Magnesium in PDB 3r7p: The Crystal Structure of I-Ltri

All present enzymatic activity of The Crystal Structure of I-Ltri:
3.1.21.1;

The structure of The Crystal Structure of I-Ltri, PDB code: 3r7p was solved by A.N.S.Mak, R.Takeuchi, D.R.Edgell, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.29 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.089, 42.595, 103.195, 90.00, 110.63, 90.00
R / Rfree (%)	19.2 / 27

The structure of The Crystal Structure of I-Ltri also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the The Crystal Structure of I-Ltri (pdb code 3r7p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of I-Ltri, PDB code: 3r7p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of I-Ltri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of I-Ltri within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg317 b:29.3 occ:1.00 O A:HOH323 1.8 27.2 1.0 OP1 D:DC15 1.9 41.5 1.0 OP2 C:DA17 2.0 40.8 1.0 OE2 A:GLU184 2.1 47.6 1.0 O A:HOH322 2.2 14.1 1.0 O A:ALA28 2.4 38.3 1.0 CD A:GLU184 3.1 46.5 1.0 P C:DA17 3.1 40.6 1.0 OP1 C:DA17 3.4 40.9 1.0 P D:DC15 3.4 43.8 1.0 OE1 A:GLU184 3.4 46.9 1.0 C A:ALA28 3.5 38.0 1.0 MN A:MN316 3.6 42.4 1.0 C5' C:DA17 3.9 40.0 1.0 O5' C:DA17 4.0 39.6 1.0 O3' D:DA14 4.0 44.3 1.0 OE2 A:GLU29 4.0 41.8 1.0 C5' D:DC15 4.1 44.1 1.0 CA A:ALA28 4.2 37.9 1.0 NE2 A:GLN211 4.2 38.2 1.0 OP3 C:DA17 4.2 39.2 1.0 O5' D:DC15 4.3 44.0 1.0 CG A:GLU184 4.4 43.5 1.0 OP2 D:DC15 4.4 44.8 1.0 OE1 A:GLN211 4.4 39.9 1.0 C4' D:DC15 4.4 43.6 1.0 N A:GLU29 4.6 38.0 1.0 C4' C:DA17 4.6 40.3 1.0 CD A:GLU29 4.6 40.0 1.0 OE1 A:GLU29 4.7 39.6 1.0 CD A:GLN211 4.7 39.9 1.0 CA A:GLU29 4.9 38.1 1.0 CB A:ALA28 4.9 38.0 1.0 O A:ASP27 4.9 38.4 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of I-Ltri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of I-Ltri within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg17 b:49.6 occ:1.00 O A:HOH336 1.8 62.3 1.0 OP1 B:DT16 2.0 51.9 1.0 OP2 E:DG16 2.3 45.1 1.0 O E:HOH28 2.5 36.3 1.0 O A:HOH320 2.9 27.3 1.0 P B:DT16 3.5 51.0 1.0 NZ A:LYS274 3.5 46.1 1.0 P E:DG16 3.6 46.2 1.0 OP3 E:DG16 3.9 43.6 1.0 O A:GLY183 4.0 41.5 1.0 C5' B:DT16 4.2 51.1 1.0 O A:ALA182 4.2 42.2 1.0 OP2 B:DT16 4.3 51.6 1.0 O5' B:DT16 4.3 50.8 1.0 O3' B:DA15 4.3 50.7 1.0 O E:HOH29 4.5 28.6 1.0 OP1 E:DG16 4.6 45.5 1.0 O5' E:DG16 4.7 46.0 1.0 CE A:LYS274 4.7 44.9 1.0 C5' E:DG16 4.8 44.8 1.0 C A:GLY183 4.9 41.3 1.0 CA A:GLY183 5.0 41.2 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of I-Ltri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of I-Ltri within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg16 b:41.3 occ:1.00 O4' D:DT13 3.9 55.0 1.0 C4' D:DT13 4.3 55.9 1.0 N3 C:DA17 4.4 37.1 1.0 O4' D:DA14 4.5 45.5 1.0 N3 D:DA12 4.6 46.4 1.0 O2 D:DT13 4.7 50.4 1.0 C1' D:DT13 4.8 54.7 1.0 C4' D:DA14 4.8 47.2 1.0 C2 D:DA12 4.9 44.8 1.0 C5' C:DG18 4.9 41.8 1.0 C5' D:DA14 4.9 49.5 1.0 O3' D:DT13 4.9 55.1 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of I-Ltri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of I-Ltri within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg2 b:31.4 occ:1.00 O D:HOH22 1.9 41.7 1.0 OP1 E:DG16 1.9 45.5 1.0 OP3 C:DA17 2.2 39.2 1.0 O3' D:DC15 2.3 44.0 1.0 O B:HOH21 2.4 32.0 1.0 P E:DG16 3.1 46.2 1.0 OP3 E:DG16 3.4 43.6 1.0 C3' D:DC15 3.5 44.0 1.0 O5' E:DG16 3.6 46.0 1.0 P C:DA17 3.6 40.6 1.0 MN A:MN316 3.8 42.4 1.0 OP1 C:DA17 3.9 40.9 1.0 C1' D:DC15 4.0 44.0 1.0 C4' D:DC15 4.0 43.6 1.0 C2' D:DC15 4.0 43.9 1.0 O E:HOH29 4.1 28.6 1.0 O4' B:DT16 4.1 52.0 1.0 C5' B:DT16 4.2 51.1 1.0 O B:HOH22 4.2 41.1 1.0 C4' B:DT16 4.3 51.0 1.0 OP2 C:DA17 4.3 40.8 1.0 OP2 E:DG16 4.4 45.1 1.0 O2 D:DC15 4.5 46.6 1.0 O4' D:DC15 4.5 43.1 1.0 N3 D:DA14 4.6 42.1 1.0 O5' C:DA17 4.6 39.6 1.0 N3 B:DA15 4.7 49.5 1.0 O4' E:DG16 4.7 45.1 1.0 OE1 A:GLU184 4.8 46.9 1.0 C5' E:DG16 4.9 44.8 1.0 C2 D:DA14 4.9 43.3 1.0

R.Takeuchi, A.R.Lambert, A.N.Mak, K.Jacoby, R.J.Dickson, G.B.Gloor, A.M.Scharenberg, D.R.Edgell, B.L.Stoddard. Tapping Natural Reservoirs of Homing Endonucleases For Targeted Gene Modification. Proc.Natl.Acad.Sci.Usa V. 108 13077 2011.
ISSN: ISSN 0027-8424
PubMed: 21784983
DOI: 10.1073/PNAS.1107719108