Magnesium in PDB 4fe1: Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

All present enzymatic activity of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution:
1.97.1.12;

The structure of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution, PDB code: 4fe1 was solved by R.Fromme, P.D.Adams, P.Fromme, M.Levitt, G.F.Schroeder, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.97 / 4.92
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	281.000, 281.000, 165.200, 90.00, 90.00, 120.00
R / Rfree (%)	27.4 / 31.5

The structure of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution also contains other interesting chemical elements:

Iron	(Fe)	12 atoms
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 96;

Binding sites:

The binding sites of Magnesium atom in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution (pdb code 4fe1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 96 binding sites of Magnesium where determined in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution, PDB code: 4fe1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:55.6 occ:1.00 MG A:CLA801 0.0 55.6 1.0 ND A:CLA801 2.0 82.6 1.0 NB A:CLA801 2.0 55.3 1.0 NC A:CLA801 2.0 56.0 1.0 NE2 A:HIS680 2.1 0.4 1.0 NA A:CLA801 2.1 54.5 1.0 C4D A:CLA801 2.9 80.0 1.0 C1B A:CLA801 3.0 54.7 1.0 C4A A:CLA801 3.0 54.2 1.0 CD2 A:HIS680 3.0 1.0 1.0 C1D A:CLA801 3.0 84.4 1.0 C4C A:CLA801 3.1 56.3 1.0 C4B A:CLA801 3.1 55.5 1.0 C1C A:CLA801 3.1 56.2 1.0 CE1 A:HIS680 3.1 0.4 1.0 C1A A:CLA801 3.1 54.3 1.0 CHB A:CLA801 3.3 54.3 1.0 CHD A:CLA801 3.4 88.0 1.0 CHC A:CLA801 3.4 56.1 1.0 CHA A:CLA801 3.5 54.5 1.0 CAB B:CLA801 3.8 0.2 1.0 C3D A:CLA801 4.1 82.6 1.0 C3B B:CLA801 4.1 0.0 1.0 C2B A:CLA801 4.2 54.5 1.0 ND1 A:HIS680 4.2 0.9 1.0 CG A:HIS680 4.2 0.3 1.0 C2D A:CLA801 4.2 76.6 1.0 C3B A:CLA801 4.2 55.0 1.0 C3A A:CLA801 4.3 53.9 1.0 C3C A:CLA801 4.3 56.8 1.0 C2C A:CLA801 4.3 56.7 1.0 C2A A:CLA801 4.4 53.9 1.0 C4B B:CLA801 4.6 0.9 1.0 C2B B:CLA801 4.7 0.6 1.0 CBD A:CLA801 4.7 89.2 1.0 CHC B:CLA801 4.8 0.3 1.0

Magnesium binding site 2 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:0.8 occ:1.00 MG A:CLA802 0.0 0.8 1.0 ND A:CLA802 2.0 0.4 1.0 NB A:CLA802 2.0 83.8 1.0 NC A:CLA802 2.0 0.7 1.0 NA A:CLA802 2.1 78.1 1.0 C4D A:CLA802 2.9 0.4 1.0 C1B A:CLA802 3.0 84.2 1.0 C4A A:CLA802 3.0 77.7 1.0 C1D A:CLA802 3.0 0.2 1.0 C4C A:CLA802 3.0 0.4 1.0 C1C A:CLA802 3.0 0.7 1.0 C4B A:CLA802 3.1 93.3 1.0 C1A A:CLA802 3.1 82.9 1.0 CHB A:CLA802 3.3 80.9 1.0 CHD A:CLA802 3.4 0.8 1.0 CHC A:CLA802 3.4 0.1 1.0 CHA A:CLA802 3.4 94.1 1.0 CBB B:CLA803 3.6 54.7 1.0 OD1 A:ASN604 4.0 47.1 1.0 C3D A:CLA802 4.1 0.2 1.0 C2B A:CLA802 4.2 85.1 1.0 C2D A:CLA802 4.2 0.1 1.0 C3B A:CLA802 4.2 94.5 1.0 C20 A:CLA801 4.3 45.7 1.0 C3C A:CLA802 4.3 0.1 1.0 C2C A:CLA802 4.3 46.3 1.0 C3A A:CLA802 4.3 70.1 1.0 C2 A:CLA801 4.4 49.0 1.0 C2A A:CLA802 4.4 76.5 1.0 C5 A:CLA801 4.6 48.3 1.0 C3 A:CLA801 4.7 48.8 1.0 ND2 A:ASN604 4.7 46.0 1.0 CG A:ASN604 4.7 46.8 1.0 CAB B:CLA803 4.8 54.3 1.0 CB B:ALA664 4.9 55.8 1.0 CBD A:CLA802 4.9 78.2 1.0

