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Magnesium in PDB 4lgy: Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis

Enzymatic activity of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis

All present enzymatic activity of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis:
6.3.5.3;

Protein crystallography data

The structure of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis, PDB code: 4lgy was solved by A.S.Tanwar, V.D.Goyal, D.Choudhary, S.Panjikar, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.50 / 1.48
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 146.329, 146.329, 140.841, 90.00, 90.00, 120.00
R / Rfree (%) 14.2 / 16.6

Other elements in 4lgy:

The structure of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis (pdb code 4lgy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis, PDB code: 4lgy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4lgy

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Magnesium binding site 1 out of 7 in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:5.6
occ:1.00
 O1B A:ADP1301 2.0 6.2 1.0
OD1 A:ASP884 2.0 6.0 1.0
OD1 A:ASP679 2.1 6.1 1.0
OD1 A:ASN722 2.1 5.0 1.0
O A:HOH2425 2.1 6.8 1.0
O A:HOH2423 2.2 6.3 1.0
CG A:ASP884 3.0 6.0 1.0
CG A:ASP679 3.1 7.5 1.0
CG A:ASN722 3.1 5.4 1.0
PB A:ADP1301 3.2 6.0 1.0
OD2 A:ASP884 3.3 7.2 1.0
ND2 A:ASN722 3.6 6.0 1.0
O3B A:ADP1301 3.7 6.2 1.0
O2B A:ADP1301 3.8 6.2 1.0
CB A:ASP679 3.8 5.7 1.0
OD2 A:ASP679 3.9 7.2 1.0
O A:HOH1430 3.9 6.4 1.0
OG A:SER886 4.1 8.0 1.0
O A:HOH1742 4.2 14.2 1.0
NE2 A:HIS883 4.2 8.3 1.0
CA A:ASP679 4.3 6.2 1.0
CD2 A:HIS883 4.4 3.9 1.0
O A:ASP884 4.4 7.6 1.0
CB A:ASP884 4.4 5.3 1.0
O3A A:ADP1301 4.4 6.3 1.0
O A:HOH1428 4.4 6.9 1.0
CB A:ASN722 4.5 5.8 1.0
N A:ASP884 4.6 5.6 1.0
C A:ASP884 4.8 6.5 1.0
CA A:ASN722 4.8 5.2 1.0
OE2 A:GLU718 4.8 7.6 1.0
CA A:ASP884 4.8 5.9 1.0
O A:ASP679 4.9 7.3 1.0
CB A:SER886 5.0 7.7 1.0

Magnesium binding site 2 out of 7 in 4lgy

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Magnesium binding site 2 out of 7 in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:7.1
occ:1.00
 OE2 A:GLU718 2.0 7.6 1.0
O3B A:ADP1301 2.0 6.2 1.0
O A:HOH2422 2.0 9.9 1.0
O A:HOH2424 2.1 9.0 1.0
O A:HOH2427 2.1 7.8 1.0
O A:HOH1420 2.1 8.4 1.0
CD A:GLU718 3.1 8.7 1.0
PB A:ADP1301 3.3 6.0 1.0
OE1 A:GLU718 3.5 10.2 1.0
O2B A:ADP1301 3.6 6.2 1.0
O A:HOH1588 3.9 9.6 1.0
O A:HOH2423 4.0 6.3 1.0
ND2 A:ASN722 4.1 6.0 1.0
O3A A:ADP1301 4.1 6.3 1.0
O A:HOH1793 4.2 13.5 1.0
O1A A:ADP1301 4.3 8.5 1.0
OE2 A:GLU699 4.3 14.4 1.0
OD2 A:ASP887 4.3 11.6 1.0
O A:ILE697 4.4 6.8 1.0
CG A:GLU718 4.4 8.0 1.0
O1B A:ADP1301 4.5 6.2 1.0
OG A:SER886 4.5 8.0 1.0
CB A:SER886 4.7 7.7 1.0
PA A:ADP1301 4.8 6.6 1.0
O A:HOH2426 4.9 7.9 1.0
O A:GLU699 4.9 8.4 1.0

Magnesium binding site 3 out of 7 in 4lgy

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Magnesium binding site 3 out of 7 in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:6.7
occ:1.00
 O2B A:ADP1301 2.0 6.2 1.0
O2A A:ADP1301 2.0 6.3 1.0
O A:HOH1404 2.1 5.9 1.0
O A:HOH2426 2.1 7.9 1.0
O A:HOH1428 2.1 6.9 1.0
O A:HOH2421 2.2 7.3 1.0
PA A:ADP1301 3.2 6.6 1.0
PB A:ADP1301 3.3 6.0 1.0
O3A A:ADP1301 3.5 6.3 1.0
O1A A:ADP1301 3.9 8.5 1.0
O A:HOH1420 4.0 8.4 1.0
O A:HOH1568 4.0 10.4 1.0
OG A:SER886 4.1 8.0 1.0
O A:HOH2425 4.1 6.8 1.0
O1B A:ADP1301 4.1 6.2 1.0
OE1 A:GLU896 4.2 7.6 1.0
OE2 A:GLU896 4.2 7.0 1.0
O A:HOH1430 4.3 6.4 1.0
O3B A:ADP1301 4.4 6.2 1.0
O5' A:ADP1301 4.5 5.3 1.0
O A:HOH1619 4.5 12.6 1.0
O A:THR645 4.5 7.1 1.0
OD2 A:ASP887 4.6 11.6 1.0
O A:VAL646 4.6 6.4 1.0
CD A:GLU896 4.7 7.7 1.0
O A:ASP887 4.7 7.3 1.0
C5' A:ADP1301 4.8 6.1 1.0
CB A:ASP887 4.9 8.3 1.0

