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Magnesium in PDB 2is6: Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex

Protein crystallography data

The structure of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex, PDB code: 2is6 was solved by W.Yang, J.Y.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.336, 96.609, 110.930, 90.00, 94.05, 90.00
R / Rfree (%) 21 / 24

Other elements in 2is6:

The structure of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex (pdb code 2is6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex, PDB code: 2is6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2is6

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Magnesium binding site 1 out of 4 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


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 Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg681

b:36.9
occ:1.00
F1 A:MGF699 2.0 33.6 1.0
O1B A:ADP700 2.0 29.6 1.0
O A:HOH839 2.1 32.4 1.0
O A:HOH838 2.1 24.3 1.0
OG1 A:THR36 2.1 31.1 1.0
O A:HOH837 2.2 33.0 1.0
CB A:THR36 3.2 32.5 1.0
PB A:ADP700 3.2 33.1 1.0
MG A:MGF699 3.3 35.2 1.0
O3B A:ADP700 3.5 32.2 1.0
OE2 A:GLU221 3.9 31.7 1.0
N A:THR36 3.9 32.6 1.0
OD1 A:ASP220 4.0 34.5 1.0
CA A:THR36 4.1 33.0 1.0
OD2 A:ASP220 4.1 33.9 1.0
O2A A:ADP700 4.1 35.8 1.0
O3A A:ADP700 4.2 33.5 1.0
O A:HOH748 4.3 34.0 1.0
O2B A:ADP700 4.3 31.5 1.0
CG2 A:THR36 4.3 32.8 1.0
O1A A:ADP700 4.4 33.4 1.0
F3 A:MGF699 4.5 33.7 1.0
O A:HOH702 4.5 32.4 1.0
CG A:ASP220 4.5 32.8 1.0
CA A:GLY564 4.5 33.0 1.0
PA A:ADP700 4.5 34.3 1.0
O A:GLY564 4.6 37.1 1.0
O A:HOH771 4.6 31.9 1.0
CD A:GLU221 4.8 33.3 1.0
CB A:LYS35 4.9 30.0 1.0
C A:LYS35 4.9 32.7 1.0
F2 A:MGF699 5.0 35.9 1.0

Magnesium binding site 2 out of 4 in 2is6

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Magnesium binding site 2 out of 4 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


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 Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg699

b:35.2
occ:1.00
MG A:MGF699 0.0 35.2 1.0
F1 A:MGF699 1.6 33.6 1.0
F3 A:MGF699 1.8 33.7 1.0
O3B A:ADP700 1.9 32.2 1.0
F2 A:MGF699 2.0 35.9 1.0
O A:HOH702 2.0 32.4 1.0
PB A:ADP700 3.2 33.1 1.0
MG A:MG681 3.3 36.9 1.0
O A:HOH748 3.4 34.0 1.0
O1B A:ADP700 3.4 29.6 1.0
OE2 A:GLU221 3.8 31.7 1.0
NH2 A:ARG605 3.8 24.6 1.0
O A:HOH839 3.8 32.4 1.0
NH2 A:ARG284 3.9 30.3 1.0
O2B A:ADP700 4.0 31.5 1.0
OE1 A:GLN251 4.0 31.4 1.0
NZ A:LYS35 4.1 27.1 1.0
N A:GLY32 4.1 36.9 1.0
NE2 A:GLN251 4.1 30.0 1.0
O A:HOH838 4.1 24.3 1.0
CA A:ALA31 4.3 34.8 1.0
O3A A:ADP700 4.4 33.5 1.0
O A:HOH837 4.4 33.0 1.0
NH1 A:ARG284 4.4 32.7 1.0
CA A:GLY564 4.5 33.0 1.0
CD A:GLN251 4.5 31.7 1.0
CE A:LYS35 4.5 29.1 1.0
CB A:ALA31 4.6 31.9 1.0
CZ A:ARG284 4.6 35.3 1.0
N A:GLY564 4.7 31.5 1.0
NH1 A:ARG605 4.7 24.0 1.0
CZ A:ARG605 4.7 29.8 1.0
C A:ALA31 4.8 35.5 1.0
CD A:GLU221 4.8 33.3 1.0

Magnesium binding site 3 out of 4 in 2is6

Go back to Magnesium Binding Sites List in 2is6
Magnesium binding site 3 out of 4 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


