Calcium in PDB 8rpx: Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target

The structure of Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target, PDB code: 8rpx was solved by D.Rafalski, K.Krakowska, M.Gilski, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.81 / 1.81
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.635, 167.059, 56.514, 90, 90, 90
R / Rfree (%)	20.5 / 24.3

The binding sites of Calcium atom in the Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target (pdb code 8rpx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target, PDB code: 8rpx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:32.2 occ:1.00 OE1 A:GLN80 2.2 36.4 1.0 O A:HOH317 2.2 29.4 1.0 O A:VAL81 2.3 29.0 1.0 OP1 G:DT5 2.3 34.9 0.5 OP1 F:DA5 2.3 30.8 0.5 O F:HOH109 2.4 26.1 1.0 OD2 A:ASP70 2.5 34.8 1.0 CD A:GLN80 3.3 40.2 1.0 CG A:ASP70 3.4 42.8 1.0 C A:VAL81 3.4 31.2 1.0 P G:DT5 3.5 34.2 0.5 P F:DA5 3.5 35.9 0.5 OD1 A:ASP70 3.5 39.1 1.0 N A:VAL81 3.8 38.4 1.0 O5' F:DA5 3.9 33.0 0.5 O5' G:DT5 3.9 33.6 0.5 C5' F:DA5 3.9 28.0 0.5 O A:HOH301 4.0 35.7 1.0 C5' G:DT5 4.0 33.6 0.5 NE2 A:GLN80 4.0 40.1 1.0 CA A:VAL81 4.1 34.1 1.0 OP2 F:DA5 4.3 30.3 0.5 OP2 G:DT5 4.3 34.4 0.5 OE2 A:GLU50 4.3 33.5 1.0 O G:HOH107 4.4 29.9 1.0 CB A:VAL81 4.5 31.1 1.0 CG A:GLN80 4.5 36.5 1.0 N A:LYS82 4.5 30.8 1.0 C A:GLN80 4.6 38.8 1.0 CD A:LYS82 4.6 29.6 1.0 O A:HOH369 4.6 39.2 1.0 O G:HOH103 4.7 34.0 1.0 O3' F:5CM4 4.7 38.3 0.6 O3' G:5CM4 4.7 34.1 0.4 CE A:LYS82 4.7 32.4 1.0 OP2 F:DG6 4.7 31.2 0.4 OP2 G:DG6 4.7 34.3 0.6 O A:HOH333 4.8 45.9 1.0 CB A:ASP70 4.8 44.3 1.0 CA A:LYS82 4.8 31.6 1.0 O3' F:DA5 4.9 29.6 0.5 O3' G:DT5 4.9 33.6 0.5 CG A:LYS82 4.9 34.5 1.0

Calcium binding site 2 out of 5 in the Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:27.8 occ:1.00 OP1 F:DA5 2.2 32.6 0.5 OP1 G:DT5 2.2 33.3 0.5 O B:HOH310 2.3 28.4 1.0 OE1 B:GLN80 2.3 31.1 1.0 O B:VAL81 2.3 26.7 1.0 OD2 B:ASP70 2.4 31.6 1.0 O G:HOH110 2.4 25.2 1.0 CG B:ASP70 3.3 35.0 1.0 CD B:GLN80 3.4 33.1 1.0 OD1 B:ASP70 3.4 41.8 1.0 P G:DT5 3.5 31.4 0.5 C B:VAL81 3.5 26.9 1.0 P F:DA5 3.5 31.3 0.5 N B:VAL81 3.8 27.6 1.0 O5' F:DA5 3.9 32.0 0.5 O5' G:DT5 3.9 31.0 0.5 O B:HOH301 3.9 27.2 1.0 C5' F:DA5 3.9 28.9 0.5 C5' G:DT5 3.9 30.9 0.5 NE2 B:GLN80 4.0 33.0 1.0 CA B:VAL81 4.1 25.3 1.0 OP2 F:DA5 4.3 28.9 0.5 OP2 G:DT5 4.3 37.1 0.5 OE2 B:GLU50 4.3 40.2 1.0 O G:HOH112 4.4 30.3 1.0 CB B:VAL81 4.5 30.5 1.0 CG B:GLN80 4.6 29.6 1.0 O F:HOH107 4.6 29.6 1.0 N B:LYS82 4.6 27.4 1.0 C B:GLN80 4.6 36.1 1.0 CB B:ASP70 4.6 34.0 1.0 O3' G:5CM4 4.6 34.7 0.6 O3' F:5CM4 4.7 27.3 0.4 CD B:LYS82 4.7 25.2 1.0 CE B:LYS82 4.7 27.6 1.0 OP2 G:DG6 4.7 30.4 0.5 OP2 F:DG6 4.7 37.6 0.6 O B:HOH394 4.8 35.3 1.0 CA B:LYS82 4.9 26.9 1.0 O3' F:DA5 5.0 30.8 0.5 O3' G:DT5 5.0 33.0 0.5 O B:HOH302 5.0 41.3 1.0

