Atomistry » Calcium » PDB 1mts-1n7d » 1n3e
Atomistry »
  Calcium »
    PDB 1mts-1n7d »
      1n3e »

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

Protein crystallography data

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

Other elements in 1n3e:

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:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1n3e

Go back to Calcium Binding Sites List in 1n3e
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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
C:Ca492

b:27.9
occ:1.00
 OD1 B:ASP220 2.0 22.3 1.0
OD1 A:ASP20 2.1 26.7 1.0
OP3 D:DG415 2.2 25.8 1.0
O3' C:DC414 2.3 27.0 1.0
OP3 F:DG465 2.4 24.8 1.0
O3' E:DC464 2.6 24.6 1.0
CG B:ASP220 3.2 21.1 1.0
CG A:ASP20 3.3 24.3 1.0
C3' C:DC414 3.3 30.6 1.0
P D:DG415 3.5 26.1 1.0
C3' E:DC464 3.6 22.4 1.0
O5' D:DG415 3.7 27.2 1.0
O A:GLY19 3.7 23.1 1.0
CA D:CA493 3.8 18.5 1.0
P F:DG465 3.8 28.8 1.0
OD2 B:ASP220 3.8 17.4 1.0
CA F:CA491 3.9 29.7 1.0
C4' C:DC414 3.9 32.4 1.0
O C:HOH1211 4.0 41.5 1.0
O E:HOH1109 4.0 46.7 1.0
O5' F:DG465 4.0 25.3 1.0
OD2 A:ASP20 4.0 25.8 1.0
O B:GLY219 4.1 26.0 1.0
C4' E:DC464 4.1 23.8 1.0
OP2 D:DG415 4.3 26.8 1.0
CB A:ASP20 4.3 22.6 1.0
CB B:ASP220 4.4 17.7 1.0
C A:GLY19 4.4 21.4 1.0
CA A:ASP20 4.5 21.6 1.0
C B:GLY219 4.6 22.8 1.0
C2' C:DC414 4.6 30.8 1.0
OP2 F:DG465 4.6 28.3 1.0
CA B:ASP220 4.6 19.6 1.0
OP1 D:DG415 4.7 27.7 1.0
N A:ASP20 4.7 20.5 1.0
N B:ASP220 4.8 21.2 1.0
C2' E:DC464 4.9 23.7 1.0
OP1 F:DG465 4.9 30.8 1.0
C5' C:DC414 4.9 33.4 1.0
OP1 E:DC464 4.9 22.1 1.0
O4' C:DC414 5.0 33.2 1.0

Calcium binding site 2 out of 6 in 1n3e

Go back to Calcium Binding Sites List in 1n3e
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
D:Ca493

b:18.5
occ:1.00
 OD2 B:ASP220 2.2 17.4 1.0
O A:GLY19 2.3 23.1 1.0
OP1 E:DC464 2.3 22.1 1.0
O A:HOH1033 2.3 18.5 1.0
OP3 D:DG415 2.4 25.8 1.0
OP1 D:DG415 2.6 27.7 1.0
P D:DG415 3.0 26.1 1.0
CG B:ASP220 3.1 21.1 1.0
OD1 B:ASP220 3.3 22.3 1.0
C A:GLY19 3.3 21.4 1.0
P E:DC464 3.8 23.6 1.0
CA C:CA492 3.8 27.9 1.0
CA A:GLY19 3.8 21.3 1.0
O5' D:DG415 3.8 27.2 1.0
O D:HOH1022 3.9 38.0 1.0
O A:ASP18 4.1 22.4 1.0
O3' E:DA463 4.2 27.0 1.0
OE1 B:GLN247 4.3 22.6 1.0
OP2 D:DG415 4.3 26.8 1.0
NE2 B:GLN247 4.4 21.3 1.0
C5' E:DC464 4.4 24.0 1.0
C4' E:DC464 4.4 23.8 1.0
OD1 A:ASP20 4.4 26.7 1.0
CB B:ASP220 4.5 17.7 1.0
N A:ASP20 4.5 20.5 1.0
C5' D:DG415 4.6 26.9 1.0
O5' E:DC464 4.6 23.7 1.0
CD B:GLN247 4.7 23.7 1.0
OP2 E:DC464 4.8 24.6 1.0
N A:GLY19 4.8 21.5 1.0
C A:ASP18 4.8 22.7 1.0
CA A:ASP20 4.8 21.6 1.0

