Calcium in PDB 3slp: Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex

All present enzymatic activity of Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex:
3.1.11.3;

The structure of Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex, PDB code: 3slp was solved by C.E.Bell, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.59 / 2.30
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.115, 80.115, 241.041, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 28.1

The structure of Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex (pdb code 3slp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex, PDB code: 3slp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex


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 Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca227 b:66.2 occ:1.00 OD1 A:ASP119 2.8 30.6 1.0 O A:HOH367 3.0 35.6 1.0 O A:HOH488 3.0 35.9 1.0 OE2 A:GLU129 3.0 33.0 1.0 OD2 A:ASP119 3.0 29.6 1.0 O A:HOH312 3.0 28.0 1.0 CG A:ASP119 3.3 31.8 1.0 CD A:GLU129 3.8 32.2 1.0 OE1 A:GLU129 3.9 32.3 1.0 NE2 A:GLN19 4.5 68.0 1.0 CB A:ASP119 4.8 32.4 1.0 O A:LEU130 4.9 26.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex


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 Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca227 b:42.7 occ:1.00 O B:HOH231 2.2 22.0 1.0 OD2 B:ASP119 2.4 21.0 1.0 O B:LEU130 2.4 19.6 1.0 OE2 B:GLU129 2.7 15.4 1.0 O B:HOH232 2.8 26.2 1.0 O B:HOH307 2.9 35.5 1.0 CG B:ASP119 3.3 19.6 1.0 CD B:GLU129 3.5 17.7 1.0 OD1 B:ASP119 3.5 22.4 1.0 C B:LEU130 3.6 19.8 1.0 OE1 B:GLU129 3.9 19.4 1.0 O B:HOH271 3.9 47.5 1.0 O B:HOH251 3.9 26.9 1.0 N B:LEU130 4.1 18.7 1.0 O B:HOH308 4.2 32.3 1.0 NZ B:LYS131 4.2 18.9 1.0 CA B:LEU130 4.2 19.4 1.0 O B:HOH449 4.4 23.5 1.0 CD B:LYS131 4.5 16.4 1.0 CB B:LEU130 4.5 19.4 1.0 N B:LYS131 4.6 19.8 1.0 CB B:ASP119 4.7 20.7 1.0 O B:HOH240 4.7 26.3 1.0 CG B:GLU129 4.7 17.0 1.0 CE B:LYS131 4.9 16.6 1.0 CA B:LYS131 4.9 19.6 1.0 OE1 B:GLU85 5.0 32.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Lambda Exonuclease in Complex with A 12 Bp Symmetric Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca227 b:88.2 occ:1.00 O C:HOH336 2.2 21.4 1.0 O C:HOH460 2.3 82.7 1.0 OD1 C:ASP119 2.7 27.2 1.0 O C:HOH481 2.9 27.5 1.0 OE1 C:GLU129 3.3 35.6 1.0 OE2 C:GLU129 3.4 29.3 1.0 CG C:ASP119 3.4 29.9 1.0 O C:SER117 3.5 32.2 1.0 OD2 C:ASP119 3.6 28.7 1.0 CD C:GLU129 3.8 33.3 1.0 O3 C:PO4229 4.1 0.5 1.0 NE2 C:GLN157 4.4 26.5 1.0 NE2 C:GLN19 4.4 70.8 1.0 N C:ASP119 4.5 29.9 1.0 O C:HOH234 4.6 19.2 1.0 C C:SER117 4.6 31.0 1.0 CB C:ASP119 4.8 30.1 1.0 O1 C:PO4229 4.8 0.4 1.0 C C:PRO118 4.8 29.7 1.0 CA C:ASP119 4.9 29.9 1.0

J.Zhang, K.A.Mccabe, C.E.Bell. Crystal Structures of {Lambda} Exonuclease in Complex with Dna Suggest An Electrostatic Ratchet Mechanism For Processivity. Proc.Natl.Acad.Sci.Usa V. 108 11872 2011.
ISSN: ISSN 0027-8424
PubMed: 21730170
DOI: 10.1073/PNAS.1103467108