Magnesium in PDB 6lym: Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase

All present enzymatic activity of Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase:
6.3.5.3;

The structure of Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase, PDB code: 6lym was solved by N.Sharma, A.S.Tanwar, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.21 / 2.46
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	147.296, 147.296, 141.455, 90, 90, 120
R / Rfree (%)	15.8 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase (pdb code 6lym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase, PDB code: 6lym:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase


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 D657A Mutant of Formylglycinamidine Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:12.9 occ:1.00 O3B A:ADP1301 1.9 16.1 1.0 O A:HOH1577 2.0 11.8 1.0 OD1 A:ASN722 2.1 13.3 1.0 OD1 A:ASP884 2.1 14.7 1.0 OD1 A:ASP679 2.1 14.0 1.0 O A:HOH1644 2.1 9.4 1.0 PB A:ADP1301 3.1 16.9 1.0 CG A:ASP679 3.1 14.7 1.0 CG A:ASN722 3.1 15.0 1.0 CG A:ASP884 3.1 14.3 1.0 OD2 A:ASP884 3.5 13.6 1.0 ND2 A:ASN722 3.6 15.3 1.0 O1B A:ADP1301 3.6 18.0 1.0 O2B A:ADP1301 3.6 16.9 1.0 O A:HOH1593 3.8 17.8 1.0 CB A:ASP679 3.9 14.4 1.0 OD2 A:ASP679 4.0 15.2 1.0 OG A:SER886 4.1 15.8 1.0 CA A:ASP679 4.3 14.1 1.0 NE2 A:HIS883 4.3 14.4 1.0 O A:ASP884 4.3 17.2 1.0 O3A A:ADP1301 4.3 15.9 1.0 O A:HOH1782 4.3 23.4 1.0 O A:HOH1542 4.4 11.8 1.0 CD2 A:HIS883 4.4 14.5 1.0 CB A:ASN722 4.5 15.3 1.0 CB A:ASP884 4.5 14.3 1.0 N A:ASP884 4.7 15.2 1.0 OE2 A:GLU718 4.8 13.7 1.0 C A:ASP884 4.8 15.8 1.0 CA A:ASN722 4.8 15.4 1.0 CB A:SER886 4.8 15.9 1.0 CA A:ASP884 4.9 15.0 1.0 O A:ASP679 4.9 13.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase


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 D657A Mutant of Formylglycinamidine Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:18.4 occ:1.00 O A:HOH1460 2.0 14.3 1.0 O A:HOH1544 2.0 10.8 1.0 O A:HOH1431 2.1 19.6 1.0 O1B A:ADP1301 2.1 18.0 1.0 OE2 A:GLU718 2.1 13.7 1.0 O A:HOH1523 2.1 13.2 1.0 CD A:GLU718 3.1 13.7 1.0 PB A:ADP1301 3.4 16.9 1.0 OE1 A:GLU718 3.5 13.6 1.0 O2B A:ADP1301 3.7 16.9 1.0 O A:HOH1424 3.9 18.6 1.0 O3A A:ADP1301 4.1 15.9 1.0 O A:HOH1577 4.1 11.8 1.0 O A:HOH1625 4.2 15.9 1.0 O2A A:ADP1301 4.2 16.6 1.0 OE1 A:GLU699 4.2 19.3 1.0 OD2 A:ASP887 4.2 18.4 1.0 ND2 A:ASN722 4.3 15.3 1.0 CG A:GLU718 4.4 13.8 1.0 O A:ILE697 4.4 15.3 1.0 OG A:SER886 4.5 15.8 1.0 O3B A:ADP1301 4.6 16.1 1.0 CB A:SER886 4.6 15.9 1.0 PA A:ADP1301 4.8 16.8 1.0 O A:HOH1629 4.8 17.0 1.0 O A:GLU699 4.8 16.1 1.0 N A:GLU699 5.0 16.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase


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 D657A Mutant of Formylglycinamidine Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1304 b:10.8 occ:1.00 O A:HOH1629 2.0 17.0 1.0 O A:HOH1542 2.0 11.8 1.0 O1A A:ADP1301 2.0 14.7 1.0 O2B A:ADP1301 2.1 16.9 1.0 O A:HOH1437 2.1 6.2 1.0 O A:HOH1433 2.3 11.7 1.0 PA A:ADP1301 3.2 16.8 1.0 PB A:ADP1301 3.4 16.9 1.0 O3A A:ADP1301 3.6 15.9 1.0 OG A:SER886 3.8 15.8 1.0 O A:HOH1544 4.0 10.8 1.0 O2A A:ADP1301 4.0 16.6 1.0 O A:HOH1632 4.1 18.3 1.0 OE1 A:GLU896 4.1 17.1 1.0 O A:HOH1644 4.1 9.4 1.0 O3B A:ADP1301 4.2 16.1 1.0 OE2 A:GLU896 4.2 15.3 1.0 O A:HOH1593 4.4 17.8 1.0 O A:THR645 4.4 13.0 1.0 O A:HOH1774 4.5 14.4 1.0 O1B A:ADP1301 4.5 18.0 1.0 O A:VAL646 4.5 13.6 1.0 OD2 A:ASP887 4.5 18.4 1.0 O5' A:ADP1301 4.5 16.2 1.0 CD A:GLU896 4.6 16.4 1.0 O A:ASP887 4.7 14.3 1.0 CB A:ASP887 4.8 16.3 1.0 C5' A:ADP1301 4.9 15.3 1.0 CA A:VAL646 4.9 14.4 1.0 N A:ASP887 5.0 15.4 1.0

N.Sharma, A.S.Tanwar, R.Anand. Crystal Structure of D657A Mutant of Formylglycinamidine Synthetase To Be Published.