Atomistry » Magnesium » PDB 5chg-5cqz » 5cnv
Atomistry »
  Magnesium »
    PDB 5chg-5cqz »
      5cnv »

Magnesium in PDB 5cnv: Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 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 Bound to Gdp and Ttp at 3.20 Angstroms Resolution, PDB code: 5cnv was solved by P.Y.-T.Chen, C.M.Zimanyi, M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.73 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 274.776, 157.753, 165.768, 90.00, 119.49, 90.00
R / Rfree (%) 19 / 21.9

Other elements in 5cnv:

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 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 Bound to Gdp and Ttp at 3.20 Angstroms Resolution (pdb code 5cnv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution, PDB code: 5cnv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 1 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 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 Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:93.5
occ:1.00
 O1B A:TTP804 2.1 93.7 0.8
O2B A:DAT802 2.1 89.2 1.0
O1A A:TTP804 2.1 92.4 0.8
O1G A:TTP804 2.1 93.9 0.8
O2A A:DAT802 2.1 88.4 1.0
O A:HOH901 2.1 89.7 1.0
PB A:DAT802 3.0 89.3 1.0
PB A:TTP804 3.1 95.5 0.8
O1B A:DAT802 3.2 88.2 1.0
PA A:DAT802 3.3 86.1 1.0
PA A:TTP804 3.3 98.5 0.8
PG A:TTP804 3.4 94.3 0.8
O3A A:DAT802 3.5 86.7 1.0
O3A A:TTP804 3.5 93.2 0.8
O3B A:TTP804 3.6 91.8 0.8
NZ A:LYS91 4.0 84.5 1.0
O5' A:TTP804 4.2 91.7 0.8
O2G A:TTP804 4.2 89.6 0.8
NZ A:LYS9 4.2 87.5 1.0
O5' A:DAT802 4.2 83.5 1.0
O3B A:DAT802 4.4 87.2 1.0
O1A A:DAT802 4.4 82.2 1.0
O3G A:TTP804 4.5 92.6 0.8
O2B A:TTP804 4.5 88.0 0.8
O2A A:TTP804 4.5 94.7 0.8
CE A:LYS9 4.9 89.3 1.0

Magnesium binding site 2 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 2 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 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 Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:81.7
occ:1.00
 O2B A:TTP805 2.1 81.1 1.0
O2A A:TTP805 2.1 82.2 1.0
O3G A:TTP805 2.1 82.2 1.0
O A:HOH906 2.1 82.6 1.0
O A:HOH907 2.1 81.9 1.0
O A:HOH905 2.1 77.7 1.0
PB A:TTP805 3.1 81.7 1.0
PA A:TTP805 3.3 81.8 1.0
PG A:TTP805 3.3 84.9 1.0
O3A A:TTP805 3.5 83.5 1.0
O3B A:TTP805 3.6 82.7 1.0
O1G A:TTP805 3.9 86.9 1.0
O1A A:TTP805 4.3 78.1 1.0
C5' A:TTP805 4.3 79.8 1.0
O5' A:TTP805 4.3 79.8 1.0
O A:ASP232 4.5 79.9 1.0
O1B A:TTP805 4.5 82.1 1.0
O2G A:TTP805 4.5 84.4 1.0
NH2 A:ARG262 4.6 80.9 1.0
CB A:SER233 4.7 79.2 1.0

