Sodium in PDB 1n3e: Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence)

The structure of Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence), PDB code: 1n3e was solved by B.Chevalier, M.Turmel, C.Lemieux, R.J.Monnat, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.18 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.730, 68.440, 301.490, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.5

The structure of Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence) also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence) (pdb code 1n3e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence), PDB code: 1n3e:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na495 b:34.2 occ:1.00 O A:HOH1081 2.5 27.6 1.0 O A:ASN136 2.6 31.2 1.0 O A:ALA134 2.8 26.7 1.0 C A:ASN136 3.6 30.5 1.0 O B:HOH1144 3.6 56.1 1.0 C A:ALA134 3.9 26.6 1.0 CA A:ASP137 4.0 35.9 1.0 O A:LEU135 4.1 27.8 1.0 N A:ASP137 4.2 32.9 1.0 C A:LEU135 4.3 26.9 1.0 OD1 A:ASP137 4.3 42.6 1.0 N A:SER138 4.3 37.8 1.0 O A:ALA133 4.5 32.5 1.0 N A:ASN136 4.6 26.3 1.0 NE2 B:GLN250 4.7 50.1 1.0 CA A:ASN136 4.7 28.3 1.0 CA A:ALA134 4.7 28.5 1.0 C A:ASP137 4.7 36.8 1.0 N A:LEU135 4.8 25.8 1.0 CA A:LEU135 4.9 26.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na494 b:24.5 occ:1.00 O B:ALA334 2.4 26.2 1.0 O B:HOH1233 2.4 46.3 1.0 O B:ASN336 2.5 30.9 1.0 C B:ALA334 3.6 25.3 1.0 C B:ASN336 3.6 29.4 1.0 O B:LEU335 4.0 29.6 1.0 C B:LEU335 4.0 27.3 1.0 CA B:ASP337 4.2 32.0 1.0 N B:ASN336 4.3 27.3 1.0 N B:ASP337 4.3 30.7 1.0 O B:ALA333 4.4 25.4 1.0 N B:LEU335 4.5 25.7 1.0 CA B:ALA334 4.5 25.1 1.0 CA B:LEU335 4.5 26.8 1.0 CA B:ASN336 4.6 28.5 1.0 OD1 B:ASP337 4.6 37.7 1.0 N B:SER338 4.6 32.9 1.0 NE2 A:GLN50 4.9 57.1 1.0 C B:ASP337 4.9 32.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence) within 5.0Å range: probe atom residue distance (Å) B Occ G:Na995 b:38.2 occ:1.00 O G:ASN636 2.5 29.5 1.0 O G:ALA634 2.7 30.5 1.0 O G:HOH1136 2.7 44.2 1.0 C G:ASN636 3.6 30.5 1.0 C G:ALA634 3.8 30.7 1.0 CA G:ASP637 4.1 35.6 1.0 O G:LEU635 4.2 33.1 1.0 N G:ASP637 4.3 33.2 1.0 C G:LEU635 4.3 30.6 1.0 OD1 G:ASP637 4.4 39.9 1.0 N G:SER638 4.4 36.1 1.0 O G:ALA633 4.5 32.9 1.0 CA G:ALA634 4.5 31.0 1.0 N G:ASN636 4.6 30.1 1.0 CA G:ASN636 4.7 30.1 1.0 N G:LEU635 4.8 30.4 1.0 C G:ASP637 4.8 35.6 1.0 CA G:LEU635 4.9 30.3 1.0 NE2 H:GLN750 5.0 54.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence I (Palindrome of Left Side of Wildtype Dna Target Sequence) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na994 b:49.5 occ:1.00 O H:ASN836 2.5 44.0 1.0 O H:HOH1204 2.6 48.1 1.0 O H:ALA834 2.7 34.7 1.0 C H:ASN836 3.6 42.9 1.0 C H:ALA834 3.8 34.6 1.0 O H:LEU835 4.0 38.3 1.0 CA H:ASP837 4.1 46.2 1.0 C H:LEU835 4.2 38.0 1.0 N H:ASP837 4.2 44.6 1.0 OD1 H:ASP837 4.4 46.0 1.0 NE2 G:GLN550 4.4 52.2 1.0 N H:SER838 4.4 47.0 1.0 N H:ASN836 4.5 38.5 1.0 O H:ALA833 4.6 32.9 1.0 CA H:ALA834 4.6 34.4 1.0 CA H:ASN836 4.7 40.6 1.0 N H:LEU835 4.7 34.9 1.0 CA H:LEU835 4.8 36.4 1.0 C H:ASP837 4.8 46.9 1.0

B.Chevalier, M.Turmel, C.Lemieux, R.J.Monnat, B.L.Stoddard. Flexible Dna Target Site Recognition By Divergent Homing Endonuclease Isoschizomers I-Crei and I-Msoi J.Mol.Biol. V. 329 253 2003.
ISSN: ISSN 0022-2836
PubMed: 12758074
DOI: 10.1016/S0022-2836(03)00447-9