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Calcium in PDB 1n3f: Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right Side of Wildtype Dna Target Sequence)

Protein crystallography data

The structure of Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right Side of Wildtype Dna Target Sequence), PDB code: 1n3f 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) 19.85 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.320, 76.390, 81.060, 90.00, 108.75, 90.00
R / Rfree (%) 19.5 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right Side of Wildtype Dna Target Sequence) (pdb code 1n3f). 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 II (Palindrome of Right Side of Wildtype Dna Target Sequence), PDB code: 1n3f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1n3f

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Calcium binding site 1 out of 6 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right 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 II (Palindrome of Right Side of Wildtype Dna Target Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca498

b:34.8
occ:1.00
 OP1 D:DG415 2.0 16.6 1.0
OD1 A:ASP20 2.1 22.6 1.0
OD1 B:ASP220 2.1 22.7 1.0
OP1 F:DG465 2.1 17.4 1.0
O3' E:DA464 2.3 20.0 1.0
O3' C:DA414 2.4 21.5 1.0
CG A:ASP20 3.2 20.2 1.0
C3' C:DA414 3.2 24.6 1.0
C3' E:DA464 3.3 20.1 1.0
CG B:ASP220 3.3 19.5 1.0
P D:DG415 3.3 23.0 1.0
P F:DG465 3.4 22.5 1.0
O5' D:DG415 3.7 22.6 1.0
OD2 A:ASP20 3.7 18.6 1.0
O5' F:DG465 3.7 19.5 1.0
CA D:CA499 3.7 36.5 1.0
OD2 B:ASP220 3.8 18.6 1.0
CA F:CA497 3.8 37.5 1.0
C4' E:DA464 3.9 22.1 1.0
OP3 D:DG415 3.9 24.3 1.0
O B:GLY219 3.9 19.2 1.0
C4' C:DA414 4.0 24.8 1.0
O D:HOH1003 4.0 19.9 1.0
O A:GLY19 4.1 17.8 1.0
OP3 F:DG465 4.1 25.4 1.0
O F:HOH1002 4.2 21.2 1.0
CB A:ASP20 4.5 18.1 1.0
CB B:ASP220 4.5 19.9 1.0
OP2 D:DG415 4.5 20.8 1.0
C B:GLY219 4.5 22.6 1.0
C2' C:DA414 4.6 24.6 1.0
C2' E:DA464 4.6 19.9 1.0
CA B:ASP220 4.6 19.2 1.0
OP2 F:DG465 4.6 18.6 1.0
CA A:ASP20 4.6 19.1 1.0
C A:GLY19 4.6 22.5 1.0
OP1 E:DA464 4.7 23.2 1.0
C5' E:DA464 4.7 21.2 1.0
OP1 C:DA414 4.8 22.2 1.0
C5' C:DA414 4.8 26.7 1.0
N B:ASP220 4.9 20.4 1.0
N A:ASP20 4.9 20.1 1.0
O4' E:DA464 5.0 23.4 1.0

Calcium binding site 2 out of 6 in 1n3f

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Calcium binding site 2 out of 6 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right 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 II (Palindrome of Right Side of Wildtype Dna Target Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca499

b:36.5
occ:1.00
 OP1 E:DA464 2.0 23.2 1.0
OD2 A:ASP20 2.1 18.6 1.0
O B:GLY219 2.1 19.2 1.0
O B:HOH1001 2.2 18.5 1.0
OP1 D:DG415 2.3 16.6 1.0
OP2 D:DG415 2.3 20.8 1.0
P D:DG415 2.7 23.0 1.0
CG A:ASP20 3.1 20.2 1.0
C B:GLY219 3.1 22.6 1.0
OD1 A:ASP20 3.4 22.6 1.0
P E:DA464 3.5 20.4 1.0
CA B:GLY219 3.6 21.9 1.0
CA C:CA498 3.7 34.8 1.0
O5' D:DG415 3.8 22.6 1.0
O B:HOH1031 3.9 28.2 1.0
O3' E:DG463 4.0 23.8 1.0
OP3 D:DG415 4.0 24.3 1.0
NE2 A:GLN47 4.0 18.4 1.0
O B:ASP218 4.1 21.0 1.0
OE1 A:GLN47 4.2 19.2 1.0
C5' E:DA464 4.2 21.2 1.0
OD1 B:ASP220 4.2 22.7 1.0
N B:ASP220 4.3 20.4 1.0
O5' E:DA464 4.4 17.5 1.0
C4' E:DA464 4.4 22.1 1.0
CB A:ASP20 4.4 18.1 1.0
C5' D:DG415 4.5 21.7 1.0
OP2 E:DA464 4.5 22.6 1.0
CD A:GLN47 4.5 22.3 1.0
O B:HOH1075 4.7 26.7 1.0
N B:GLY219 4.7 18.6 1.0
CA B:ASP220 4.7 19.2 1.0
C B:ASP218 4.9 22.3 1.0
O3' E:DA464 4.9 20.0 1.0
C3' E:DA464 4.9 20.1 1.0

