Atomistry » Sodium » PDB 1t4b-1u8r » 1t9i
Atomistry »
  Sodium »
    PDB 1t4b-1u8r »
      1t9i »

Sodium in PDB 1t9i: I-Crei(D20N)/Dna Complex

Protein crystallography data

The structure of I-Crei(D20N)/Dna Complex, PDB code: 1t9i was solved by B.Chevalier, D.Sussman, C.Otis, D.Boudreau, M.Turmel, C.Lemieux, K.Stephens, R.J.Monnat Jr., B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.800, 67.310, 89.350, 90.00, 92.40, 90.00
R / Rfree (%) 19.4 / 21.1

Other elements in 1t9i:

The structure of I-Crei(D20N)/Dna Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the I-Crei(D20N)/Dna Complex (pdb code 1t9i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the I-Crei(D20N)/Dna Complex, PDB code: 1t9i:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1t9i

Go back to Sodium Binding Sites List in 1t9i
Sodium binding site 1 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of I-Crei(D20N)/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na806

b:46.5
occ:1.00
O C:HOH1178 2.2 22.5 1.0
O D:HOH1282 2.3 34.3 1.0
O D:HOH1164 2.4 36.7 1.0
O D:HOH1449 2.5 33.0 1.0
O D:HOH1269 2.5 51.3 1.0
O C:HOH1410 2.6 30.8 1.0
O D:HOH1586 4.2 37.2 1.0
N3 C:DA503 4.3 10.3 1.0
C2 C:DA503 4.6 10.0 1.0
O C:HOH1101 4.6 21.6 1.0
O4' D:DC574 4.8 26.8 1.0
O4' C:DA504 4.8 19.0 1.0
N3 D:DG573 4.9 30.8 1.0
O4' D:DG573 4.9 33.0 1.0
C4' C:DA504 4.9 15.3 1.0

Sodium binding site 2 out of 4 in 1t9i

Go back to Sodium Binding Sites List in 1t9i
Sodium binding site 2 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of I-Crei(D20N)/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na805

b:38.0
occ:1.00
O D:HOH1256 2.2 24.3 1.0
O C:HOH1464 2.4 38.4 1.0
O C:HOH1622 2.4 40.7 1.0
O C:HOH1582 2.4 44.3 1.0
O C:HOH1055 2.4 35.5 1.0
O D:HOH1563 2.5 45.6 1.0
O D:HOH1429 4.4 37.1 1.0
O C:HOH1221 4.4 23.2 1.0
N3 D:DA553 4.5 18.5 1.0
C2 D:DA553 4.6 19.4 1.0
O C:HOH1431 4.6 37.2 1.0
N2 D:DG552 4.6 16.1 1.0
O2 C:DC523 4.8 38.6 1.0
O4' C:DG524 4.8 41.7 1.0
O4' D:DA554 4.9 19.6 1.0
O4' C:DC523 4.9 40.1 1.0

Sodium binding site 3 out of 4 in 1t9i

Go back to Sodium Binding Sites List in 1t9i
Sodium binding site 3 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of I-Crei(D20N)/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:21.9
occ:1.00
O A:HOH1044 2.3 33.8 1.0
O A:HOH1273 2.3 33.4 1.0
O A:ASN136 2.4 10.2 1.0
O B:HOH1314 2.4 28.0 1.0
O A:HOH1576 2.4 55.3 1.0
O A:HOH1618 2.4 40.7 1.0
O A:ALA134 2.6 14.3 1.0
O A:HOH1247 3.2 31.6 1.0
C A:ASN136 3.6 11.0 1.0
C A:ALA134 3.7 11.9 1.0
C A:LEU135 4.1 11.4 1.0
O A:LEU135 4.2 12.3 1.0
CA A:ASP137 4.3 11.3 1.0
O B:HOH1487 4.3 43.3 1.0
O A:ALA133 4.3 12.1 1.0
N A:ASP137 4.4 11.3 1.0
N A:ASN136 4.4 11.1 1.0
N A:SER138 4.4 11.9 1.0
CA A:ALA134 4.5 12.5 1.0
OE1 B:GLN350 4.5 31.1 1.0
N A:LEU135 4.6 11.2 1.0
O A:HOH1421 4.6 38.3 1.0
CA A:ASN136 4.6 9.8 1.0
O A:HOH1235 4.6 29.7 1.0
CA A:LEU135 4.6 11.1 1.0
OD1 A:ASP137 4.7 16.3 1.0
C A:ASP137 4.9 10.8 1.0

Sodium binding site 4 out of 4 in 1t9i

Go back to Sodium Binding Sites List in 1t9i
Sodium binding site 4 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of I-Crei(D20N)/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:20.1
occ:1.00
O B:HOH1218 2.3 29.8 1.0
O B:HOH1209 2.3 27.5 1.0
O B:HOH1610 2.4 40.7 1.0
O B:ASN436 2.4 12.8 1.0
O A:HOH1017 2.4 35.0 1.0
O B:HOH1277 2.5 22.1 1.0
O B:HOH1090 2.7 21.6 1.0
O B:ALA434 2.7 17.5 1.0
C B:ASN436 3.6 11.3 1.0
C B:ALA434 3.8 15.6 1.0
CA B:ASP437 4.2 12.5 1.0
O B:LEU435 4.3 14.2 1.0
N B:SER438 4.3 12.4 1.0
C B:LEU435 4.3 14.7 1.0
N B:ASP437 4.4 12.4 1.0
O B:ALA433 4.4 13.7 1.0
N B:ASN436 4.5 13.1 1.0
CA B:ALA434 4.6 14.0 1.0
OE1 A:GLN50 4.6 28.7 1.0
OD1 B:ASP437 4.7 16.5 1.0
CA B:ASN436 4.7 11.3 1.0
N B:LEU435 4.7 14.9 1.0
C B:ASP437 4.8 11.8 1.0
O B:HOH1213 4.8 23.4 1.0
NE2 A:GLN50 4.8 25.8 1.0
CA B:LEU435 4.8 13.6 1.0
O B:HOH1527 4.9 42.0 1.0

Reference:

B.Chevalier, D.Sussman, C.Otis, A.J.Noel, M.Turmel, C.Lemieux, K.Stephens, R.J.Monnat Jr., B.L.Stoddard. Metal-Dependent Dna Cleavage Mechanism of the I-Crei Laglidadg Homing Endonuclease. Biochemistry V. 43 14015 2004.
ISSN: ISSN 0006-2960
PubMed: 15518550
DOI: 10.1021/BI048970C
Page generated: Sun Oct 6 22:37:55 2024

Last articles

Mg in 9J2F
Mg in 9IZ4
Mg in 9MM2
Mg in 9MF6
Mg in 9MED
Mg in 9JKP
Mg in 9MEC
Mg in 9HM9
Mg in 9GOB
Mg in 9GO5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy