Magnesium in PDB 1evw: L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.

The structure of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna., PDB code: 1evw was solved by E.A.Galburt, M.S.Jurica, B.S.Chevalier, D.Erho, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.000, 73.100, 92.700, 90.00, 95.40, 90.00
R / Rfree (%)	27.3 / 32

The structure of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. (pdb code 1evw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna., PDB code: 1evw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg601 b:6.6 occ:1.00 OD1 C:ASN119 2.4 2.0 1.0 OP1 P:DG13 3.3 4.9 1.0 CG C:ASN119 3.5 2.0 1.0 O3' H:DA12 3.6 84.4 1.0 O C:ASN119 3.6 2.0 1.0 ND1 C:HIS101 3.6 2.0 1.0 CE1 C:HIS101 3.9 2.0 1.0 O C:HIS98 4.0 15.6 1.0 ND2 C:ASN119 4.1 2.0 1.0 OG C:SER97 4.2 37.7 1.0 OD1 C:ASN123 4.2 12.4 1.0 C C:ASN119 4.3 3.0 1.0 OP2 P:DG13 4.4 4.9 1.0 C5' H:DA12 4.4 84.4 1.0 P P:DG13 4.5 4.9 1.0 C4' H:DA12 4.6 84.4 1.0 N C:HIS98 4.6 2.0 1.0 C3' H:DA12 4.7 84.4 1.0 CG C:ASN123 4.7 12.4 1.0 CB C:ASN119 4.8 2.0 1.0 CA C:ASN119 4.9 3.0 1.0 CG C:HIS101 4.9 2.0 1.0 ND2 C:ASN123 4.9 12.4 1.0 O5' H:DA12 5.0 84.4 1.0 C C:HIS98 5.0 2.0 1.0 N C:LYS120 5.0 10.3 1.0

Magnesium binding site 2 out of 4 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg602 b:6.6 occ:1.00 OD1 D:ASN119 2.3 2.4 1.0 OP3 N:DG14 2.7 9.6 1.0 OP1 N:DG14 3.3 9.6 1.0 CG D:ASN119 3.4 2.4 1.0 P N:DG14 3.6 9.6 1.0 ND2 D:ASN119 3.8 2.4 1.0 O D:ASN119 3.9 2.4 1.0 C4' G:DA13 4.0 90.7 1.0 ND1 D:HIS101 4.2 12.6 1.0 O5' N:DG14 4.3 9.6 1.0 C D:ASN119 4.4 2.0 1.0 OD1 D:ASN123 4.4 2.0 1.0 CE1 D:HIS101 4.5 12.6 1.0 O D:HIS98 4.6 11.6 1.0 O4' G:DA13 4.6 90.7 1.0 O5' G:DA13 4.7 90.7 1.0 C5' G:DA13 4.7 90.7 1.0 CB D:ASN119 4.7 2.4 1.0 OG D:SER97 4.7 3.0 1.0 C3' G:DA13 4.8 90.7 1.0 CG D:ASN123 4.8 2.0 1.0 ND2 D:ASN123 4.9 2.0 1.0 OP2 N:DG14 4.9 9.6 1.0 N D:HIS98 4.9 2.8 1.0 N D:LYS120 4.9 24.6 1.0 C2' G:DA13 5.0 90.7 1.0 O3' G:DA13 5.0 90.7 1.0

Magnesium binding site 3 out of 4 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:6.6 occ:1.00 OD1 A:ASN119 2.3 2.1 1.0 O3' F:DA12 2.8 95.5 1.0 OP1 O:DG13 2.8 10.3 1.0 CG A:ASN119 3.4 2.1 1.0 OP3 O:DG13 3.7 10.3 1.0 C5' F:DA12 3.8 95.5 1.0 ND2 A:ASN119 3.8 2.1 1.0 P O:DG13 3.8 10.3 1.0 O A:ASN119 3.9 2.1 1.0 C3' F:DA12 3.9 95.5 1.0 C4' F:DA12 4.0 95.5 1.0 ND1 A:HIS101 4.1 3.5 1.0 CE1 A:HIS101 4.4 3.5 1.0 O A:HIS98 4.4 55.8 1.0 C A:ASN119 4.4 2.0 1.0 OD1 A:ASN123 4.5 9.4 1.0 N A:HIS98 4.7 2.0 1.0 O5' F:DA12 4.7 95.5 1.0 CB A:ASN119 4.7 2.1 1.0 O5' O:DG13 4.8 10.3 1.0

Magnesium binding site 4 out of 4 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:6.6 occ:1.00 OD1 B:ASN119 2.5 14.6 1.0 O B:HIS98 3.0 54.6 1.0 OP1 M:DG14 3.2 6.3 1.0 OG B:SER97 3.3 15.3 1.0 CG B:ASN119 3.6 14.6 1.0 ND1 B:HIS101 3.6 17.3 1.0 O B:ASN119 3.7 14.6 1.0 CE1 B:HIS101 3.7 17.3 1.0 N B:HIS98 3.8 2.0 1.0 OP3 M:DG14 3.9 6.3 1.0 C B:HIS98 4.0 2.0 1.0 P M:DG14 4.0 6.3 1.0 ND2 B:ASN119 4.1 14.6 1.0 CA B:HIS98 4.3 2.0 1.0 C B:ASN119 4.4 24.5 1.0 CB B:HIS98 4.4 54.6 1.0 CB B:SER97 4.5 15.3 1.0 C B:SER97 4.5 2.0 1.0 CA B:SER97 4.6 2.0 1.0 OP2 M:DG14 4.7 6.3 1.0 CB B:ASN119 4.8 14.6 1.0 CA B:ASN119 4.8 24.5 1.0 CG B:HIS101 4.8 17.3 1.0 NE2 B:HIS101 4.9 17.3 1.0 CB B:ARG122 4.9 2.0 1.0 OD1 B:ASN123 5.0 48.5 1.0

E.A.Galburt, M.S.Chadsey, M.S.Jurica, B.S.Chevalier, D.Erho, W.Tang, R.J.Monnat Jr., B.L.Stoddard. Conformational Changes and Cleavage By the Homing Endonuclease I-Ppoi: A Critical Role For A Leucine Residue in the Active Site. J.Mol.Biol. V. 300 877 2000.
ISSN: ISSN 0022-2836
PubMed: 10891275
DOI: 10.1006/JMBI.2000.3874