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Magnesium in PDB 4col: Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site

Enzymatic activity of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site

All present enzymatic activity of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site:
1.17.4.2;

Protein crystallography data

The structure of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site, PDB code: 4col was solved by O.Aurelius, R.Johansson, V.Bagenholm, T.Beck, A.Balhuizen, D.Lundin, B.M.Sjoberg, E.Mulliez, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.136 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.000, 94.120, 86.710, 90.00, 112.03, 90.00
R / Rfree (%) 19.11 / 22.55

Other elements in 4col:

The structure of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site (pdb code 4col). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site, PDB code: 4col:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4col

Go back to Magnesium Binding Sites List in 4col
Magnesium binding site 1 out of 2 in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site


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 Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:38.0
occ:1.00
 OE1 A:GLN207 1.9 40.0 1.0
O1A A:DTP702 2.0 39.4 1.0
O2G A:DTP702 2.1 44.4 1.0
O1B A:DTP702 2.1 41.4 1.0
OE1 A:GLN210 2.1 39.5 1.0
O A:HOH2069 2.2 37.1 1.0
CD A:GLN207 3.0 41.3 1.0
CD A:GLN210 3.2 39.0 1.0
PB A:DTP702 3.2 46.6 1.0
PA A:DTP702 3.3 40.0 1.0
PG A:DTP702 3.3 46.4 1.0
NE2 A:GLN207 3.4 42.7 1.0
O3A A:DTP702 3.6 41.3 1.0
NE2 A:GLN210 3.6 41.0 1.0
O3B A:DTP702 3.7 49.0 1.0
O A:HOH2067 3.8 40.8 1.0
O3G A:DTP702 3.8 46.1 1.0
O5' A:DTP702 3.9 38.4 1.0
CG A:GLN207 4.3 37.8 1.0
NE1 A:TRP203 4.4 48.7 1.0
CD2 B:HIS151 4.4 42.9 1.0
CG A:GLN210 4.4 38.8 1.0
H2'1 A:DTP702 4.5 48.6 1.0
O1G A:DTP702 4.5 45.8 1.0
H8 A:DTP702 4.5 42.6 1.0
O2A A:DTP702 4.6 41.6 1.0
CA A:GLN207 4.6 35.8 1.0
O2B A:DTP702 4.6 45.5 1.0
CB A:GLN207 4.6 37.9 1.0
CB A:GLN210 4.7 35.9 1.0
O A:HOH2099 4.8 28.6 1.0
NE2 B:HIS151 4.9 46.0 1.0
CG2 B:THR154 5.0 36.9 1.0

Magnesium binding site 2 out of 2 in 4col

Go back to Magnesium Binding Sites List in 4col
Magnesium binding site 2 out of 2 in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site


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 Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:39.5
occ:1.00
 OE1 B:GLN207 2.0 41.8 1.0
O2A B:DTP702 2.0 40.2 1.0
O2G B:DTP702 2.1 48.5 1.0
OE1 B:GLN210 2.1 39.9 1.0
O2B B:DTP702 2.1 40.3 1.0
O B:HOH2050 2.1 36.3 1.0
CD B:GLN207 3.0 41.4 1.0
CD B:GLN210 3.1 39.6 1.0
PA B:DTP702 3.2 41.3 1.0
PB B:DTP702 3.3 44.5 1.0
PG B:DTP702 3.3 48.8 1.0
NE2 B:GLN207 3.4 42.3 1.0
NE2 B:GLN210 3.5 40.6 1.0
O3A B:DTP702 3.6 43.1 1.0
O3B B:DTP702 3.7 49.5 1.0
O3G B:DTP702 3.7 46.7 1.0
O5' B:DTP702 3.9 40.0 1.0
O B:HOH2048 3.9 37.2 1.0
CG B:GLN207 4.4 44.1 1.0
CG B:GLN210 4.4 39.1 1.0
H2'1 B:DTP702 4.4 44.7 1.0
H8 B:DTP702 4.4 42.3 1.0
O1A B:DTP702 4.5 42.6 1.0
CD2 A:HIS151 4.5 48.0 1.0
O1G B:DTP702 4.6 49.6 1.0
NE1 B:TRP203 4.6 58.4 1.0
CB B:GLN210 4.6 39.7 1.0
O1B B:DTP702 4.6 42.9 1.0
CA B:GLN207 4.7 38.5 1.0
CB B:GLN207 4.7 41.5 1.0
CG2 A:THR154 4.9 33.8 1.0
NE2 A:HIS151 5.0 49.9 1.0

Reference:

O.Aurelius, R.Johansson, V.Bagenholm, T.Beck, A.Balhuizen, D.Lundin, B.M.Sjoberg, E.Mulliez, D.T.Logan. The Crystal Structure of the Thermotoga Maritima Anaerobic Ribonucleotide Reductase Lacks A Radical Cysteine Pre-Positioned in the Active Site To Be Published.
Page generated: Thu Aug 15 16:51:20 2024

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