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Calcium in PDB 3s5u: Crystal Structure of Crispr Associated Protein

Protein crystallography data

The structure of Crystal Structure of Crispr Associated Protein, PDB code: 3s5u was solved by A.Ke, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.112, 140.091, 148.434, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 27.5

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Crispr Associated Protein (pdb code 3s5u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of Crispr Associated Protein, PDB code: 3s5u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 3s5u

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Calcium binding site 1 out of 16 in the Crystal Structure of Crispr Associated Protein


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 Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca220

b:47.6
occ:1.00
 OE2 A:GLU150 2.2 41.2 1.0
OD1 A:ASP142 2.2 49.5 1.0
OE1 A:GLU138 2.3 48.6 1.0
O A:GLU138 2.6 45.7 1.0
OD2 G:ASP118 2.8 39.3 1.0
CG A:ASP142 3.1 48.9 1.0
CD A:GLU150 3.3 41.7 1.0
OD2 A:ASP142 3.4 47.0 1.0
C A:GLU138 3.5 45.8 1.0
CD A:GLU138 3.6 48.1 1.0
OE1 A:GLU150 3.8 39.4 1.0
CG G:ASP118 3.8 42.0 1.0
CB G:ASP118 3.9 41.2 1.0
CB A:GLU138 4.2 44.7 1.0
N A:THR139 4.3 46.7 1.0
CA A:GLU138 4.4 44.9 1.0
CA A:THR139 4.4 47.6 1.0
OE2 A:GLU138 4.5 48.4 1.0
CG A:GLU138 4.5 44.5 1.0
CB A:ASP142 4.5 48.1 1.0
CG A:GLU150 4.6 41.8 1.0
CB A:GLU146 4.8 42.8 1.0
N A:GLU138 4.8 44.0 1.0
CA A:ASP142 4.8 48.2 1.0
OD1 G:ASP118 5.0 42.8 1.0
CG A:GLU146 5.0 47.8 1.0

Calcium binding site 2 out of 16 in 3s5u

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Calcium binding site 2 out of 16 in the Crystal Structure of Crispr Associated Protein


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 Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca221

b:37.2
occ:1.00
 OE2 A:GLU128 2.1 43.3 1.0
OD1 A:ASP122 2.2 41.0 1.0
O A:GLY123 2.3 41.8 1.0
O G:ALA132 2.4 41.0 1.0
O A:HOH223 2.6 29.5 1.0
O A:HOH239 2.7 44.2 1.0
OE1 A:GLU128 2.8 45.6 1.0
CD A:GLU128 2.8 43.6 1.0
CG A:ASP122 3.3 43.3 1.0
C A:GLY123 3.5 42.0 1.0
C G:ALA132 3.6 41.4 1.0
OD2 A:ASP122 3.9 46.1 1.0
N A:GLY123 3.9 43.4 1.0
CG A:GLU128 4.3 39.5 1.0
CA A:GLY123 4.3 42.6 1.0
CA G:LEU133 4.4 42.4 1.0
O A:HOH242 4.4 47.1 1.0
N G:LEU133 4.4 41.7 1.0
CB A:ASP122 4.4 43.2 1.0
C G:LEU133 4.5 43.5 1.0
N A:ILE124 4.5 41.2 1.0
N G:GLY134 4.6 43.5 1.0
CA A:ILE124 4.6 40.7 1.0
CA G:ALA132 4.6 41.4 1.0
O G:LEU133 4.9 45.4 1.0

Calcium binding site 3 out of 16 in 3s5u

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Calcium binding site 3 out of 16 in the Crystal Structure of Crispr Associated Protein


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 Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca220

