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Magnesium in PDB 2o6m: H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna

Protein crystallography data

The structure of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna, PDB code: 2o6m was solved by J.H.Eastberg, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.30 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.850, 113.850, 88.880, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 24.4

Other elements in 2o6m:

The structure of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna (pdb code 2o6m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna, PDB code: 2o6m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2o6m

Go back to Magnesium Binding Sites List in 2o6m
Magnesium binding site 1 out of 2 in the H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg605

b:16.9
occ:1.00
OD1 B:ASN319 2.3 15.9 1.0
O B:HOH701 2.3 22.4 1.0
O B:HOH702 2.4 9.6 1.0
OP1 C:DG414 2.4 17.4 1.0
O B:HOH703 2.5 17.1 1.0
O3' C:DA413 2.5 16.9 1.0
P C:DG414 3.0 25.5 1.0
CG B:ASN319 3.4 15.9 1.0
C3' C:DA413 3.7 16.9 1.0
N B:GLN298 3.8 18.5 1.0
O B:ASN319 3.8 13.2 1.0
ND2 B:ASN319 4.0 15.9 1.0
O B:GLN298 4.1 18.5 1.0
C4' C:DA413 4.1 16.9 1.0
OP2 C:DG414 4.1 17.4 1.0
O5' C:DG414 4.1 25.5 1.0
O C:HOH827 4.3 30.1 1.0
C B:ASN319 4.3 13.2 1.0
OG B:SER297 4.4 14.9 1.0
CA B:GLN298 4.5 18.5 1.0
CB B:GLN298 4.5 38.6 1.0
OD1 B:ASN323 4.6 11.1 1.0
C B:GLN298 4.6 18.5 1.0
CA B:SER297 4.6 21.3 1.0
CB B:ASN319 4.6 15.9 1.0
C B:SER297 4.6 21.3 1.0
C2' C:DA413 4.7 16.9 1.0
ND1 B:HIS301 4.7 13.2 1.0
CA B:ASN319 4.7 13.2 1.0
CE1 B:HIS301 4.8 13.2 1.0
C5' C:DA413 4.9 16.9 1.0

Magnesium binding site 2 out of 2 in 2o6m

Go back to Magnesium Binding Sites List in 2o6m
Magnesium binding site 2 out of 2 in the H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg606

b:14.9
occ:1.00
O A:HOH706 2.2 14.8 1.0
OD1 A:ASN119 2.3 12.7 1.0
OP1 D:DG514 2.4 18.0 1.0
O3' D:DA513 2.4 15.9 1.0
O A:HOH704 2.4 14.4 1.0
O A:HOH705 2.5 14.6 1.0
P D:DG514 2.9 17.3 1.0
CG A:ASN119 3.4 12.7 1.0
C3' D:DA513 3.6 15.9 1.0
O A:ASN119 3.8 10.2 1.0
C4' D:DA513 3.9 15.9 1.0
N A:GLN98 3.9 18.6 1.0
ND2 A:ASN119 3.9 12.7 1.0
OP2 D:DG514 4.0 18.0 1.0
O5' D:DG514 4.0 17.3 1.0
O A:GLN98 4.1 18.6 1.0
C A:ASN119 4.3 10.2 1.0
OG A:SER97 4.3 18.1 1.0
OD1 A:ASN123 4.4 21.3 1.0
CB A:GLN98 4.4 38.2 1.0
O D:HOH934 4.5 36.9 1.0
CA A:GLN98 4.6 18.6 1.0
C2' D:DA513 4.6 15.9 1.0
CA A:SER97 4.6 12.3 1.0
CB A:ASN119 4.6 12.7 1.0
C A:SER97 4.6 12.3 1.0
C A:GLN98 4.7 18.6 1.0
C5' D:DA513 4.7 15.9 1.0
ND1 A:HIS101 4.8 18.4 1.0
CA A:ASN119 4.8 10.2 1.0
CE1 A:HIS101 4.9 18.4 1.0
N A:LYS120 4.9 13.8 1.0

Reference:

J.H.Eastberg, J.Eklund, R.Monnat, B.L.Stoddard. Mutability of An Hnh Nuclease Imidazole General Base and Exchange of A Deprotonation Mechanism. Biochemistry V. 46 7215 2007.
ISSN: ISSN 0006-2960
PubMed: 17516660
DOI: 10.1021/BI700418D
Page generated: Mon Dec 14 07:31:48 2020

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