Calcium binding site 3 out of 6 in 1n3f

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Calcium binding site 3 out of 6 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right 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 II (Palindrome of Right Side of Wildtype Dna Target Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca497

b:37.5
occ:1.00
 O A:GLY19 2.1 17.8 1.0
OP1 C:DA414 2.1 22.2 1.0
OD2 B:ASP220 2.1 18.6 1.0
OP1 F:DG465 2.2 17.4 1.0
O A:HOH1007 2.3 19.6 1.0
OP2 F:DG465 2.3 18.6 1.0
P F:DG465 2.7 22.5 1.0
CG B:ASP220 3.1 19.5 1.0
C A:GLY19 3.1 22.5 1.0
OD1 B:ASP220 3.4 22.7 1.0
P C:DA414 3.5 23.4 1.0
CA A:GLY19 3.7 22.9 1.0
O5' F:DG465 3.7 19.5 1.0
O F:HOH1042 3.8 26.4 1.0
CA C:CA498 3.8 34.8 1.0
O3' C:DG413 4.0 23.5 1.0
OP3 F:DG465 4.0 25.4 1.0
NE2 B:GLN247 4.1 21.1 1.0
O A:ASP18 4.2 21.4 1.0
OD1 A:ASP20 4.2 22.6 1.0
OE1 B:GLN247 4.2 25.6 1.0
C5' C:DA414 4.3 26.7 1.0
N A:ASP20 4.3 20.1 1.0
C5' F:DG465 4.4 19.2 1.0
C4' C:DA414 4.4 24.8 1.0
O5' C:DA414 4.4 20.0 1.0
CB B:ASP220 4.5 19.9 1.0
OP2 C:DA414 4.5 23.1 1.0
CD B:GLN247 4.6 24.1 1.0
O A:HOH1041 4.6 27.6 1.0
CA A:ASP20 4.7 19.1 1.0
N A:GLY19 4.8 20.7 1.0
O3' C:DA414 4.9 21.5 1.0
C A:ASP18 4.9 22.3 1.0
C3' C:DA414 4.9 24.6 1.0
O3' E:DA464 5.0 20.0 1.0

Calcium binding site 4 out of 6 in 1n3f

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Calcium binding site 4 out of 6 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right 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 II (Palindrome of Right Side of Wildtype Dna Target Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca998

b:41.4
occ:1.00
 OP3 J:DG915 2.1 20.6 1.0
OD1 G:ASP520 2.1 24.1 1.0
OD1 H:ASP720 2.1 24.8 1.0
OP3 L:DG965 2.1 25.1 1.0
O3' I:DA914 2.3 26.6 1.0
O3' K:DA964 2.4 28.6 1.0
C3' I:DA914 3.2 26.4 1.0
CG G:ASP520 3.2 25.0 1.0
CG H:ASP720 3.2 22.2 1.0
C3' K:DA964 3.3 25.7 1.0
P J:DG915 3.4 26.1 1.0
P L:DG965 3.4 27.9 1.0
O5' J:DG915 3.7 25.0 1.0
O5' L:DG965 3.7 26.1 1.0
OD2 H:ASP720 3.7 23.6 1.0
OD2 G:ASP520 3.7 26.5 1.0
CA J:CA997 3.7 38.1 1.0
CA L:CA999 3.8 40.5 1.0
O H:GLY719 3.9 21.8 1.0
C4' I:DA914 3.9 29.2 1.0
C4' K:DA964 3.9 29.2 1.0
O G:GLY519 4.0 22.5 1.0
OP2 J:DG915 4.0 26.2 1.0
OP2 L:DG965 4.1 30.3 1.0
O L:HOH1026 4.1 26.2 1.0
O J:HOH1036 4.1 28.5 1.0
CB H:ASP720 4.5 23.6 1.0
CB G:ASP520 4.5 21.3 1.0
C2' I:DA914 4.5 28.9 1.0
C H:GLY719 4.6 22.9 1.0
OP1 J:DG915 4.6 24.9 1.0
C G:GLY519 4.6 24.5 1.0
C2' K:DA964 4.6 26.3 1.0
OP1 L:DG965 4.6 24.6 1.0
CA H:ASP720 4.6 22.9 1.0
CA G:ASP520 4.6 23.7 1.0
C5' K:DA964 4.7 25.9 1.0
C5' I:DA914 4.7 28.9 1.0
OP1 K:DA964 4.7 23.3 1.0
OP1 I:DA914 4.8 27.6 1.0
N G:ASP520 4.9 23.9 1.0
N H:ASP720 4.9 22.8 1.0