b:48.1
occ:1.00
 O B:HOH227 2.1 42.9 1.0
O B:GLY123 2.2 54.2 1.0
OE2 B:GLU128 2.3 52.0 1.0
O D:ALA132 2.4 51.7 1.0
O B:HOH223 2.5 39.0 1.0
OD1 B:ASP122 2.7 62.3 1.0
OE1 B:GLU128 2.8 53.3 1.0
CD B:GLU128 2.9 51.4 1.0
CG B:ASP122 3.3 58.5 1.0
C B:GLY123 3.5 53.8 1.0
OD2 B:ASP122 3.5 59.1 1.0
C D:ALA132 3.7 51.9 1.0
N D:GLY134 4.2 50.7 1.0
CA B:ILE124 4.2 49.9 1.0
N B:ILE124 4.3 51.8 1.0
N B:GLY123 4.4 56.0 1.0
CG B:GLU128 4.4 47.9 1.0
CA B:GLY123 4.5 55.0 1.0
CB B:ASP122 4.5 57.0 1.0
N D:LEU133 4.5 51.2 1.0
CA D:LEU133 4.5 51.4 1.0
C B:ASP122 4.6 56.5 1.0
N B:ILE125 4.7 47.3 1.0
CA D:ALA132 4.7 52.4 1.0
C D:LEU133 4.8 51.8 1.0
O B:ASP122 5.0 57.1 1.0
C B:ILE124 5.0 48.8 1.0
CA D:GLY134 5.0 49.4 1.0

Calcium binding site 4 out of 16 in 3s5u

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Calcium binding site 4 out of 16 in the Crystal Structure of Crispr Associated Protein


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 Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca221

b:59.1
occ:1.00
 OD2 D:ASP118 2.2 56.0 1.0
OE2 B:GLU150 2.4 39.1 1.0
OE1 B:GLU138 2.4 47.7 1.0
OD1 B:ASP142 2.4 44.2 1.0
O B:GLU138 2.6 45.0 1.0
CG D:ASP118 3.4 56.4 1.0
CG B:ASP142 3.6 44.2 1.0
CD B:GLU150 3.6 42.0 1.0
CD B:GLU138 3.7 47.0 1.0
C B:GLU138 3.7 44.6 1.0
OE1 B:GLU146 3.7 49.1 1.0
OD2 B:ASP142 4.1 41.5 1.0
OE1 B:GLU150 4.1 41.4 1.0
CB D:ASP118 4.3 55.4 1.0
CB B:GLU138 4.3 43.2 1.0
OD1 D:ASP118 4.3 59.5 1.0
OG B:SER141 4.4 47.9 1.0
OE2 B:GLU138 4.5 46.8 1.0
CA B:GLU138 4.5 43.5 1.0
CG B:GLU138 4.6 43.9 1.0
N B:THR139 4.6 45.8 1.0
CA B:THR139 4.7 46.9 1.0
CB B:ASP142 4.7 44.3 1.0
CB B:GLU146 4.7 40.8 1.0
CG B:GLU150 4.8 43.5 1.0
CD B:GLU146 4.8 45.1 1.0
CA B:ASP142 4.8 44.6 1.0
N B:ASP142 4.9 45.9 1.0
N B:GLU138 4.9 42.0 1.0

Calcium binding site 5 out of 16 in 3s5u

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Calcium binding site 5 out of 16 in the Crystal Structure of Crispr Associated Protein


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 Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca220

b:49.8
occ:1.00
 O C:GLY123 2.2 47.4 1.0
O E:ALA132 2.3 46.0 1.0
OE2 C:GLU128 2.4 52.6 1.0
OD1 C:ASP122 2.4 49.4 1.0
O C:HOH227 2.4 49.2 1.0
OE1 C:GLU128 2.7 52.4 1.0
CD C:GLU128 2.9 51.6 1.0
C C:GLY123 3.4 47.0 1.0
C E:ALA132 3.5 46.4 1.0
CG C:ASP122 3.6 47.7 1.0
N C:GLY123 3.9 46.8 1.0
CA C:GLY123 4.2 46.9 1.0
OD2 C:ASP122 4.2 50.1 1.0
N E:LEU133 4.3 46.6 1.0
CA E:LEU133 4.4 47.0 1.0
N C:ILE124 4.4 46.4 1.0
CG C:GLU128 4.4 48.7 1.0
CA C:ILE124 4.5 46.3 1.0
C E:LEU133 4.5 48.1 1.0
CA E:ALA132 4.5 46.7 1.0
CB C:ASP122 4.6 46.1 1.0
N E:GLY134 4.8 48.5 1.0
C C:ASP122 4.9 46.6 1.0
O E:LEU133 5.0 48.6 1.0

Calcium binding site 6 out of 16 in 3s5u

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Calcium binding site 6 out of 16 in the Crystal Structure of Crispr Associated Protein