Magnesium binding site 3 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:0.6 occ:1.00 MG A:CLA803 0.0 0.6 1.0 ND A:CLA803 2.0 95.9 1.0 NB A:CLA803 2.0 0.0 1.0 NC A:CLA803 2.0 98.6 1.0 NA A:CLA803 2.1 94.5 1.0 SD A:MET688 2.4 0.8 1.0 C4D A:CLA803 2.9 93.9 1.0 C1B A:CLA803 3.0 0.6 1.0 C4A A:CLA803 3.0 0.5 1.0 C1D A:CLA803 3.0 99.2 1.0 C4C A:CLA803 3.0 0.9 1.0 C1C A:CLA803 3.1 96.2 1.0 C4B A:CLA803 3.1 0.2 1.0 C1A A:CLA803 3.1 95.7 1.0 CHB A:CLA803 3.3 0.3 1.0 CHD A:CLA803 3.4 97.4 1.0 CG A:MET688 3.4 57.9 1.0 CHC A:CLA803 3.4 99.7 1.0 CHA A:CLA803 3.4 93.3 1.0 CE A:MET688 3.7 60.4 1.0 NE1 B:TRP588 3.7 66.1 1.0 CB A:MET688 3.9 57.3 1.0 C3D A:CLA803 4.1 93.2 1.0 C2B A:CLA803 4.2 0.2 1.0 C2D A:CLA803 4.2 91.9 1.0 C3B A:CLA803 4.2 0.5 1.0 C3C A:CLA803 4.3 93.2 1.0 C2C A:CLA803 4.3 90.2 1.0 C3A A:CLA803 4.3 0.1 1.0 CZ2 B:TRP588 4.4 0.3 1.0 CE2 B:TRP588 4.4 66.3 1.0 C2A A:CLA803 4.4 99.1 1.0 CD1 B:TRP588 4.8 64.9 1.0 CH2 A:TRP697 4.8 0.4 1.0 CBD A:CLA803 4.8 0.5 1.0

Magnesium binding site 4 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:0.1 occ:1.00 MG A:CLA804 0.0 0.1 1.0 ND A:CLA804 2.0 98.0 1.0 NE2 A:HIS56 2.0 82.2 1.0 NB A:CLA804 2.0 0.2 1.0 NC A:CLA804 2.0 0.2 1.0 NA A:CLA804 2.1 89.0 1.0 CE1 A:HIS56 2.8 80.7 1.0 C4D A:CLA804 2.9 89.6 1.0 C1B A:CLA804 3.0 0.5 1.0 C4A A:CLA804 3.0 90.3 1.0 C1D A:CLA804 3.0 0.2 1.0 C4C A:CLA804 3.0 0.9 1.0 C1C A:CLA804 3.1 0.7 1.0 C4B A:CLA804 3.1 0.8 1.0 CD2 A:HIS56 3.1 81.5 1.0 C1A A:CLA804 3.1 90.1 1.0 CHB A:CLA804 3.3 89.7 1.0 CHD A:CLA804 3.4 0.2 1.0 CHC A:CLA804 3.4 0.2 1.0 CHA A:CLA804 3.5 89.2 1.0 ND1 A:HIS56 4.0 79.0 1.0 C3D A:CLA804 4.1 86.6 1.0 CG A:HIS56 4.2 79.5 1.0 C2B A:CLA804 4.2 0.6 1.0 C2D A:CLA804 4.2 84.6 1.0 C3B A:CLA804 4.2 96.5 1.0 C3C A:CLA804 4.3 0.4 1.0 C2C A:CLA804 4.3 0.7 1.0 C3A A:CLA804 4.4 92.8 1.0 C2A A:CLA804 4.4 92.7 1.0 CBB A:CLA805 4.7 0.3 1.0 CBD A:CLA804 4.9 90.6 1.0

Magnesium binding site 5 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:89.1 occ:1.00 MG A:CLA805 0.0 89.1 1.0 ND A:CLA805 2.0 88.5 1.0 NB A:CLA805 2.0 91.1 1.0 NC A:CLA805 2.0 97.8 1.0 NA A:CLA805 2.1 0.7 1.0 CMB A:CLA830 2.3 0.1 1.0 C4D A:CLA805 2.9 0.9 1.0 C1B A:CLA805 3.0 91.9 1.0 C4A A:CLA805 3.0 0.8 1.0 C1D A:CLA805 3.0 88.2 1.0 C4C A:CLA805 3.0 0.9 1.0 C1C A:CLA805 3.1 94.9 1.0 C4B A:CLA805 3.1 98.8 1.0 C1A A:CLA805 3.1 0.6 1.0 CHB A:CLA805 3.3 91.7 1.0 CHD A:CLA805 3.4 88.2 1.0 CHC A:CLA805 3.4 94.3 1.0 NE2 A:HIS76 3.5 0.7 1.0 CHA A:CLA805 3.5 0.4 1.0 C2B A:CLA830 3.7 83.7 1.0 CD2 A:HIS76 4.0 1.0 1.0 C3D A:CLA805 4.1 0.6 1.0 C2B A:CLA805 4.2 0.3 1.0 C2D A:CLA805 4.2 88.0 1.0 C3B A:CLA805 4.2 0.5 1.0 C3C A:CLA805 4.3 1.0 1.0 C2C A:CLA805 4.3 99.8 1.0 C3A A:CLA805 4.3 0.0 1.0 C2A A:CLA805 4.4 0.7 1.0 CE1 A:HIS76 4.5 0.7 1.0 C3B A:CLA830 4.6 78.8 1.0 C1B A:CLA830 4.7 82.5 1.0 CAB A:CLA830 4.8 89.4 1.0 CBD A:CLA805 4.9 89.5 1.0 CHB A:CLA830 4.9 70.9 1.0 CBB A:CLA830 4.9 95.7 1.0

Magnesium binding site 6 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg806 b:75.4 occ:1.00 MG A:CLA806 0.0 75.4 1.0 ND A:CLA806 2.0 0.4 1.0 NB A:CLA806 2.0 74.8 1.0 NC A:CLA806 2.0 97.6 1.0 NA A:CLA806 2.1 0.4 1.0 C4D A:CLA806 2.9 0.2 1.0 C1B A:CLA806 3.0 73.8 1.0 C4A A:CLA806 3.0 0.4 1.0 NE2 A:HIS79 3.0 0.0 1.0 C1D A:CLA806 3.0 1.0 1.0 C4C A:CLA806 3.0 95.7 1.0 C1C A:CLA806 3.0 77.5 1.0 C4B A:CLA806 3.1 75.3 1.0 C1A A:CLA806 3.1 0.5 1.0 CHB A:CLA806 3.3 0.7 1.0 CHD A:CLA806 3.4 0.3 1.0 CHC A:CLA806 3.4 76.4 1.0 CHA A:CLA806 3.4 0.9 1.0 C16 A:CLA806 3.7 69.9 1.0 CE1 A:HIS79 3.9 0.3 1.0 CD2 A:HIS79 4.0 0.8 1.0 C3D A:CLA806 4.1 0.4 1.0 C2B A:CLA806 4.2 73.6 1.0 C2D A:CLA806 4.2 0.3 1.0 C3B A:CLA806 4.2 74.6 1.0 C3C A:CLA806 4.3 92.0 1.0 C2C A:CLA806 4.3 98.2 1.0 C14 A:CLA806 4.3 94.4 1.0 C3A A:CLA806 4.3 0.5 1.0 C15 A:CLA806 4.4 68.5 1.0 C2A A:CLA806 4.4 0.6 1.0 C13 A:CLA806 4.4 98.1 1.0 C17 A:CLA806 4.5 70.5 1.0 C18 A:CLA806 4.5 72.0 1.0 CMA A:CLA805 4.8 89.6 1.0 CBD A:CLA806 4.9 0.2 1.0 C19 A:CLA806 5.0 71.0 1.0

