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Magnesium in PDB 4r7g: Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment

Enzymatic activity of Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment

All present enzymatic activity of Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment:
6.3.5.3;

Protein crystallography data

The structure of Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment, PDB code: 4r7g was solved by A.S.Tanwar, D.J.Sindhikara, F.Hirata, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 146.570, 146.570, 141.320, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment (pdb code 4r7g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment, PDB code: 4r7g:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4r7g

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Magnesium binding site 1 out of 3 in the Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:18.5
occ:1.00
 O3B A:ADP1310 2.2 1.5 0.5
OD1 A:ASP679 2.3 30.3 1.0
OD1 A:ASP884 2.4 15.5 1.0
OD1 A:ASN722 2.5 13.4 1.0
O1B A:ADP1310 3.1 1.5 0.5
PB A:ADP1310 3.1 1.5 0.5
CG A:ASP884 3.2 13.4 1.0
CG A:ASN722 3.4 15.7 1.0
OD2 A:ASP884 3.4 13.2 1.0
CG A:ASP679 3.4 30.0 1.0
ND2 A:ASN722 3.6 13.8 1.0
OG A:SER886 3.7 24.8 1.0
O2B A:ADP1310 3.8 1.5 0.5
O A:ASP884 4.0 23.9 1.0
OD2 A:ASP679 4.1 30.2 1.0
O A:HOH1535 4.2 20.9 1.0
CB A:SER886 4.3 22.8 1.0
CB A:ASP679 4.4 28.3 1.0
O3A A:ADP1310 4.4 1.5 0.5
NE2 A:HIS883 4.5 4.3 1.0
CB A:ASP884 4.6 12.2 1.0
CD2 A:HIS883 4.6 4.7 1.0
C A:ASP884 4.6 23.9 1.0
OE2 A:GLU718 4.6 28.5 1.0
N A:ASP884 4.7 21.0 1.0
CA A:ASP679 4.8 23.7 1.0
CA A:ASP884 4.8 22.6 1.0
CB A:ASN722 4.8 17.2 1.0
MG A:MG1303 4.9 18.8 1.0

Magnesium binding site 2 out of 3 in 4r7g

Go back to Magnesium Binding Sites List in 4r7g
Magnesium binding site 2 out of 3 in the Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:28.9
occ:1.00
 O2B A:ADP1310 2.3 1.5 0.5
O A:HOH1615 2.3 60.0 1.0
OE2 A:GLU718 2.6 28.5 1.0
CD A:GLU718 3.5 26.1 1.0
O A:ILE697 3.7 12.2 1.0
PB A:ADP1310 3.7 1.5 0.5
O A:HOH1609 3.8 31.9 1.0
OE1 A:GLU718 3.8 27.5 1.0
ND2 A:ASN722 4.0 13.8 1.0
O1A A:ADP1310 4.1 1.5 0.5
O3B A:ADP1310 4.3 1.5 0.5
CB A:TYR388 4.4 5.5 1.0
O3A A:ADP1310 4.4 1.5 0.5
C A:ILE697 4.5 11.4 1.0
CG A:GLU718 4.7 26.2 1.0
OE1 A:GLU699 4.7 24.3 1.0
O1B A:ADP1310 4.7 1.5 0.5
O A:GLU699 4.8 17.3 1.0
N A:GLU699 4.8 14.3 1.0
PA A:ADP1310 4.9 1.5 0.5
CG2 A:ILE697 4.9 1.0 1.0

Magnesium binding site 3 out of 3 in 4r7g

Go back to Magnesium Binding Sites List in 4r7g
Magnesium binding site 3 out of 3 in the Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:18.8
occ:1.00
 O1B A:ADP1310 2.2 1.5 0.5
O A:HOH1444 2.4 26.7 1.0
O2A A:ADP1310 2.7 1.5 0.5
PB A:ADP1310 3.5 1.5 0.5
OE1 A:GLU896 3.6 11.2 1.0
OG A:SER886 3.7 24.8 1.0
PA A:ADP1310 3.8 1.5 0.5
O3A A:ADP1310 3.8 1.5 0.5
OE2 A:GLU896 3.9 10.8 1.0
O A:ASP887 4.1 21.8 1.0
CD A:GLU896 4.2 10.6 1.0
O2B A:ADP1310 4.3 1.5 0.5
O A:HOH1535 4.4 20.9 1.0
O1A A:ADP1310 4.5 1.5 0.5
O A:VAL646 4.6 8.4 1.0
CG1 A:VAL892 4.6 6.6 1.0
O3B A:ADP1310 4.6 1.5 0.5
CB A:ASP887 4.9 26.4 1.0
O A:THR645 4.9 15.2 1.0
MG A:MG1301 4.9 18.5 1.0
O A:HOH1557 4.9 38.9 1.0
O A:HOH1615 4.9 60.0 1.0
O5' A:ADP1310 4.9 1.5 0.5

Reference:

A.S.Tanwar, D.J.Sindhikara, F.Hirata, R.Anand. Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway By Combining 3D-Rism Theory with Experiment Acs Chem.Biol. 2014.
ISSN: ESSN 1554-8937
PubMed: 25551173
DOI: 10.1021/CB501015R
Page generated: Mon Aug 11 23:11:02 2025

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