 1.0
O1A D:DTP803 3.2 0.6 1.0
O D:ASP232 3.5 0.4 1.0
PB D:DTP803 3.6 0.6 1.0
O3B D:DTP803 3.6 0.6 1.0
O3A D:DTP803 3.7 0.6 1.0
PA D:DTP803 3.9 0.6 1.0
O3G D:DTP803 4.0 0.6 1.0
C5' D:DTP803 4.2 0.6 1.0
NH2 D:ARG262 4.4 0.8 1.0
O5' D:DTP803 4.4 0.6 1.0
OD2 D:ASP232 4.5 0.1 1.0
CB D:SER233 4.7 0.1 1.0
C D:ASP232 4.7 0.4 1.0

Reference:

C.M.Zimanyi, N.Ando, E.J.Brignole, F.J.Asturias, J.Stubbe, C.L.Drennan. Tangled Up in Knots: Structures of Inactivated Forms of E. Coli Class Ia Ribonucleotide Reductase. Structure V. 20 1374 2012.
ISSN: ISSN 0969-2126
PubMed: 22727814
DOI: 10.1016/J.STR.2012.05.009
Page generated: Fri Aug 16 14:36:51 2024

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