Magnesium binding site 7 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg807 b:0.3 occ:1.00 MG A:CLA807 0.0 0.3 1.0 ND A:CLA807 2.0 0.3 1.0 NB A:CLA807 2.0 93.8 1.0 NE2 A:HIS93 2.0 0.0 1.0 NC A:CLA807 2.0 99.2 1.0 NA A:CLA807 2.1 95.0 1.0 C4D A:CLA807 2.9 0.5 1.0 C1B A:CLA807 3.0 91.5 1.0 CD2 A:HIS93 3.0 0.9 1.0 CE1 A:HIS93 3.0 0.9 1.0 C4A A:CLA807 3.0 92.5 1.0 C1D A:CLA807 3.0 1.0 1.0 C4B A:CLA807 3.1 93.8 1.0 C4C A:CLA807 3.1 0.1 1.0 C1C A:CLA807 3.1 98.4 1.0 C1A A:CLA807 3.1 96.1 1.0 CHB A:CLA807 3.3 90.9 1.0 CHD A:CLA807 3.4 0.8 1.0 CHC A:CLA807 3.4 95.8 1.0 CHA A:CLA807 3.5 98.7 1.0 ND1 A:HIS93 4.1 0.0 1.0 CG A:HIS93 4.1 0.6 1.0 C3D A:CLA807 4.1 0.2 1.0 C2B A:CLA807 4.2 89.9 1.0 C2D A:CLA807 4.2 0.9 1.0 C3B A:CLA807 4.2 91.3 1.0 C3C A:CLA807 4.3 0.1 1.0 C2C A:CLA807 4.3 0.9 1.0 C3A A:CLA807 4.4 91.7 1.0 C2A A:CLA807 4.4 94.2 1.0 CBD A:CLA807 4.9 1.0 1.0 CD2 A:PHE92 5.0 0.8 1.0

Magnesium binding site 8 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg808 b:77.9 occ:1.00 MG A:CLA808 0.0 77.9 1.0 OE1 A:GLN115 1.8 0.7 1.0 ND A:CLA808 2.0 76.4 1.0 NB A:CLA808 2.0 78.7 1.0 NC A:CLA808 2.0 75.5 1.0 NA A:CLA808 2.1 0.7 1.0 CD A:GLN115 2.8 82.1 1.0 C4D A:CLA808 2.9 0.5 1.0 C1B A:CLA808 3.0 1.0 1.0 C4A A:CLA808 3.0 0.7 1.0 C1D A:CLA808 3.0 74.8 1.0 C4C A:CLA808 3.0 74.1 1.0 C4B A:CLA808 3.0 77.9 1.0 C1C A:CLA808 3.0 75.3 1.0 C1A A:CLA808 3.1 0.1 1.0 CHB A:CLA808 3.3 0.5 1.0 C4 A:CLA828 3.3 85.2 1.0 NE2 A:GLN115 3.3 83.0 1.0 CHD A:CLA808 3.4 73.8 1.0 CHC A:CLA808 3.4 80.3 1.0 CHA A:CLA808 3.5 0.5 1.0 CG A:GLN115 4.1 84.0 1.0 C3D A:CLA808 4.1 75.8 1.0 C2B A:CLA808 4.2 80.4 1.0 C2D A:CLA808 4.2 93.0 1.0 C3B A:CLA808 4.2 79.0 1.0 C3C A:CLA808 4.3 91.6 1.0 CB A:GLN115 4.3 83.9 1.0 C2C A:CLA808 4.3 73.9 1.0 C3A A:CLA808 4.3 0.6 1.0 C2A A:CLA808 4.4 0.3 1.0 C3 A:CLA828 4.8 78.1 1.0 CBD A:CLA808 4.8 0.0 1.0 CD1 A:ILE137 4.8 79.1 1.0