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 Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg681

b:33.4
occ:1.00
F1 B:MGF701 1.9 36.5 1.0
OG1 B:THR36 2.0 26.4 1.0
O1B B:ADP702 2.0 30.1 1.0
O B:HOH732 2.1 36.8 1.0
O B:HOH777 2.2 30.5 1.0
O B:HOH778 2.2 29.4 1.0
CB B:THR36 3.1 29.5 1.0
MG B:MGF701 3.3 34.5 1.0
PB B:ADP702 3.3 32.7 1.0
O3B B:ADP702 3.6 32.0 1.0
OE2 B:GLU221 3.8 30.7 1.0
N B:THR36 3.8 32.3 1.0
OD1 B:ASP220 3.9 37.0 1.0
OD2 B:ASP220 4.0 35.2 1.0
CA B:THR36 4.0 30.6 1.0
O2A B:ADP702 4.2 29.8 1.0
CG2 B:THR36 4.2 28.6 1.0
O B:HOH752 4.2 38.1 1.0
O3A B:ADP702 4.3 30.6 1.0
O2B B:ADP702 4.3 33.6 1.0
CG B:ASP220 4.3 34.0 1.0
O B:HOH883 4.4 39.7 1.0
O B:GLY564 4.5 32.8 1.0
F3 B:MGF701 4.5 31.1 1.0
O B:HOH703 4.5 29.0 1.0
O1A B:ADP702 4.5 34.5 1.0
CA B:GLY564 4.5 28.3 1.0
PA B:ADP702 4.6 33.9 1.0
CD B:GLU221 4.8 35.5 1.0
CB B:LYS35 4.9 31.8 1.0
C B:LYS35 4.9 32.7 1.0
F2 B:MGF701 5.0 29.6 1.0
C B:GLY564 5.0 29.5 1.0

Magnesium binding site 4 out of 4 in 2is6

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Magnesium binding site 4 out of 4 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:34.5
occ:1.00
MG B:MGF701 0.0 34.5 1.0
F1 B:MGF701 1.6 36.5 1.0
F3 B:MGF701 1.9 31.1 1.0
F2 B:MGF701 1.9 29.6 1.0
O B:HOH703 2.0 29.0 1.0
O3B B:ADP702 2.1 32.0 1.0
MG B:MG681 3.3 33.4 1.0
PB B:ADP702 3.3 32.7 1.0
O1B B:ADP702 3.5 30.1 1.0
O B:HOH752 3.5 38.1 1.0
OE2 B:GLU221 3.7 30.7 1.0
O B:HOH732 3.9 36.8 1.0
NH2 B:ARG284 4.0 35.3 1.0
OE1 B:GLN251 4.0 34.0 1.0
O2B B:ADP702 4.1 33.6 1.0
NH2 B:ARG605 4.2 28.3 1.0
O B:HOH778 4.2 29.4 1.0
O B:HOH777 4.2 30.5 1.0
NZ B:LYS35 4.3 32.2 1.0
NE2 B:GLN251 4.3 30.0 1.0
N B:GLY32 4.3 32.1 1.0
CA B:GLY564 4.3 28.3 1.0
NH1 B:ARG605 4.4 28.0 1.0
CA B:ALA31 4.4 32.7 1.0
NH1 B:ARG284 4.4 33.8 1.0
O3A B:ADP702 4.5 30.6 1.0
CB B:ALA31 4.5 35.0 1.0
CD B:GLN251 4.6 34.4 1.0
N B:GLY564 4.6 28.0 1.0
CD B:GLU221 4.6 35.5 1.0
CZ B:ARG284 4.7 34.4 1.0
CE B:LYS35 4.7 31.5 1.0
CZ B:ARG605 4.8 31.1 1.0
OE1 B:GLU221 4.9 35.8 1.0
C B:ALA31 4.9 31.8 1.0
C B:GLY564 5.0 29.5 1.0

Reference:

J.Y.Lee, W.Yang. Uvrd Helicase Unwinds Dna One Base Pair at A Time By A Two-Part Power Stroke. Cell(Cambridge,Mass.) V. 127 1349 2006.
ISSN: ISSN 0092-8674
PubMed: 17190599
DOI: 10.1016/J.CELL.2006.10.049
Page generated: Mon Dec 14 07:27:42 2020

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