Magnesium binding site 4 out of 7 in 4lgy

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Magnesium binding site 4 out of 7 in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1337

b:27.1
occ:1.00
 O A:HOH3007 2.2 20.2 1.0
O A:HOH1470 2.7 10.5 1.0
O A:HOH2998 2.9 8.9 1.0
O A:PHE1169 3.2 8.2 1.0
O A:HOH3005 3.4 20.9 1.0
O A:HOH1448 3.9 7.2 1.0
C A:PHE1169 4.1 5.8 1.0
O A:HOH2669 4.3 36.1 1.0
O A:HOH3000 4.4 16.1 1.0
CB A:ARG1168 4.4 6.3 1.0
N A:PHE1169 4.4 5.4 1.0
CA A:SER1170 4.5 5.6 1.0
CD A:ARG1168 4.5 6.9 1.0
O A:HOH3003 4.7 21.2 1.0
O A:HOH1481 4.7 11.0 1.0
N A:SER1170 4.7 5.8 1.0
OG A:SER1170 4.7 7.8 1.0
O A:PRO1234 4.8 6.8 1.0
CG A:PRO1234 4.8 6.7 1.0
CG A:GLN674 4.9 5.4 1.0
CA A:PHE1169 4.9 5.5 1.0
CB A:GLN674 4.9 4.9 1.0
CG A:ARG1168 5.0 6.8 1.0

Magnesium binding site 5 out of 7 in 4lgy

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Magnesium binding site 5 out of 7 in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1338

b:31.6
occ:1.00
 OG1 A:THR1232 2.8 12.7 1.0
O A:HOH2483 3.1 18.4 1.0
O1 A:GOL1327 3.3 16.2 1.0
N A:THR1232 3.4 7.3 1.0
C A:GLU1231 3.5 7.6 1.0
CA A:THR1232 3.7 7.3 1.0
CB A:GLU1231 3.8 8.9 1.0
O A:GLU1231 3.8 8.8 1.0
C1 A:GOL1327 3.9 24.4 1.0
CB A:THR1232 3.9 8.4 1.0
CA A:GLU1231 4.0 7.8 1.0
N A:GLU1231 4.2 8.7 1.0
O A:HOH2154 4.6 23.8 1.0
OE1 A:GLN1004 4.7 17.2 1.0
CG2 A:THR1232 4.8 9.4 1.0
OG1 A:THR1230 5.0 11.4 1.0

Magnesium binding site 6 out of 7 in 4lgy

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Magnesium binding site 6 out of 7 in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1339

b:39.2
occ:1.00
 O A:HOH1632 2.6 17.6 1.0
O A:HOH2204 2.9 41.8 1.0
O A:PHE1112 3.3 18.6 1.0
CB A:ASN1113 3.6 13.5 1.0
OD1 A:ASN1113 3.6 19.9 1.0
CA A:ASN1113 3.6 12.3 1.0
C A:PHE1112 3.8 14.5 1.0
C A:CYS98 3.8 16.6 1.0
N A:ASN1113 3.9 12.2 1.0
O A:CYS98 3.9 19.5 1.0
N A:GLY99 3.9 14.3 1.0
CA A:GLY99 4.0 17.1 1.0
CG A:ASN1113 4.1 15.5 1.0
O A:ASN97 4.4 15.4 1.0
CA A:CYS98 4.4 12.6 1.0
O A:HOH1828 4.7 24.1 1.0
O A:HOH1882 4.7 21.7 1.0
CB A:PHE1112 4.8 12.3 1.0
CA A:PHE1112 4.9 11.0 1.0

Magnesium binding site 7 out of 7 in 4lgy

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Magnesium binding site 7 out of 7 in the Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1340

b:26.8
occ:1.00
 O A:ALA875 3.0 8.7 1.0
ND1 A:HIS813 3.1 9.6 1.0
NE2 A:GLN727 3.2 9.4 1.0
CE1 A:HIS813 3.2 9.8 1.0
OE1 A:GLN727 3.4 10.9 1.0
O A:HOH1616 3.6 12.6 1.0
CD A:GLN727 3.7 8.9 1.0
CA A:ALA875 3.9 7.3 1.0
C A:ALA875 3.9 6.8 1.0
O A:HOH2983 4.3 33.6 1.0
CB A:ALA875 4.4 8.3 1.0
CD A:ARG877 4.4 16.4 1.0
CG A:HIS813 4.4 7.5 1.0
NE2 A:HIS813 4.5 11.2 1.0
O A:VAL874 5.0 6.9 1.0

Reference:

A.S.Tanwar, V.D.Goyal, D.Choudhary, S.Panjikar, R.Anand. Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight From Xenon Trapping and Statistical Coupling Analysis Plos One V. 8 77781 2013.
ISSN: ESSN 1932-6203
PubMed: 24223728
DOI: 10.1371/JOURNAL.PONE.0077781
Page generated: Mon Aug 19 17:43:26 2024

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