Magnesium binding site 9 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg809 b:1.0 occ:1.00 MG A:CLA809 0.0 1.0 1.0 OE1 A:GLN123 2.0 0.9 1.0 ND A:CLA809 2.0 0.9 1.0 NB A:CLA809 2.0 0.8 1.0 NC A:CLA809 2.0 0.7 1.0 NA A:CLA809 2.1 0.1 1.0 C4D A:CLA809 2.9 0.2 1.0 C1B A:CLA809 3.0 0.1 1.0 CD A:GLN123 3.0 0.7 1.0 C4A A:CLA809 3.0 0.9 1.0 C1D A:CLA809 3.0 0.9 1.0 C4C A:CLA809 3.0 0.8 1.0 C1C A:CLA809 3.1 0.5 1.0 C4B A:CLA809 3.1 0.0 1.0 C1A A:CLA809 3.1 0.7 1.0 CHB A:CLA809 3.3 0.8 1.0 CHD A:CLA809 3.4 0.4 1.0 CHC A:CLA809 3.4 0.6 1.0 CHA A:CLA809 3.5 89.4 1.0 NE2 A:GLN123 3.6 0.8 1.0 C19 A:CLA828 4.1 81.2 1.0 C3D A:CLA809 4.1 0.7 1.0 CG A:GLN123 4.1 88.4 1.0 CB A:GLN123 4.1 86.5 1.0 C2B A:CLA809 4.2 0.3 1.0 C2D A:CLA809 4.2 0.2 1.0 C3B A:CLA809 4.2 88.8 1.0 C3C A:CLA809 4.3 82.0 1.0 C2C A:CLA809 4.3 82.8 1.0 C3A A:CLA809 4.3 0.8 1.0 C2A A:CLA809 4.4 0.0 1.0 C18 A:CLA828 4.4 0.8 1.0 CBD A:CLA809 4.9 0.0 1.0

Magnesium binding site 10 out of 96 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg810 b:0.7 occ:1.00 MG A:CLA810 0.0 0.7 1.0 ND A:CLA810 2.0 0.4 1.0 NB A:CLA810 2.0 0.4 1.0 NC A:CLA810 2.0 0.1 1.0 NE2 A:HIS179 2.1 0.6 1.0 NA A:CLA810 2.1 0.2 1.0 C4D A:CLA810 2.9 0.4 1.0 CE1 A:HIS179 2.9 0.9 1.0 C1B A:CLA810 3.0 0.1 1.0 C4A A:CLA810 3.0 0.1 1.0 C1D A:CLA810 3.0 0.5 1.0 C4C A:CLA810 3.1 0.6 1.0 C1C A:CLA810 3.1 0.3 1.0 C4B A:CLA810 3.1 0.4 1.0 C1A A:CLA810 3.1 0.9 1.0 CD2 A:HIS179 3.2 0.9 1.0 CHB A:CLA810 3.3 0.5 1.0 CHD A:CLA810 3.4 0.2 1.0 CHC A:CLA810 3.4 0.4 1.0 CHA A:CLA810 3.5 0.7 1.0 ND1 A:HIS179 4.1 0.3 1.0 C3D A:CLA810 4.1 0.4 1.0 C2B A:CLA810 4.2 0.1 1.0 C2D A:CLA810 4.2 0.8 1.0 CG A:HIS179 4.2 0.4 1.0 C3B A:CLA810 4.2 0.8 1.0 C3C A:CLA810 4.3 0.7 1.0 C2C A:CLA810 4.3 0.5 1.0 C3A A:CLA810 4.3 0.6 1.0 C2A A:CLA810 4.4 0.0 1.0 CBD A:CLA810 4.8 0.8 1.0

A.T.Brunger, P.D.Adams, P.Fromme, R.Fromme, M.Levitt, G.F.Schroder. Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution. Structure V. 20 957 2012.
ISSN: ISSN 0969-2126
PubMed: 22681901
DOI: 10.1016/J.STR.2012.04.020