Calcium binding site 5 out of 6 in 1n3f

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Calcium binding site 5 out of 6 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right 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 II (Palindrome of Right Side of Wildtype Dna Target Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca997

b:38.1
occ:1.00
 OP1 K:DA964 2.0 23.3 1.0
OD2 G:ASP520 2.1 26.5 1.0
O H:GLY719 2.1 21.8 1.0
OP3 J:DG915 2.2 20.6 1.0
O H:HOH1020 2.2 20.0 1.0
OP1 J:DG915 2.4 24.9 1.0
P J:DG915 2.7 26.1 1.0
CG G:ASP520 3.0 25.0 1.0
C H:GLY719 3.2 22.9 1.0
OD1 G:ASP520 3.3 24.1 1.0
P K:DA964 3.5 25.4 1.0
CA H:GLY719 3.7 23.1 1.0
O5' J:DG915 3.7 25.0 1.0
CA I:CA998 3.7 41.4 1.0
O J:HOH1027 3.9 30.9 1.0
NE2 G:GLN547 3.9 19.6 1.0
O3' K:DG963 3.9 26.3 1.0
OP2 J:DG915 4.0 26.2 1.0
OD1 H:ASP720 4.1 24.8 1.0
C5' K:DA964 4.2 25.9 1.0
OE1 G:GLN547 4.2 23.0 1.0
O H:ASP718 4.2 22.7 1.0
N H:ASP720 4.3 22.8 1.0
O5' K:DA964 4.3 24.7 1.0
C4' K:DA964 4.4 29.2 1.0
CB G:ASP520 4.4 21.3 1.0
C5' J:DG915 4.4 23.6 1.0
OP2 K:DA964 4.5 24.5 1.0
CD G:GLN547 4.5 24.2 1.0
O H:HOH1072 4.7 34.1 1.0
CA H:ASP720 4.7 22.9 1.0
N H:GLY719 4.8 18.9 1.0
O3' K:DA964 4.8 28.6 1.0
C3' K:DA964 4.9 25.7 1.0
C H:ASP718 4.9 23.3 1.0

Calcium binding site 6 out of 6 in 1n3f

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Calcium binding site 6 out of 6 in the Crystal Structure of I-Crei Bound to A Palindromic Dna Sequence II (Palindrome of Right 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 II (Palindrome of Right Side of Wildtype Dna Target Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca999

b:40.5
occ:1.00
 OP1 I:DA914 2.1 27.6 1.0
O H:HOH1011 2.2 24.5 1.0
O G:GLY519 2.2 22.5 1.0
OD2 H:ASP720 2.2 23.6 1.0
OP3 L:DG965 2.2 25.1 1.0
OP1 L:DG965 2.3 24.6 1.0
P L:DG965 2.7 27.9 1.0
C G:GLY519 3.2 24.5 1.0
CG H:ASP720 3.2 22.2 1.0
OD1 H:ASP720 3.5 24.8 1.0
P I:DA914 3.5 28.3 1.0
CA G:GLY519 3.6 24.3 1.0
O5' L:DG965 3.7 26.1 1.0
O L:HOH1215 3.8 33.7 1.0
CA I:CA998 3.8 41.4 1.0
O3' I:DG913 3.9 27.3 1.0
OP2 L:DG965 4.0 30.3 1.0
NE2 H:GLN747 4.1 24.3 1.0
OE1 H:GLN747 4.1 28.8 1.0
O G:ASP518 4.2 27.1 1.0
C5' I:DA914 4.2 28.9 1.0
OD1 G:ASP520 4.3 24.1 1.0
N G:ASP520 4.3 23.9 1.0
C4' I:DA914 4.4 29.2 1.0
O5' I:DA914 4.4 26.9 1.0
C5' L:DG965 4.4 26.7 1.0
CD H:GLN747 4.5 27.0 1.0
CB H:ASP720 4.5 23.6 1.0
OP2 I:DA914 4.5 28.6 1.0
O G:HOH1157 4.7 35.7 1.0
N G:GLY519 4.7 25.6 1.0
CA G:ASP520 4.8 23.7 1.0
O3' I:DA914 4.9 26.6 1.0
C G:ASP518 4.9 26.7 1.0
C3' I:DA914 4.9 26.4 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: Thu Jul 11 12:41:58 2024

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