Calcium in PDB 3uvf: Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space

The structure of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space, PDB code: 3uvf was solved by K.Jacoby, M.Metzger, B.Shen, J.Jarjour, B.Stoddard, A.Scharenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.71 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.591, 73.592, 82.031, 90.00, 90.00, 90.00
R / Rfree (%)	28 / 37.8

The structure of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space (pdb code 3uvf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space, PDB code: 3uvf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:42.7 occ:1.00 O A:HOH416 1.8 41.9 1.0 OP1 D:DA515 2.3 46.4 1.0 O A:ALA149 2.3 42.2 1.0 OP1 C:DT417 2.4 45.9 0.5 OD1 A:ASP18 2.5 40.8 1.0 OP2 C:DT417 2.8 45.6 0.5 P C:DT417 2.9 46.1 0.5 OD2 A:ASP18 3.1 41.2 1.0 CG A:ASP18 3.2 40.6 1.0 C A:ALA149 3.5 41.8 1.0 P D:DA515 3.7 46.9 1.0 O5' C:DT417 3.7 46.9 1.0 C5' C:DT417 3.8 47.2 1.0 O3' D:DA514 4.0 47.4 1.0 CA A:ALA149 4.2 41.0 1.0 O3' C:DC416 4.4 46.9 1.0 C5' D:DA515 4.4 44.5 1.0 C4' D:DA515 4.4 44.0 1.0 O5' D:DA515 4.5 45.7 1.0 N A:GLU150 4.6 42.4 1.0 C4' C:DT417 4.7 47.9 1.0 CB A:ASP18 4.8 39.7 1.0 OP2 D:DA515 4.8 48.3 1.0 O A:GLU148 4.8 42.0 1.0 CA A:GLU150 4.9 43.3 1.0 CA A:CA303 4.9 42.4 1.0 CB A:ALA149 4.9 40.4 1.0 O3' D:DA515 5.0 42.8 1.0

Calcium binding site 2 out of 6 in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:42.3 occ:1.00 O A:GLY17 2.2 40.9 1.0 OP2 D:DC516 2.5 42.9 1.0 OP1 C:DC416 2.7 47.8 1.0 O A:HOH415 2.7 42.6 1.0 OE1 A:GLU150 2.8 42.9 1.0 CA A:CA303 2.9 42.4 1.0 C A:GLY17 3.2 40.2 1.0 C5' D:DC516 3.6 42.3 1.0 O A:GLU16 3.7 40.4 1.0 CA A:GLY17 3.7 40.5 1.0 P C:DC416 3.8 49.1 1.0 P D:DC516 3.9 42.9 1.0 CD A:GLU150 4.0 43.1 1.0 O5' D:DC516 4.1 42.7 1.0 O3' C:DT415 4.2 49.1 1.0 N A:ASP18 4.3 39.5 1.0 OP2 C:DC416 4.4 50.6 1.0 NE2 A:GLN173 4.4 45.3 1.0 O3' D:DA515 4.5 42.8 1.0 C A:GLU16 4.6 40.0 1.0 OE2 A:GLU150 4.7 43.9 1.0 N A:GLY17 4.7 40.0 1.0 CA A:ASP18 4.7 39.6 1.0 C4' D:DC516 4.7 42.5 1.0 OD2 A:ASP18 4.9 41.2 1.0 CG A:GLU150 5.0 42.5 1.0

Calcium binding site 3 out of 6 in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:42.4 occ:1.00 OE1 A:GLU150 2.2 42.9 1.0 OP2 D:DC516 2.2 42.9 1.0 O A:GLY17 2.3 40.9 1.0 OD2 A:ASP18 2.6 41.2 1.0 OP2 C:DT417 2.7 45.6 0.5 CA A:CA302 2.9 42.3 1.0 P D:DC516 2.9 42.9 1.0 OP1 C:DC416 3.0 47.8 1.0 O3' D:DA515 3.1 42.8 1.0 CD A:GLU150 3.1 43.1 1.0 C A:GLY17 3.2 40.2 1.0 CG A:GLU150 3.4 42.5 1.0 OP1 D:DC516 3.8 43.6 1.0 CG A:ASP18 3.8 40.6 1.0 P C:DT417 3.9 46.1 0.5 CA A:GLY17 3.9 40.5 1.0 O3' C:DC416 4.0 46.9 1.0 N A:ASP18 4.1 39.5 1.0 CA A:ASP18 4.1 39.6 1.0 C4' C:DC416 4.2 48.2 1.0 O5' D:DC516 4.2 42.7 1.0 P C:DC416 4.3 49.1 1.0 OE2 A:GLU150 4.3 43.9 1.0 C5' C:DC416 4.4 48.9 1.0 C5' D:DC516 4.5 42.3 1.0 C3' C:DC416 4.5 47.8 1.0 C3' D:DA515 4.5 43.0 1.0 CB A:ASP18 4.6 39.7 1.0 O3' C:DT415 4.7 49.1 1.0 CB A:GLU150 4.7 43.4 1.0 O A:ALA149 4.7 42.2 1.0 OD1 A:ASP18 4.7 40.8 1.0 OP1 C:DT417 4.8 45.9 0.5 O5' C:DC416 4.9 49.7 1.0 CA A:CA301 4.9 42.7 1.0 O5' C:DT417 4.9 46.9 1.0

