Magnesium in PDB 6nju: Mouse Endonuclease G Mutant H97A Bound to A-Dna

Protein crystallography data

The structure of Mouse Endonuclease G Mutant H97A Bound to A-Dna, PDB code: 6nju was solved by C.M.Vander Zanden, E.N.Ho, R.S.Czarny, A.B.Robertson, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.99 / 2.35
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 107.983, 107.983, 357.419, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 29.2

Other elements in 6nju:

The structure of Mouse Endonuclease G Mutant H97A Bound to A-Dna also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mouse Endonuclease G Mutant H97A Bound to A-Dna (pdb code 6nju). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mouse Endonuclease G Mutant H97A Bound to A-Dna, PDB code: 6nju:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6nju

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Magnesium binding site 1 out of 4 in the Mouse Endonuclease G Mutant H97A Bound to A-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse Endonuclease G Mutant H97A Bound to A-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:33.4
occ:1.00
 OD1 A:ASN128 2.1 29.2 1.0
O A:HOH404 2.4 31.4 1.0
O A:HOH428 2.4 24.2 1.0
O A:HOH401 2.5 31.7 1.0
O A:HOH405 2.5 34.9 1.0
CG A:ASN128 3.3 30.2 1.0
ND2 A:ASN128 3.9 23.8 1.0
OE2 A:GLU136 3.9 29.0 1.0
N A:ALA97 4.0 32.8 1.0
O A:ASN128 4.1 30.4 1.0
O A:HOH423 4.2 26.4 1.0
OE1 A:GLU136 4.2 32.2 1.0
OE1 A:GLN123 4.2 37.5 1.0
O A:ALA97 4.2 27.1 1.0
CA A:GLY96 4.5 27.2 1.0
CD A:GLU136 4.5 26.9 1.0
CB A:ASN128 4.5 29.4 1.0
C A:GLY96 4.6 33.0 1.0
CD1 A:TRP132 4.7 24.9 1.0
CA A:ASN128 4.7 29.1 1.0
C A:ASN128 4.7 29.4 1.0
O A:HOH446 4.7 24.8 1.0
CB A:ALA97 4.8 27.0 1.0
CA A:ALA97 4.8 28.2 1.0
C A:ALA97 5.0 29.0 1.0

Magnesium binding site 2 out of 4 in 6nju

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Magnesium binding site 2 out of 4 in the Mouse Endonuclease G Mutant H97A Bound to A-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse Endonuclease G Mutant H97A Bound to A-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:22.2
occ:1.00
 O B:HOH414 2.3 26.8 1.0
OD1 B:ASN128 2.3 30.5 1.0
O B:HOH408 2.4 31.9 1.0
O B:HOH419 2.5 26.7 1.0
O B:HOH424 2.5 36.2 1.0
CG B:ASN128 3.5 29.6 1.0
N B:ALA97 3.8 27.4 1.0
O B:ALA97 3.9 30.0 1.0
OE1 B:GLU136 4.1 37.5 1.0
OE2 B:GLU136 4.1 32.8 1.0
ND2 B:ASN128 4.1 22.4 1.0
CA B:GLY96 4.2 21.1 1.0
OE1 B:GLN123 4.3 28.3 1.0
C B:GLY96 4.4 25.2 1.0
CD B:GLU136 4.5 32.7 1.0
O B:ASN128 4.5 35.2 1.0
CD1 B:TRP132 4.6 30.5 1.0
CA B:ALA97 4.6 28.2 1.0
CB B:ALA97 4.7 25.1 1.0
C B:ALA97 4.7 26.2 1.0
CB B:ASN128 4.7 22.8 1.0
CA B:ASN128 5.0 24.2 1.0

Magnesium binding site 3 out of 4 in 6nju

Go back to Magnesium Binding Sites List in 6nju
Magnesium binding site 3 out of 4 in the Mouse Endonuclease G Mutant H97A Bound to A-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mouse Endonuclease G Mutant H97A Bound to A-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:35.5
occ:1.00
 OD1 C:ASN128 2.1 26.3 1.0
O C:HOH421 2.2 25.6 1.0
O C:HOH422 2.3 27.2 1.0
O C:HOH413 2.4 31.8 1.0
O C:HOH418 2.8 26.0 1.0
CG C:ASN128 3.2 27.2 1.0
ND2 C:ASN128 3.7 20.2 1.0
N C:ALA97 4.0 26.7 1.0
O C:HOH435 4.0 23.2 1.0
O C:ASN128 4.1 33.9 1.0
OE1 C:GLU136 4.1 28.0 1.0
O C:ALA97 4.3 26.7 1.0
OE1 C:GLN123 4.3 28.1 1.0
CA C:GLY96 4.4 21.1 1.0
OE2 C:GLU136 4.4 30.4 1.0
CB C:ASN128 4.5 27.9 1.0
C C:GLY96 4.6 30.2 1.0
O C:HOH470 4.7 24.5 1.0
CD C:GLU136 4.7 27.5 1.0
C C:ASN128 4.8 29.6 1.0
CA C:ASN128 4.8 27.4 1.0
CA C:ALA97 4.8 24.7 1.0
CB C:ALA97 4.8 26.7 1.0
CD1 C:TRP132 5.0 26.7 1.0

Magnesium binding site 4 out of 4 in 6nju

Go back to Magnesium Binding Sites List in 6nju
Magnesium binding site 4 out of 4 in the Mouse Endonuclease G Mutant H97A Bound to A-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mouse Endonuclease G Mutant H97A Bound to A-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:34.1
occ:1.00
 OD1 D:ASN128 2.1 26.6 1.0
O D:HOH426 2.4 19.6 1.0
O D:HOH425 2.5 22.4 1.0
O D:HOH406 2.6 25.3 1.0
CG D:ASN128 3.2 26.1 1.0
O D:HOH448 3.3 37.9 1.0
O D:ASN128 3.9 26.0 1.0
ND2 D:ASN128 3.9 26.7 1.0
O D:HOH435 4.2 25.3 1.0
N D:ALA97 4.2 22.9 1.0
OE2 D:GLU136 4.2 25.6 1.0
OE1 D:GLN123 4.3 28.9 1.0
CB D:ASN128 4.4 26.8 1.0
OE1 D:GLU136 4.5 33.5 1.0
O D:ALA97 4.5 25.1 1.0
C D:ASN128 4.5 30.0 1.0
CA D:GLY96 4.6 15.5 1.0
CA D:ASN128 4.6 23.2 1.0
O D:HOH460 4.6 17.6 1.0
CD1 D:TRP132 4.8 29.9 1.0
CD D:GLU136 4.8 22.9 1.0
C D:GLY96 4.8 25.2 1.0

Reference:

C.M.Vander Zanden, E.N.Ho, R.S.Czarny, A.B.Robertson, P.S.Ho. Structural Adaptation of Vertebrate Endonuclease G For 5-Hydroxymethylcytosine Recognition and Function To Be Published.
Page generated: Mon Dec 14 23:40:23 2020

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