Calcium binding site 3 out of 5 in the Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:52.1 occ:1.00 O C:VAL81 2.0 77.9 1.0 OD2 C:ASP70 2.2 94.9 1.0 O I:HOH104 2.5 73.8 1.0 O C:HOH532 2.5 62.6 1.0 OE1 C:GLN80 2.6 81.2 1.0 OP1 I:DT5 2.9 67.5 0.5 OP1 H:DA5 3.0 69.6 0.5 C C:VAL81 3.1 79.7 1.0 CG C:ASP70 3.1 85.5 1.0 N C:VAL81 3.5 85.6 1.0 OD1 C:ASP70 3.5 90.8 1.0 CA C:VAL81 3.6 83.3 1.0 CD C:GLN80 3.6 84.2 1.0 CB C:VAL81 3.8 82.7 1.0 OE2 C:GLU50 4.0 80.5 1.0 NE2 C:GLN80 4.1 85.4 1.0 N C:LYS82 4.2 78.6 1.0 P I:DT5 4.3 59.8 0.5 P H:DA5 4.3 63.1 0.5 CB C:ASP70 4.3 86.6 1.0 C5' H:DA5 4.4 53.0 0.5 O H:HOH206 4.4 38.3 1.0 C5' I:DT5 4.4 57.4 0.5 C C:GLN80 4.5 88.1 1.0 O C:HOH516 4.6 72.9 1.0 O5' I:DT5 4.6 57.8 0.5 O5' H:DA5 4.6 53.1 0.5 CG1 C:VAL81 4.6 80.4 1.0 O C:HOH518 4.6 57.9 1.0 CA C:LYS82 4.7 75.3 1.0 CG C:GLN80 4.8 86.7 1.0 OP2 I:DG6 4.9 55.0 0.5 CG2 C:VAL81 4.9 86.5 1.0 OP2 H:DG6 4.9 51.1 0.5 CD C:GLU50 4.9 87.1 1.0 CG C:GLU50 4.9 79.8 1.0 O3' I:DT5 5.0 54.6 0.5 O3' H:DA5 5.0 54.1 0.5

Calcium binding site 4 out of 5 in the Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca205 b:34.3 occ:1.00 OE1 D:GLN80 2.2 42.8 1.0 OP1 H:DA5 2.3 38.2 0.5 OP1 I:DT5 2.3 43.0 0.5 O D:VAL81 2.3 31.9 1.0 OD2 D:ASP70 2.4 40.1 1.0 O D:HOH309 2.4 29.9 1.0 O I:HOH109 2.5 36.8 1.0 CG D:ASP70 3.2 43.9 1.0 CD D:GLN80 3.4 40.0 1.0 OD1 D:ASP70 3.4 46.1 1.0 C D:VAL81 3.5 30.4 1.0 P H:DA5 3.5 42.1 0.5 P I:DT5 3.5 43.9 0.5 N D:VAL81 3.8 34.7 1.0 O5' H:DA5 3.9 45.9 0.5 C5' H:DA5 3.9 47.1 0.5 O5' I:DT5 3.9 45.0 0.5 C5' I:DT5 4.0 46.4 0.5 NE2 D:GLN80 4.0 37.4 1.0 O D:HOH301 4.1 42.2 1.0 CA D:VAL81 4.1 29.8 1.0 OP2 H:DA5 4.2 49.1 0.5 OP2 I:DT5 4.3 46.5 0.5 OE2 D:GLU50 4.3 43.4 1.0 O H:HOH205 4.4 32.0 1.0 CB D:VAL81 4.5 28.7 1.0 CG D:GLN80 4.5 42.2 1.0 N D:LYS82 4.6 31.8 1.0 CB D:ASP70 4.6 33.2 1.0 C D:GLN80 4.6 44.9 1.0 O D:HOH353 4.7 44.6 1.0 O H:HOH202 4.7 42.2 1.0 CE D:LYS82 4.7 42.8 1.0 CD D:LYS82 4.7 39.5 1.0 O3' H:5CM4 4.7 40.4 0.5 O3' I:5CM4 4.7 43.4 0.5 OP2 I:DG6 4.9 44.8 0.5 CA D:LYS82 4.9 30.2 1.0 OP2 H:DG6 4.9 38.7 0.5 O3' H:DA5 5.0 39.0 0.5 O3' I:DT5 5.0 42.9 0.5 CG D:LYS82 5.0 45.5 1.0

Calcium binding site 5 out of 5 in the Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Nhoi Restriction Endonuclease in Complex with Quadruply Methylated Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:31.4 occ:1.00 O E:HOH331 2.2 30.5 1.0 OE1 E:GLN80 2.2 30.7 1.0 O E:VAL81 2.3 31.6 1.0 OP1 K:DT5 2.3 42.4 0.9 OP1 J:DA5 2.3 62.6 0.6 OD2 E:ASP70 2.4 35.3 1.0 O J:HOH106 2.5 30.7 1.0 CG E:ASP70 3.2 41.4 1.0 CD E:GLN80 3.3 29.7 1.0 OD1 E:ASP70 3.4 38.5 1.0 C E:VAL81 3.4 37.6 1.0 P J:DA5 3.6 62.5 0.6 P K:DT5 3.6 41.9 0.9 N E:VAL81 3.7 32.0 1.0 C5' J:DA5 3.9 62.4 0.6 C5' K:DT5 3.9 44.4 0.9 NE2 E:GLN80 3.9 33.6 1.0 O E:HOH301 4.0 26.6 1.0 O5' K:DT5 4.0 44.2 0.9 O5' J:DA5 4.0 62.7 0.6 CA E:VAL81 4.0 36.5 1.0 O K:HOH110 4.3 33.4 1.0 OE2 E:GLU50 4.3 45.3 1.0 OP2 K:DT5 4.4 36.1 0.9 OP2 J:DA5 4.4 63.1 0.6 CB E:VAL81 4.4 40.9 1.0 CG E:GLN80 4.5 30.0 1.0 C E:GLN80 4.5 32.9 1.0 N E:LYS82 4.5 34.3 1.0 CB E:ASP70 4.6 38.8 1.0 O E:HOH314 4.7 37.2 1.0 CD E:LYS82 4.7 34.4 1.0 O3' J:5CM4 4.7 61.2 0.8 O3' K:5CM4 4.7 50.3 0.8 CE E:LYS82 4.8 33.8 1.0 O E:HOH366 4.8 36.8 1.0 OP2 K:DG6 4.8 55.2 0.8 OP2 J:DG6 4.8 66.2 0.8 CA E:LYS82 4.9 33.3 1.0 CA E:GLN80 4.9 31.8 1.0 O3' J:DA5 4.9 64.4 0.6 O3' K:DT5 4.9 52.5 0.9

K.Krakowska, D.Rafalski, K.Skowronek, M.Wojciechowski, A.A.Kazrani, M.Gilski, S.Y.Xu, M.Bochtler. Structural Analysis of the Bisi Family of Modification Dependent Restriction Endonucleases To Be Published.