Magnesium binding site 3 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 3 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 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 Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:0.7
occ:1.00
 O2B B:TTP804 2.1 0.7 0.8
O2A B:TTP804 2.1 0.2 0.8
O3G B:TTP804 2.1 0.6 0.8
O1B B:DAT802 2.1 0.4 1.0
O B:HOH901 2.1 0.9 1.0
O1A B:DAT802 2.1 0.7 1.0
PB B:DAT802 3.0 0.0 1.0
PB B:TTP804 3.1 0.7 0.8
O3B B:DAT802 3.2 0.8 1.0
PA B:TTP804 3.3 0.2 0.8
PA B:DAT802 3.3 0.5 1.0
PG B:TTP804 3.4 0.4 0.8
O3A B:DAT802 3.5 0.6 1.0
O3A B:TTP804 3.6 0.5 0.8
O3B B:TTP804 3.6 0.2 0.8
O5' B:DAT802 4.2 0.3 1.0
O5' B:TTP804 4.2 0.2 0.8
NZ B:LYS91 4.3 99.3 1.0
NZ B:LYS9 4.3 99.6 1.0
O1G B:TTP804 4.3 0.1 0.8
O2G B:TTP804 4.3 0.1 0.8
O2B B:DAT802 4.4 0.2 1.0
O1A B:TTP804 4.5 0.2 0.8
O2A B:DAT802 4.5 0.7 1.0
O1B B:TTP804 4.5 0.6 0.8

Magnesium binding site 4 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 4 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 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 Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg806

b:81.6
occ:1.00
 O1B B:TTP805 2.1 83.9 1.0
O1A B:TTP805 2.1 80.7 1.0
O1G B:TTP805 2.1 82.2 1.0
O B:HOH903 2.1 82.3 1.0
O B:HOH904 2.1 80.5 1.0
O B:HOH905 2.1 85.3 1.0
PB B:TTP805 3.1 82.4 1.0
PG B:TTP805 3.3 86.7 1.0
PA B:TTP805 3.3 81.6 1.0
O3A B:TTP805 3.5 81.0 1.0
O3B B:TTP805 3.6 84.7 1.0
O3G B:TTP805 3.8 88.2 1.0
O B:ASP232 4.2 82.6 1.0
O5' B:TTP805 4.3 82.0 1.0
O2A B:TTP805 4.3 81.0 1.0
C5' B:TTP805 4.4 82.6 1.0
NH2 B:ARG262 4.5 84.7 1.0
O2B B:TTP805 4.5 80.3 1.0
O2G B:TTP805 4.5 83.2 1.0
CB B:SER233 4.7 82.4 1.0

Magnesium binding site 5 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 5 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:73.2
occ:1.00
 O2B C:TTP804 2.1 74.7 0.8
O2A C:TTP804 2.1 77.6 0.8
O1B C:DAT802 2.1 76.6 1.0
O C:HOH901 2.1 75.7 1.0
O1A C:DAT802 2.1 77.1 1.0
O3G C:TTP804 2.1 78.5 0.8
PB C:DAT802 3.1 75.9 1.0
PB C:TTP804 3.1 81.1 0.8
PA C:DAT802 3.3 72.7 1.0
PA C:TTP804 3.3 82.3 0.8
O3B C:DAT802 3.4 72.8 1.0
PG C:TTP804 3.4 78.5 0.8
O3A C:DAT802 3.5 72.3 1.0
O3A C:TTP804 3.5 80.1 0.8
O3B C:TTP804 3.6 76.7 0.8
O5' C:DAT802 4.1 69.7 1.0
NZ C:LYS91 4.1 70.8 1.0
O5' C:TTP804 4.3 78.4 0.8
O2G C:TTP804 4.3 76.5 0.8
NZ C:LYS9 4.3 71.5 1.0
O1A C:TTP804 4.4 76.0 0.8
O1G C:TTP804 4.4 73.9 0.8
O2B C:DAT802 4.4 70.9 1.0
O1B C:TTP804 4.5 76.0 0.8
O2A C:DAT802 4.5 69.2 1.0
CE C:LYS9 5.0 72.2 1.0

