Calcium in PDB 6uki: Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)

The structure of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0), PDB code: 6uki was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.97 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.411, 94.998, 97.868, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.4

The binding sites of Calcium atom in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) (pdb code 6uki). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0), PDB code: 6uki:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca301 b:55.4 occ:1.00 OP1 A:DC9 2.1 68.5 1.0 O X:ALA47 2.2 66.5 1.0 O X:HOH401 2.2 29.0 1.0 OD2 X:ASP34 2.3 42.9 1.0 OE1 X:GLU46 2.3 60.8 1.0 CD X:GLU46 3.1 55.1 1.0 P A:DC9 3.1 49.1 1.0 CG X:ASP34 3.2 43.1 1.0 NZ X:LYS48 3.3 36.2 1.0 C X:ALA47 3.4 54.4 1.0 OD1 X:ASP34 3.4 56.5 1.0 OP2 A:DC9 3.4 34.5 1.0 OE2 X:GLU46 3.8 56.9 1.0 CG X:GLU46 3.9 52.2 1.0 N X:ALA47 3.9 48.0 1.0 O5' A:DC9 4.0 42.7 1.0 CG X:LYS48 4.1 43.0 1.0 O X:HOH403 4.1 55.2 1.0 CA X:ALA47 4.2 48.5 1.0 OP2 A:DT10 4.3 50.4 1.0 CA A:CA101 4.3 54.6 1.0 OE1 X:GLU7 4.3 84.9 1.0 C5' A:DC9 4.3 37.7 1.0 O3' A:DG8 4.4 54.5 1.0 N X:LYS48 4.4 50.5 1.0 CE X:LYS48 4.4 46.4 1.0 CB X:ASP34 4.6 33.9 1.0 CB X:ALA47 4.6 41.8 1.0 CA X:LYS48 4.6 45.2 1.0 C X:GLU46 4.7 43.4 1.0 O A:HOH202 4.8 41.4 1.0 CD X:LYS48 4.9 45.0 1.0 CB X:LYS48 4.9 42.5 1.0

Calcium binding site 2 out of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:54.6 occ:1.00 OD1 X:ASP34 2.3 56.5 1.0 O X:HOH403 2.4 55.2 1.0 O3' A:DG8 2.6 54.5 1.0 OP1 A:DC9 2.7 68.5 1.0 P A:DC9 3.3 49.1 1.0 CG X:ASP34 3.5 43.1 1.0 O X:GLU27 3.6 75.0 1.0 C3' A:DG8 3.9 56.7 1.0 OE1 X:GLU7 3.9 84.9 1.0 C4' A:DG8 4.0 46.7 1.0 OD2 X:ASP34 4.1 42.9 1.0 CA X:CA301 4.3 55.4 1.0 O5' A:DC9 4.3 42.7 1.0 C5' A:DC9 4.3 37.7 1.0 O X:THR32 4.4 75.5 1.0 O X:ASP29 4.4 59.8 1.0 OP2 A:DC9 4.4 34.5 1.0 O X:GLY26 4.5 81.5 1.0 CA X:ASP34 4.5 36.0 1.0 C2' A:DG8 4.5 62.4 1.0 O X:HOH401 4.6 29.0 1.0 CB X:ASP34 4.6 33.9 1.0 N X:ASP34 4.6 47.1 1.0 OE1 X:GLU46 4.7 60.8 1.0 C5' A:DG8 4.8 40.9 1.0 C X:GLU27 4.8 69.4 1.0 C X:SER33 4.9 55.0 1.0 CD X:GLU7 4.9 83.8 1.0 OE2 X:GLU46 5.0 56.9 1.0

Calcium binding site 3 out of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range: probe atom residue distance (Å) B Occ Y:Ca301 b:52.5 occ:1.00 OP1 D:DC9 2.2 51.5 1.0 O Y:HOH402 2.2 32.8 1.0 O Y:ALA47 2.3 54.5 1.0 OD2 Y:ASP34 2.3 56.7 1.0 O D:HOH201 2.5 55.9 1.0 OE1 Y:GLU46 2.7 46.1 1.0 CG Y:ASP34 3.1 51.1 1.0 OE2 Y:GLU46 3.1 76.2 1.0 CD Y:GLU46 3.2 60.5 1.0 OD1 Y:ASP34 3.4 45.6 1.0 P D:DC9 3.4 51.0 1.0 C Y:ALA47 3.4 52.5 1.0 N Y:ALA47 3.7 52.3 1.0 OP2 D:DC9 3.7 35.7 1.0 CA Y:ALA47 4.0 51.2 1.0 O5' D:DC9 4.2 48.7 1.0 O Y:HOH401 4.2 41.9 1.0 NZ Y:LYS48 4.3 37.7 1.0 CA D:CA101 4.3 63.0 1.0 CB Y:ALA47 4.4 34.5 1.0 CE Y:LYS48 4.4 44.9 1.0 CB Y:ASP34 4.4 39.5 1.0 OE2 Y:GLU7 4.4 59.7 1.0 CD Y:LYS48 4.4 55.4 1.0 C Y:GLU46 4.5 48.0 1.0 N Y:LYS48 4.5 53.4 1.0 CG Y:GLU46 4.5 54.0 1.0 C5' D:DC9 4.6 45.9 1.0 OP2 D:DT10 4.6 39.8 1.0 O3' D:DG8 4.6 72.2 1.0 CG Y:LYS48 4.6 53.9 1.0 CA Y:GLU46 4.8 42.5 1.0 CB Y:GLU46 4.8 36.0 1.0 CA Y:LYS48 4.8 53.2 1.0

Calcium binding site 4 out of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:63.0 occ:1.00 O Y:HOH401 2.2 41.9 1.0 OD1 Y:ASP34 2.4 45.6 1.0 O3' D:DG8 2.6 72.2 1.0 OP1 D:DC9 2.9 51.5 1.0 P D:DC9 3.3 51.0 1.0 CG Y:ASP34 3.6 51.1 1.0 C3' D:DG8 3.8 61.6 1.0 C4' D:DG8 3.9 47.4 1.0 O Y:ASP29 3.9 68.8 1.0 OE2 Y:GLU46 3.9 76.2 1.0 O Y:THR32 4.1 67.9 1.0 OP2 D:DC9 4.2 35.7 1.0 OD2 Y:ASP34 4.3 56.7 1.0 CA Y:CA301 4.3 52.5 1.0 C5' D:DG8 4.4 48.3 1.0 N Y:ASP34 4.4 33.4 1.0 OE2 Y:GLU7 4.5 59.7 1.0 C Y:SER33 4.5 42.8 1.0 O5' D:DC9 4.5 48.7 1.0 CA Y:ASP34 4.5 45.1 1.0 C5' D:DC9 4.7 45.9 1.0 CB Y:ASP34 4.7 39.5 1.0 C2' D:DG8 4.7 63.3 1.0 CA Y:SER33 4.8 41.2 1.0 O Y:HOH402 4.8 32.8 1.0 O Y:SER33 4.9 57.3 1.0 CD Y:GLU46 5.0 60.5 1.0

J.R.Horton, J.Yang, X.Zhang, T.Petronzio, A.Fomenkov, G.G.Wilson, R.J.Roberts, X.Cheng. Structure of Hhai Endonuclease with Cognate Dna at An Atomic Resolution of 1.0 Angstrom Nucleic Acids Res. 2019.
ISSN: ESSN 1362-4962