Calcium in PDB 1oup: Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna

The structure of Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna, PDB code: 1oup was solved by H.S.Yuan, C.-L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.740, 50.110, 89.610, 90.00, 97.53, 90.00
R / Rfree (%)	19.1 / 26

The binding sites of Calcium atom in the Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna (pdb code 1oup). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna, PDB code: 1oup:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:24.0 occ:1.00 O G:HOH720 2.1 22.1 1.0 OE1 A:GLU79 2.1 17.7 1.0 OP3 G:DG7 2.2 57.8 1.0 OD1 A:ASN127 2.3 17.2 1.0 O A:HOH719 2.3 22.4 1.0 O A:HOH420 2.6 18.0 1.0 CD A:GLU79 3.1 14.1 1.0 CG A:ASN127 3.4 20.6 1.0 OE2 A:GLU79 3.5 15.3 1.0 P G:DG7 3.5 63.1 1.0 O5' G:DG7 3.9 57.2 1.0 N A:ALA80 4.0 13.7 1.0 ND2 A:ASN127 4.0 20.5 1.0 OP1 G:DG7 4.0 62.8 1.0 CA A:GLU79 4.2 15.5 1.0 O A:ASN127 4.3 26.5 1.0 C3' E:DC6 4.3 60.7 1.0 O G:HOH585 4.4 24.9 1.0 O A:ALA80 4.4 12.3 1.0 CG A:GLU79 4.4 15.2 1.0 O G:HOH578 4.5 26.6 1.0 O A:SER131 4.5 16.4 1.0 C A:GLU79 4.6 15.4 1.0 CB A:GLU79 4.6 13.9 1.0 CB A:ASN127 4.7 20.3 1.0 O3' E:DC6 4.7 63.7 1.0 CD A:ARG130 4.8 16.2 1.0 OP2 G:DG7 4.8 61.6 1.0 C5' E:DC6 4.8 58.6 1.0 CA A:ASN127 4.8 20.7 1.0 C A:ASN127 4.9 23.3 1.0 NH1 A:ARG130 4.9 14.5 1.0 C A:ALA80 4.9 12.4 1.0 CA A:ALA80 4.9 14.0 1.0 O A:TRP78 5.0 20.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Periplasmic Endonuclease Vvn Complexed with Octamer Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca300 b:26.0 occ:1.00 OE1 B:GLU79 2.2 15.6 1.0 OD1 B:ASN127 2.4 17.9 1.0 O B:HOH443 2.4 18.0 1.0 O B:HOH718 2.5 19.2 1.0 O C:HOH461 2.5 13.0 1.0 CD B:GLU79 3.4 15.0 1.0 CG B:ASN127 3.4 21.2 1.0 OP1 C:DG7 3.5 50.8 1.0 ND2 B:ASN127 3.9 15.6 1.0 OE2 B:GLU79 3.9 17.8 1.0 O B:HOH460 4.0 20.9 1.0 N B:ALA80 4.1 17.5 1.0 O B:HOH411 4.2 17.4 1.0 O B:SER131 4.3 20.5 1.0 O B:ASN127 4.3 21.8 1.0 O B:ALA80 4.3 17.7 1.0 O C:HOH600 4.4 27.9 1.0 CA B:GLU79 4.4 17.9 1.0 CG B:GLU79 4.6 17.7 1.0 CB B:ASN127 4.7 18.9 1.0 C B:GLU79 4.8 18.1 1.0 CB B:GLU79 4.8 17.1 1.0 O B:TRP78 4.9 20.1 1.0 CA B:ASN127 4.9 20.9 1.0 CD B:ARG130 5.0 17.7 1.0 P C:DG7 5.0 51.7 1.0 C B:ASN127 5.0 21.0 1.0

C.-L.Li, L.-I.Hor, Z.-F.Chang, L.-C.Tsai, W.-Z.Yang, H.S.Yuan. Dna Binding and Cleavage By the Periplasmic Nuclease Vvn: A Novel Structure with A Known Active Site. Embo J. V. 22 4014 2003.
ISSN: ISSN 0261-4189
PubMed: 12881435
DOI: 10.1093/EMBOJ/CDG377