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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

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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

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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

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