Magnesium binding site 6 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 6 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg806

b:59.9
occ:1.00
 O2B C:TTP805 2.1 57.0 1.0
O1G C:TTP805 2.1 56.8 1.0
O2A C:TTP805 2.1 54.4 1.0
O C:HOH909 2.1 54.7 1.0
O C:HOH910 2.1 65.5 1.0
O C:HOH911 2.1 52.9 1.0
PB C:TTP805 3.1 61.8 1.0
PA C:TTP805 3.2 53.2 1.0
PG C:TTP805 3.2 61.2 1.0
O3A C:TTP805 3.3 58.6 1.0
O3B C:TTP805 3.5 61.0 1.0
O2G C:TTP805 3.7 65.0 1.0
C5' C:TTP805 4.2 54.5 1.0
O5' C:TTP805 4.3 53.2 1.0
O1A C:TTP805 4.3 54.9 1.0
O C:ASP232 4.4 52.3 1.0
NH2 C:ARG262 4.5 54.5 1.0
O1B C:TTP805 4.5 61.8 1.0
O3G C:TTP805 4.5 62.0 1.0
CB C:SER233 4.6 53.1 1.0

Magnesium binding site 7 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 7 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:95.7
occ:1.00
 O1B D:TTP804 2.1 97.9 0.8
O1A D:TTP804 2.1 98.3 0.8
O2A D:DAT802 2.1 95.6 1.0
O2B D:DAT802 2.1 99.4 1.0
O D:HOH901 2.1 96.4 1.0
O1G D:TTP804 2.1 99.4 0.8
PB D:DAT802 3.1 99.7 1.0
PB D:TTP804 3.1 0.1 0.8
PA D:TTP804 3.2 0.4 0.8
PA D:DAT802 3.3 96.4 1.0
O3B D:DAT802 3.3 98.2 1.0
PG D:TTP804 3.4 0.7 0.8
O3A D:TTP804 3.4 99.2 0.8
O3A D:DAT802 3.5 96.0 1.0
O3B D:TTP804 3.5 99.3 0.8
O5' D:TTP804 4.0 96.4 0.8
O5' D:DAT802 4.2 93.3 1.0
NZ D:LYS9 4.3 95.8 1.0
O2G D:TTP804 4.3 99.9 0.8
NZ D:LYS91 4.4 87.7 1.0
O3G D:TTP804 4.4 97.8 0.8
O1A D:DAT802 4.5 92.8 1.0
O1B D:DAT802 4.5 96.7 1.0
O2B D:TTP804 4.5 97.9 0.8
O2A D:TTP804 4.5 99.3 0.8
C8 D:DAT802 4.9 92.8 1.0

Magnesium binding site 8 out of 8 in 5cnv

Go back to Magnesium Binding Sites List in 5cnv
Magnesium binding site 8 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg806

b:54.9
occ:1.00
 O2B D:TTP805 2.1 55.3 1.0
O1A D:TTP805 2.1 52.7 1.0
O D:HOH910 2.1 54.2 1.0
O D:HOH911 2.1 54.7 1.0
O D:HOH912 2.1 56.8 1.0
O2G D:TTP805 2.1 53.9 1.0
PB D:TTP805 3.1 54.2 1.0
PG D:TTP805 3.2 53.6 1.0
PA D:TTP805 3.3 53.6 1.0
O3A D:TTP805 3.5 56.8 1.0
O3B D:TTP805 3.6 55.6 1.0
O3G D:TTP805 3.7 54.9 1.0
C5' D:TTP805 4.1 52.0 1.0
O5' D:TTP805 4.2 50.4 1.0
NH2 D:ARG262 4.3 53.7 1.0
O D:ASP232 4.3 52.2 1.0
O2A D:TTP805 4.5 52.0 1.0
O1B D:TTP805 4.5 54.4 1.0
O1G D:TTP805 4.5 54.3 1.0
CB D:SER233 4.7 50.0 1.0

Reference:

C.M.Zimanyi, P.Y.Chen, G.Kang, M.A.Funk, C.L.Drennan. Molecular Basis For Allosteric Specificity Regulation in Class Ia Ribonucleotide Reductase From Escherichia Coli. Elife V. 5 07141 2016.
ISSN: ESSN 2050-084X
PubMed: 26754917
DOI: 10.7554/ELIFE.07141
Page generated: Sun Sep 29 02:15:21 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