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Magnesium in PDB 4l78: Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl

Enzymatic activity of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl

All present enzymatic activity of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl:
6.3.5.3;

Protein crystallography data

The structure of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl, PDB code: 4l78 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) 19.57 / 2.18
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 146.680, 146.680, 141.221, 90.00, 90.00, 120.00
R / Rfree (%) 13.9 / 18.8

Other elements in 4l78:

The structure of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Xenon (Xe) 5 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl (pdb code 4l78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl, PDB code: 4l78:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4l78

Go back to Magnesium Binding Sites List in 4l78
Magnesium binding site 1 out of 4 in the Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:12.8
occ:1.00
 O2B A:ADP1301 2.0 12.8 1.0
OD1 A:ASP884 2.0 12.6 1.0
OD1 A:ASP679 2.1 11.0 1.0
O A:HOH1491 2.1 11.4 1.0
OD1 A:ASN722 2.1 11.6 1.0
O A:HOH1440 2.2 9.9 1.0
CG A:ASP884 3.0 11.8 1.0
CG A:ASP679 3.1 12.5 1.0
PB A:ADP1301 3.2 14.0 1.0
CG A:ASN722 3.2 12.0 1.0
OD2 A:ASP884 3.4 11.2 1.0
ND2 A:ASN722 3.7 11.1 1.0
O1B A:ADP1301 3.7 13.1 1.0
O3B A:ADP1301 3.8 13.2 1.0
CB A:ASP679 3.9 10.9 1.0
OD2 A:ASP679 3.9 11.7 1.0
O A:HOH1592 3.9 10.1 1.0
OG A:SER886 4.1 12.0 1.0
NE2 A:HIS883 4.1 13.2 1.0
CD2 A:HIS883 4.3 11.5 1.0
O A:HOH1663 4.3 14.6 1.0
CA A:ASP679 4.3 12.1 1.0
O A:HOH1542 4.4 11.7 1.0
CB A:ASP884 4.4 11.4 1.0
O3A A:ADP1301 4.4 12.6 1.0
CB A:ASN722 4.5 11.3 1.0
O A:ASP884 4.5 15.3 1.0
N A:ASP884 4.6 13.0 1.0
OE2 A:GLU718 4.8 13.8 1.0
CA A:ASN722 4.8 11.7 1.0
C A:ASP884 4.8 13.6 1.0
CA A:ASP884 4.8 12.8 1.0

Magnesium binding site 2 out of 4 in 4l78

Go back to Magnesium Binding Sites List in 4l78
Magnesium binding site 2 out of 4 in the Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:14.8
occ:1.00
 OE2 A:GLU718 2.0 13.8 1.0
O A:HOH1467 2.1 12.2 1.0
O A:HOH1531 2.1 15.8 1.0
O1B A:ADP1301 2.1 13.1 1.0
O A:HOH1525 2.1 13.2 1.0
O A:HOH2037 2.2 12.1 1.0
CD A:GLU718 3.1 12.7 1.0
OE1 A:GLU718 3.4 12.3 1.0
PB A:ADP1301 3.4 14.0 1.0
O3B A:ADP1301 3.7 13.2 1.0
O A:HOH1703 4.0 17.0 1.0
O A:HOH1440 4.0 9.9 1.0
O A:HOH1611 4.1 14.2 1.0
ND2 A:ASN722 4.1 11.1 1.0
O1A A:ADP1301 4.2 12.2 1.0
O3A A:ADP1301 4.2 12.6 1.0
OD2 A:ASP887 4.3 15.9 1.0
OE1 A:GLU699 4.3 19.0 1.0
O A:ILE697 4.4 13.8 1.0
CG A:GLU718 4.4 11.5 1.0
OG A:SER886 4.5 12.0 1.0
O2B A:ADP1301 4.6 12.8 1.0
CB A:SER886 4.6 11.8 1.0
O A:GLU699 4.8 13.6 1.0
PA A:ADP1301 4.9 13.2 1.0
O A:HOH1479 4.9 8.6 1.0
CB A:TYR388 5.0 11.4 1.0

Magnesium binding site 3 out of 4 in 4l78

Go back to Magnesium Binding Sites List in 4l78
Magnesium binding site 3 out of 4 in the Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:10.4
occ:1.00
 O3B A:ADP1301 2.1 13.2 1.0
O2A A:ADP1301 2.1 10.6 1.0
O A:HOH1486 2.1 12.3 1.0
O A:HOH1542 2.2 11.7 1.0
O A:HOH1454 2.2 10.6 1.0
O A:HOH1479 2.3 8.6 1.0
PA A:ADP1301 3.2 13.2 1.0
PB A:ADP1301 3.3 14.0 1.0
O3A A:ADP1301 3.6 12.6 1.0
O A:HOH1467 4.0 12.2 1.0
O1A A:ADP1301 4.0 12.2 1.0
OE2 A:GLU896 4.1 11.0 1.0
O A:HOH1666 4.1 13.9 1.0
OE1 A:GLU896 4.1 11.5 1.0
OG A:SER886 4.2 12.0 1.0
O2B A:ADP1301 4.2 12.8 1.0
O A:HOH1491 4.3 11.4 1.0
O A:THR645 4.4 12.1 1.0
O A:HOH1592 4.4 10.1 1.0
O1B A:ADP1301 4.5 13.1 1.0
O A:VAL646 4.5 13.3 1.0
O5' A:ADP1301 4.5 11.8 1.0
O A:HOH1464 4.5 18.0 1.0
CD A:GLU896 4.6 11.3 1.0
OD2 A:ASP887 4.6 15.9 1.0
O A:ASP887 4.6 11.5 1.0
C5' A:ADP1301 4.8 11.8 1.0
CB A:ASP887 4.9 12.7 1.0
CA A:VAL646 4.9 12.5 1.0

Magnesium binding site 4 out of 4 in 4l78

Go back to Magnesium Binding Sites List in 4l78
Magnesium binding site 4 out of 4 in the Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important For Structure and Function of Multidomain Protein Stpurl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1305

b:5.0
occ:1.00
 OH A:TYR251 3.5 15.6 1.0
CZ A:TYR251 3.8 14.6 1.0
CE1 A:TYR251 4.0 13.1 1.0
OD2 A:ASP250 4.2 24.4 1.0
CE2 A:TYR251 4.5 13.5 1.0
OD2 A:ASP730 4.7 15.1 1.0
CD1 A:TYR251 4.9 13.2 1.0
CB A:ASP250 5.0 19.1 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: Sat Aug 17 04:27:02 2024

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