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 Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca221

b:65.1
occ:1.00
 OE1 C:GLU138 2.2 59.8 1.0
OD1 C:ASP142 2.2 64.2 1.0
OE2 C:GLU150 2.4 52.0 1.0
O C:GLU138 2.6 55.2 1.0
OD2 E:ASP118 2.7 55.9 1.0
CG C:ASP142 3.0 61.1 1.0
OD2 C:ASP142 3.1 61.5 1.0
CD C:GLU138 3.3 60.6 1.0
CD C:GLU150 3.4 50.5 1.0
C C:GLU138 3.6 55.5 1.0
OE1 C:GLU150 3.7 50.5 1.0
CG E:ASP118 3.9 55.0 1.0
CB C:GLU138 4.1 55.4 1.0
OE2 C:GLU138 4.1 62.5 1.0
CG C:GLU138 4.2 57.8 1.0
CB C:ASP142 4.3 59.6 1.0
CA C:GLU138 4.4 55.4 1.0
CA C:THR139 4.4 57.1 1.0
N C:THR139 4.5 56.2 1.0
CB E:ASP118 4.5 53.4 1.0
CA C:ASP142 4.7 58.9 1.0
CG C:GLU150 4.7 49.7 1.0
OG C:SER141 4.7 58.6 1.0
OD1 E:ASP118 4.9 57.0 1.0
N C:GLU138 4.9 54.3 1.0
N C:ASP142 4.9 59.3 1.0
OE1 C:GLU146 5.0 59.6 1.0

Calcium binding site 7 out of 16 in 3s5u

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Calcium binding site 7 out of 16 in the Crystal Structure of Crispr Associated Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca220

b:53.1
occ:1.00
 OD2 B:ASP118 2.1 53.8 1.0
O D:GLU138 2.3 43.6 1.0
OE2 D:GLU150 2.4 41.1 1.0
OD1 D:ASP142 2.4 51.3 1.0
OE1 D:GLU138 2.9 51.5 1.0
CG B:ASP118 3.2 54.5 1.0
C D:GLU138 3.5 44.1 1.0
CD D:GLU150 3.5 40.2 1.0
CG D:ASP142 3.6 49.5 1.0
CD D:GLU138 3.6 49.8 1.0
OE1 D:GLU150 3.9 36.7 1.0
CB B:ASP118 3.9 54.4 1.0
OE2 D:GLU138 4.1 50.1 1.0
OD1 B:ASP118 4.1 56.0 1.0
OD2 D:ASP142 4.3 50.6 1.0
N D:THR139 4.3 44.6 1.0
CA D:THR139 4.3 46.0 1.0
CB D:GLU138 4.4 44.3 1.0
CA D:GLU138 4.5 44.1 1.0
OG D:SER141 4.6 46.6 1.0
CG D:GLU138 4.7 46.5 1.0
CA D:ASP142 4.7 47.0 1.0
CB D:ASP142 4.7 47.5 1.0
CB D:GLU146 4.8 43.8 1.0
CG D:GLU150 4.8 42.2 1.0
N D:ASP142 4.9 47.5 1.0
OE1 D:GLU146 4.9 53.6 1.0
N D:GLU138 5.0 43.6 1.0
C D:THR139 5.0 47.0 1.0

Calcium binding site 8 out of 16 in 3s5u

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Calcium binding site 8 out of 16 in the Crystal Structure of Crispr Associated Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca221

b:49.6
occ:1.00
 O B:HOH229 2.1 57.3 1.0
O D:GLY123 2.2 54.5 1.0
OE2 D:GLU128 2.2 54.7 1.0
OD1 D:ASP122 2.5 55.6 1.0
O B:ALA132 2.6 44.9 1.0
O D:HOH228 2.6 49.8 1.0
OE1 D:GLU128 2.8 53.1 1.0
CD D:GLU128 2.9 53.2 1.0
CG D:ASP122 3.0 54.7 1.0
OD2 D:ASP122 3.1 55.3 1.0
C D:GLY123 3.4 54.0 1.0
C B:ALA132 3.8 44.7 1.0
N D:GLY123 3.9 53.5 1.0
CB D:ASP122 4.1 53.5 1.0
CA D:GLY123 4.2 54.0 1.0
N D:ILE124 4.4 53.1 1.0
CG D:GLU128 4.4 52.4 1.0
CA D:ILE124 4.4 52.3 1.0
C D:ASP122 4.5 53.6 1.0
CA B:LEU133 4.5 43.5 1.0
C B:LEU133 4.5 44.0 1.0
N B:LEU133 4.6 44.2 1.0
O B:LEU133 4.7 45.5 1.0
N D:ILE125 4.7 51.4 1.0
CA B:ALA132 4.8 44.8 1.0
CA D:ASP122 4.9 53.2 1.0
N B:GLY134 4.9 43.4 1.0