Calcium binding site 3 out of 6 in 1n3e

Go back to Calcium Binding Sites List in 1n3e
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
F:Ca491

b:29.7
occ:1.00
 OP1 C:DC414 2.2 31.2 1.0
O B:GLY219 2.3 26.0 1.0
OP3 F:DG465 2.3 24.8 1.0
OD2 A:ASP20 2.4 25.8 1.0
O B:HOH1017 2.4 33.4 1.0
OP1 F:DG465 2.5 30.8 1.0
P F:DG465 2.9 28.8 1.0
CG A:ASP20 3.1 24.3 1.0
OD1 A:ASP20 3.2 26.7 1.0
C B:GLY219 3.3 22.8 1.0
P C:DC414 3.6 29.7 1.0
O5' F:DG465 3.9 25.3 1.0
CA B:GLY219 3.9 23.7 1.0
O F:HOH1038 3.9 46.2 1.0
CA C:CA492 3.9 27.9 1.0
O3' C:DA413 4.1 31.5 1.0
O B:ASP218 4.1 26.1 1.0
OP2 F:DG465 4.2 28.3 1.0
C5' C:DC414 4.2 33.4 1.0
OE1 A:GLN47 4.2 24.7 1.0
NE2 A:GLN47 4.3 29.4 1.0
C4' C:DC414 4.3 32.4 1.0
OD1 B:ASP220 4.4 22.3 1.0
O5' C:DC414 4.4 30.2 1.0
N B:ASP220 4.5 21.2 1.0
CB A:ASP20 4.5 22.6 1.0
C5' F:DG465 4.6 25.4 1.0
CD A:GLN47 4.7 27.8 1.0
OP2 C:DC414 4.7 30.9 1.0
CA B:ASP220 4.8 19.6 1.0
O3' C:DC414 4.8 27.0 1.0
C3' C:DC414 4.8 30.6 1.0
N B:GLY219 4.9 23.6 1.0
C B:ASP218 4.9 25.0 1.0
O3' E:DC464 5.0 24.6 1.0

Calcium binding site 4 out of 6 in 1n3e

Go back to Calcium Binding Sites List in 1n3e
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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
I:Ca993

b:30.2
occ:1.00
 OD1 G:ASP520 2.1 35.3 1.0
OD1 H:ASP720 2.2 30.8 1.0
OP3 L:DG965 2.3 32.7 1.0
O3' I:DC914 2.4 36.3 1.0
O3' K:DC964 2.5 30.9 1.0
OP3 J:DG915 2.6 25.7 1.0
CG G:ASP520 3.3 32.4 1.0
CG H:ASP720 3.4 30.9 1.0
C3' I:DC914 3.4 34.7 1.0
C3' K:DC964 3.5 32.3 1.0
P L:DG965 3.5 33.2 1.0
O5' L:DG965 3.7 31.8 1.0
P J:DG915 3.8 26.0 1.0
O L:HOH1094 3.8 44.3 1.0
O5' J:DG915 3.8 29.6 1.0
C4' I:DC914 3.9 34.1 1.0
CA L:CA992 3.9 28.8 1.0
O H:GLY719 3.9 31.6 1.0
OD2 G:ASP520 3.9 32.2 1.0
O G:GLY519 3.9 29.8 1.0
CA J:CA991 4.1 29.4 1.0
C4' K:DC964 4.1 32.3 1.0
OD2 H:ASP720 4.1 31.4 1.0
OP2 L:DG965 4.2 33.9 1.0
CB G:ASP520 4.4 28.4 1.0
C H:GLY719 4.4 31.3 1.0
CB H:ASP720 4.5 30.9 1.0
CA H:ASP720 4.5 30.8 1.0
OP2 J:DG915 4.5 23.6 1.0
CA G:ASP520 4.5 26.2 1.0
C G:GLY519 4.6 28.0 1.0
C2' K:DC964 4.7 31.5 1.0
OP1 L:DG965 4.7 35.8 1.0
C2' I:DC914 4.7 33.6 1.0
N H:ASP720 4.7 30.5 1.0
OP1 I:DC914 4.8 30.4 1.0
C5' I:DC914 4.8 34.0 1.0
N G:ASP520 4.9 26.9 1.0
O4' I:DC914 4.9 35.5 1.0
OP1 J:DG915 5.0 26.7 1.0