Calcium binding site 4 out of 6 in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:67.6 occ:1.00 OP1 F:DA515 2.1 80.8 1.0 OP1 E:DT417 2.4 70.6 0.5 OD1 B:ASP18 2.8 66.6 1.0 P E:DT417 3.0 70.6 0.5 OD2 B:ASP18 3.0 66.8 1.0 OP2 E:DT417 3.1 70.7 0.5 O B:ALA149 3.2 66.6 1.0 CG B:ASP18 3.2 66.5 1.0 P F:DA515 3.3 81.6 1.0 O5' E:DT417 3.5 70.7 1.0 C5' E:DT417 3.6 70.7 1.0 O3' F:DA514 3.6 81.8 1.0 C5' F:DA515 3.7 79.7 1.0 O5' F:DA515 3.9 80.8 1.0 C4' F:DA515 3.9 79.1 1.0 C B:ALA149 4.1 66.2 1.0 CA B:ALA149 4.5 66.1 1.0 O3' E:DC416 4.5 71.1 1.0 OP2 F:DA515 4.6 83.2 1.0 C4' E:DT417 4.6 71.0 1.0 CB B:ASP18 4.7 66.5 1.0 CB B:ALA149 4.7 65.9 1.0 OP1 F:DC516 4.8 78.1 1.0 O4' F:DA515 4.9 79.8 1.0 OP2 F:DC516 4.9 77.5 1.0 O3' F:DA515 4.9 77.9 1.0 C3' F:DA514 5.0 83.0 1.0

Calcium binding site 5 out of 6 in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca501 b:67.9 occ:1.00 OP1 E:DC416 1.5 73.1 1.0 P E:DC416 2.3 74.4 1.0 OP2 E:DC416 2.7 75.9 1.0 O3' E:DT415 2.9 74.7 1.0 OP2 F:DC516 3.0 77.5 1.0 OE2 B:GLU150 3.1 66.7 1.0 O B:HOH417 3.2 42.2 1.0 OE1 B:GLU150 3.5 67.3 1.0 CD B:GLU150 3.6 66.7 1.0 C5' F:DC516 3.7 78.0 1.0 O B:GLY17 3.7 66.4 1.0 O5' E:DC416 3.8 74.3 1.0 O5' F:DC516 3.8 77.9 1.0 P F:DC516 4.0 77.7 1.0 CG B:GLN173 4.3 68.9 1.0 C B:GLY17 4.3 66.2 1.0 C3' E:DT415 4.4 75.9 1.0 C5' E:DC416 4.5 73.2 1.0 CA B:GLY17 4.6 66.2 1.0 C4' E:DC416 4.7 72.4 1.0 C4' F:DC516 4.9 78.5 1.0 O B:GLU16 4.9 66.8 1.0 NE2 B:GLN173 5.0 68.7 1.0

Calcium binding site 6 out of 6 in the Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Expanding Lagalidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:93.6 occ:1.00 OP1 E:DG409 3.0 85.7 1.0 C4 E:PEG503 3.6 1.0 0.5 C3 E:PEG503 3.8 0.2 0.5 O2 E:PEG503 3.9 97.2 0.5 C1 E:PEG503 3.9 89.2 0.5 O4 E:PEG503 4.1 1.0 0.5 C2 E:PEG503 4.2 96.6 0.5 O1 E:PEG503 4.3 90.5 0.5 P E:DG409 4.4 83.2 1.0

K.Jacoby, M.Metzger, B.W.Shen, M.T.Certo, J.Jarjour, B.L.Stoddard, A.M.Scharenberg. Expanding Laglidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space. Nucleic Acids Res. V. 40 4954 2012.
ISSN: ISSN 0305-1048
PubMed: 22334611
DOI: 10.1093/NAR/GKR1303