Calcium binding site 9 out of 16 in 3s5u

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Calcium binding site 9 out of 16 in the Crystal Structure of Crispr Associated Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca220

b:57.0
occ:1.00
 O E:HOH229 2.1 53.7 1.0
O E:GLY123 2.1 50.7 1.0
OE2 E:GLU128 2.3 56.3 1.0
O C:ALA132 2.3 44.8 1.0
O E:HOH230 2.4 42.5 1.0
OD1 E:ASP122 2.6 56.9 1.0
OE1 E:GLU128 2.9 57.7 1.0
CD E:GLU128 2.9 55.7 1.0
C E:GLY123 3.3 50.8 1.0
C C:ALA132 3.5 45.4 1.0
CG E:ASP122 3.8 55.0 1.0
N E:GLY123 4.1 51.9 1.0
N E:ILE124 4.2 50.3 1.0
CA E:ILE124 4.3 49.5 1.0
CA E:GLY123 4.3 51.2 1.0
N C:LEU133 4.4 46.2 1.0
CG E:GLU128 4.4 53.3 1.0
CA C:ALA132 4.5 45.5 1.0
CA C:LEU133 4.6 46.8 1.0
OD2 E:ASP122 4.6 57.2 1.0
N E:ILE125 4.7 49.9 1.0
CB E:ASP122 4.8 53.0 1.0
C C:LEU133 4.8 48.0 1.0
N C:GLY134 4.8 48.4 1.0
CD1 E:ILE125 4.9 50.4 1.0
C E:ILE124 5.0 49.6 1.0

Calcium binding site 10 out of 16 in 3s5u

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Calcium binding site 10 out of 16 in the Crystal Structure of Crispr Associated Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Crispr Associated Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca221

b:54.0
occ:1.00
 OD2 C:ASP118 2.2 48.3 1.0
OD1 E:ASP142 2.2 49.0 1.0
OE1 E:GLU138 2.3 57.6 1.0
OE2 E:GLU150 2.5 53.7 1.0
O E:GLU138 2.6 49.3 1.0
O E:HOH226 2.9 37.9 1.0
CG C:ASP118 3.4 45.8 1.0
CG E:ASP142 3.4 49.0 1.0
C E:GLU138 3.5 49.8 1.0
CD E:GLU138 3.6 56.5 1.0
CD E:GLU150 3.6 51.0 1.0
OD2 E:ASP142 3.9 49.8 1.0
OE1 E:GLU150 4.0 48.9 1.0
CB C:ASP118 4.1 43.7 1.0
CB E:GLU138 4.3 50.8 1.0
N E:THR139 4.3 49.3 1.0
OD1 C:ASP118 4.3 48.1 1.0
CA E:THR139 4.4 48.9 1.0
OE2 E:GLU138 4.4 57.7 1.0
CA E:GLU138 4.4 50.4 1.0
CG E:GLU138 4.5 52.7 1.0
OG E:SER141 4.7 47.5 1.0
CB E:ASP142 4.7 48.4 1.0
CA E:ASP142 4.8 48.1 1.0
N E:GLU138 4.8 49.7 1.0
N E:ASP142 4.9 48.5 1.0
CG E:GLU150 4.9 50.1 1.0

Reference:

K.H.Nam, I.Kurinov, A.Ke. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (Crispr)-Associated CSN2 Protein Revealed CA2+-Dependent Double-Stranded Dna Binding Activity. J. Biol. Chem. V. 286 30759 2011.
ISSN: ESSN 1083-351X
PubMed: 21697083
DOI: 10.1074/JBC.M111.256263
Page generated: Sat Jul 13 19:02:45 2024

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