Calcium binding site 5 out of 6 in 1n3e

Go back to Calcium Binding Sites List in 1n3e
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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
J:Ca991

b:29.4
occ:1.00
 OP1 K:DC964 2.2 32.7 1.0
O H:HOH1001 2.3 34.5 1.0
O G:GLY519 2.3 29.8 1.0
OP3 J:DG915 2.4 25.7 1.0
OD2 H:ASP720 2.5 31.4 1.0
OP1 J:DG915 2.5 26.7 1.0
P J:DG915 2.9 26.0 1.0
CG H:ASP720 3.2 30.9 1.0
OD1 H:ASP720 3.3 30.8 1.0
C G:GLY519 3.4 28.0 1.0
P K:DC964 3.6 33.1 1.0
O5' J:DG915 3.7 29.6 1.0
O J:HOH1054 3.9 20.7 1.0
CA G:GLY519 4.0 27.0 1.0
O3' K:DA963 4.0 32.0 1.0
OE1 H:GLN747 4.0 28.8 1.0
O G:ASP518 4.1 29.0 1.0
CA I:CA993 4.1 30.2 1.0
OP2 J:DG915 4.3 23.6 1.0
NE2 H:GLN747 4.4 31.2 1.0
C4' K:DC964 4.4 32.3 1.0
C5' K:DC964 4.5 32.7 1.0
C5' J:DG915 4.5 27.2 1.0
OP2 K:DC964 4.5 33.3 1.0
N G:ASP520 4.5 26.9 1.0
O5' K:DC964 4.6 32.5 1.0
CD H:GLN747 4.6 30.0 1.0
CB H:ASP720 4.6 30.9 1.0
OD1 G:ASP520 4.6 35.3 1.0
CA G:ASP520 4.9 26.2 1.0
C G:ASP518 4.9 28.3 1.0
N G:GLY519 4.9 27.1 1.0
O3' I:DC914 5.0 36.3 1.0

Calcium binding site 6 out of 6 in 1n3e

Go back to Calcium Binding Sites List in 1n3e
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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
L:Ca992

b:28.8
occ:1.00
 OP1 I:DC914 2.1 30.4 1.0
O H:GLY719 2.3 31.6 1.0
OD2 G:ASP520 2.3 32.2 1.0
OP3 L:DG965 2.4 32.7 1.0
O G:HOH1049 2.6 27.8 1.0
OP1 L:DG965 2.6 35.8 1.0
P L:DG965 3.0 33.2 1.0
CG G:ASP520 3.1 32.4 1.0
OD1 G:ASP520 3.3 35.3 1.0
C H:GLY719 3.3 31.3 1.0
P I:DC914 3.6 31.2 1.0
CA H:GLY719 3.8 31.5 1.0
O5' L:DG965 3.8 31.8 1.0
CA I:CA993 3.9 30.2 1.0
O L:HOH1006 3.9 33.6 1.0
O H:ASP718 4.1 31.3 1.0
O3' I:DA913 4.1 33.9 1.0
OE1 G:GLN547 4.1 20.1 1.0
NE2 G:GLN547 4.2 23.2 1.0
OP2 L:DG965 4.3 33.9 1.0
C5' I:DC914 4.3 34.0 1.0
C4' I:DC914 4.4 34.1 1.0
O5' I:DC914 4.5 33.0 1.0
N H:ASP720 4.5 30.5 1.0
CB G:ASP520 4.5 28.4 1.0
C5' L:DG965 4.5 30.3 1.0
OP2 I:DC914 4.6 32.8 1.0
CD G:GLN547 4.6 23.1 1.0
OD1 H:ASP720 4.8 30.8 1.0
N H:GLY719 4.8 32.2 1.0
NZ H:LYS798 4.9 32.1 1.0
C H:ASP718 4.9 31.4 1.0
CA H:ASP720 4.9 30.8 1.0

Reference:

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
Page generated: Mon Jul 7 17:25:42 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy