Magnesium in PDB 6xup: Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat

The structure of Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat, PDB code: 6xup was solved by S.Grazulis, M.Zaremba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.72 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.798, 60.872, 101.718, 76.56, 75.59, 79.39
R / Rfree (%)	18.1 / 22.4

The structure of Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat also contains other interesting chemical elements:

Potassium	(K)	1 atom
Arsenic	(As)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat (pdb code 6xup). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat, PDB code: 6xup:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:34.0 occ:1.00 OP3 R:DA1 1.9 35.4 1.0 OE1 A:GLN159 2.1 35.8 1.0 O R:HOH104 2.1 41.5 1.0 OP1 R:DC3 2.3 35.8 1.0 OXT A:LEU427 2.4 39.8 1.0 O A:LEU427 2.7 37.1 1.0 C A:LEU427 3.0 40.0 1.0 CD A:GLN159 3.0 34.5 1.0 P R:DA1 3.2 36.6 1.0 NE2 A:GLN159 3.3 32.3 1.0 OP1 R:DA1 3.5 45.2 1.0 NH1 A:ARG380 3.5 53.8 1.0 P R:DC3 3.5 36.9 1.0 C5' R:DA1 3.9 33.6 1.0 O5' R:DA1 3.9 43.6 1.0 NZ A:LYS163 4.0 32.6 1.0 O3' R:DT2 4.0 35.5 1.0 O R:HOH105 4.1 50.9 1.0 NE2 A:GLN137 4.1 29.6 1.0 OP2 R:DC3 4.2 53.4 1.0 OP2 R:DA1 4.2 32.7 1.0 O A:HOH712 4.3 40.6 1.0 CG A:GLN159 4.4 33.0 1.0 CA A:LEU427 4.5 35.3 1.0 CE A:LYS163 4.6 35.5 1.0 OE1 A:GLN137 4.7 34.1 1.0 O5' R:DC3 4.8 36.2 1.0 O A:HOH671 4.8 43.2 1.0 CZ A:ARG380 4.8 44.8 1.0 CD A:GLN137 4.9 30.8 1.0

Magnesium binding site 2 out of 3 in the Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:59.2 occ:1.00 O A:HOH815 2.6 59.0 1.0 N A:ASN413 2.6 49.9 1.0 OD1 A:ASN132 2.6 49.3 1.0 O A:HOH607 2.7 62.4 1.0 O A:ASN413 3.2 49.3 1.0 O A:PRO411 3.3 34.4 1.0 CA A:ILE412 3.3 35.3 1.0 C A:ILE412 3.4 41.2 1.0 CA A:ASN413 3.6 54.0 1.0 CG A:ASN132 3.7 37.4 1.0 C A:ASN413 3.8 47.4 1.0 O A:HOH840 3.9 60.1 1.0 O A:HOH741 4.0 61.8 1.0 C A:PRO411 4.1 36.8 1.0 N A:ILE412 4.1 34.5 1.0 ND2 A:ASN132 4.2 32.1 1.0 O A:HOH691 4.3 46.0 1.0 CB A:ASN413 4.3 61.0 1.0 CB A:ILE412 4.5 31.6 1.0 CD1 A:LEU420 4.5 36.7 1.0 CG2 A:ILE412 4.5 35.2 1.0 O A:ILE412 4.6 46.7 1.0 CB A:ASN132 4.9 33.9 1.0 N A:PRO414 4.9 45.4 1.0

Magnesium binding site 3 out of 3 in the Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'- Patcgtggccacgat within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:39.6 occ:1.00 OP3 P:DA1 1.8 43.9 1.0 OE1 B:GLN159 2.0 44.3 1.0 OP1 P:DC3 2.1 47.0 1.0 O P:HOH103 2.2 41.0 1.0 OXT B:LEU427 2.2 46.2 1.0 O B:LEU427 2.7 46.8 1.0 C B:LEU427 2.8 52.9 1.0 CD B:GLN159 3.0 48.6 1.0 P P:DA1 3.2 58.2 1.0 NE2 B:GLN159 3.3 47.6 1.0 OP1 P:DA1 3.4 54.4 1.0 P P:DC3 3.5 47.8 1.0 NH1 B:ARG380 3.9 55.6 1.0 NZ B:LYS163 4.0 36.7 1.0 O3' P:DT2 4.0 45.3 1.0 O5' P:DA1 4.0 59.4 1.0 NE2 B:GLN137 4.1 40.4 1.0 C5' P:DA1 4.1 53.4 1.0 OP2 P:DA1 4.2 43.3 1.0 CG B:GLN159 4.4 41.1 1.0 CA B:LEU427 4.4 44.0 1.0 OE1 B:GLN137 4.4 42.5 1.0 OP2 P:DC3 4.4 57.8 1.0 CE B:LYS163 4.5 41.0 1.0 O5' P:DC3 4.6 57.5 1.0 O1 B:GOL504 4.6 52.8 1.0 CD B:GLN137 4.7 44.9 1.0 C5' P:DC3 4.8 54.5 1.0 O B:HOH643 4.8 49.0 1.0 CD B:ARG380 4.8 52.8 1.0 CB B:LEU427 4.9 34.3 1.0

E.Golovinas, E.Manakova, G.Sasnauskas, M.Zaremba. Archaeoglobus Fulgidus Argonaute Protein with Dna Oligoduplex 5'-Patcgtggccacgat To Be Published.