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Calcium in PDB 1sds: Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna

Protein crystallography data

The structure of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna, PDB code: 1sds was solved by T.Hamma, A.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 1.80
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 106.970, 141.300, 162.870, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 22.5

Other elements in 1sds:

The structure of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna also contains other interesting chemical elements:

Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna (pdb code 1sds). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna, PDB code: 1sds:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1sds

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Calcium binding site 1 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca755

b:36.5
occ:1.00
 O D:HOH987 2.3 41.2 1.0
OP2 D:U206 2.3 33.0 1.0
O6 D:G208 2.3 31.5 1.0
O D:HOH886 2.4 31.4 1.0
O D:HOH986 2.4 40.8 1.0
O D:HOH1030 2.4 54.9 1.0
C6 D:G208 3.4 27.9 1.0
P D:U206 3.7 31.4 1.0
CA D:CA756 3.9 34.7 1.0
N7 D:G208 4.1 27.4 1.0
C5 D:G208 4.1 27.6 1.0
O A:HOH950 4.3 31.8 1.0
OP2 D:U207 4.4 33.5 1.0
O5' D:U206 4.4 31.6 1.0
O D:HOH1031 4.4 52.9 1.0
C5' D:U206 4.4 31.2 1.0
O3' D:A205 4.5 28.8 1.0
N1 D:G208 4.6 28.2 1.0
C5 D:U207 4.6 25.8 1.0
OP1 D:U206 4.6 31.0 1.0
O4 D:U207 4.9 27.6 1.0

Calcium binding site 2 out of 10 in 1sds

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Calcium binding site 2 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca756

b:34.7
occ:1.00
 O2' D:A205 2.6 29.8 1.0
O4 D:U207 2.8 27.6 1.0
O D:HOH987 3.0 41.2 1.0
O D:HOH1033 3.0 59.5 1.0
O6 D:G208 3.1 31.5 1.0
OP2 D:U206 3.2 33.0 1.0
O3' D:A205 3.2 28.8 1.0
O D:HOH996 3.3 39.8 1.0
P D:U206 3.7 31.4 1.0
C4 D:U207 3.7 28.3 1.0
C2' D:A205 3.7 28.5 1.0
C6 D:G208 3.7 27.9 1.0
CA D:CA755 3.9 36.5 1.0
N1 D:G208 3.9 28.2 1.0
C3' D:A205 4.0 27.3 1.0
C5 D:U207 4.1 25.8 1.0
OP1 D:U206 4.2 31.0 1.0
C1' D:A205 4.6 25.6 1.0
O D:HOH1034 4.7 47.1 1.0
C5 D:G208 4.9 27.6 1.0
N3 D:U207 5.0 25.5 1.0

Calcium binding site 3 out of 10 in 1sds

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Calcium binding site 3 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca757

b:30.1
occ:0.90
 OP2 D:A212 2.3 26.4 1.0
O D:HOH852 2.3 19.9 0.9
O D:HOH910 2.3 29.2 0.9
O D:HOH957 2.4 38.9 0.9
O D:HOH956 2.5 35.8 0.9
O D:HOH1036 2.7 50.9 1.0
O D:HOH1017 3.6 42.1 1.0
P D:A212 3.6 25.2 1.0
O2' D:G211 4.1 25.4 1.0
O5' D:A212 4.2 23.7 1.0
O6 D:G214 4.3 26.7 1.0
O D:HOH1109 4.3 40.3 1.0
OP1 D:A212 4.5 24.4 1.0
N7 D:G213 4.6 20.5 1.0
O3' D:G211 4.8 24.2 1.0
O6 D:G213 4.8 22.7 1.0
O D:HOH1037 4.8 35.0 1.0
OP2 D:G213 4.8 23.8 1.0
O D:HOH1038 5.0 46.4 1.0

Calcium binding site 4 out of 10 in 1sds

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Calcium binding site 4 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca752

b:32.0
occ:1.00
 OP2 E:U206 2.3 26.8 1.0
O E:HOH1013 2.3 38.2 1.0
O E:HOH1026 2.3 48.6 1.0
O E:HOH899 2.3 37.5 1.0
O6 E:G208 2.4 29.4 1.0
O E:HOH1020 2.5 45.7 1.0
C6 E:G208 3.5 30.0 1.0
P E:U206 3.7 27.0 1.0
CA E:CA754 3.9 33.9 1.0
N7 E:G208 4.1 28.0 1.0
C5 E:G208 4.1 26.7 1.0
C5' E:U206 4.4 27.3 1.0
OP2 E:U207 4.4 28.7 1.0
O5' E:U206 4.4 29.1 1.0
O B:HOH1029 4.5 44.3 1.0
OP1 E:U206 4.6 28.9 1.0
C5 E:U207 4.6 27.0 1.0
O3' E:A205 4.6 25.0 1.0
N1 E:G208 4.6 27.3 1.0
O4 E:U207 4.9 26.2 1.0

Calcium binding site 5 out of 10 in 1sds

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Calcium binding site 5 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca754

b:33.9
occ:1.00
 O2' E:A205 2.7 25.9 1.0
O4 E:U207 2.7 26.2 1.0
O6 E:G208 3.0 29.4 1.0
OP2 E:U206 3.1 26.8 1.0
O E:HOH975 3.1 38.7 1.0
O E:HOH1020 3.1 45.7 1.0
O3' E:A205 3.2 25.0 1.0
O E:HOH895 3.5 32.8 1.0
P E:U206 3.6 27.0 1.0
C4 E:U207 3.7 27.1 1.0
C6 E:G208 3.7 30.0 1.0
C2' E:A205 3.8 23.0 1.0
N1 E:G208 3.9 27.3 1.0
CA E:CA752 3.9 32.0 1.0
C3' E:A205 4.0 24.6 1.0
C5 E:U207 4.1 27.0 1.0
OP1 E:U206 4.2 28.9 1.0
C1' E:A205 4.7 23.6 1.0
C5 E:G208 4.9 26.7 1.0
N3 E:U207 4.9 23.8 1.0

Calcium binding site 6 out of 10 in 1sds

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Calcium binding site 6 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca759

b:56.2
occ:0.90
 O E:HOH1039 2.3 31.1 0.9
O2 E:U210 4.4 28.5 1.0
O2' E:U210 4.5 24.5 1.0
O E:HOH927 4.7 35.9 1.0

Calcium binding site 7 out of 10 in 1sds

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Calcium binding site 7 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca751

b:29.6
occ:1.00
 OP2 F:U206 2.2 24.9 1.0
O F:HOH874 2.3 32.9 1.0
O F:HOH995 2.3 41.0 1.0
O6 F:G208 2.3 28.6 1.0
O F:HOH1024 2.4 45.3 1.0
O F:HOH953 2.5 39.9 1.0
O F:HOH1023 2.5 47.5 1.0
C6 F:G208 3.5 28.4 1.0
P F:U206 3.7 25.4 1.0
CA F:CA753 3.9 29.1 1.0
N7 F:G208 4.1 27.1 1.0
C5 F:G208 4.1 26.8 1.0
O5' F:U206 4.4 26.6 1.0
C5' F:U206 4.4 25.3 1.0
OP2 F:U207 4.5 27.3 1.0
O C:HOH936 4.5 33.3 1.0
O F:HOH1025 4.5 44.2 1.0
OP1 F:U206 4.5 23.9 1.0
C5 F:U207 4.5 24.6 1.0
O3' F:A205 4.5 22.6 1.0
N1 F:G208 4.6 28.8 1.0
O F:HOH1077 4.7 52.3 1.0
O4 F:U207 4.9 25.7 1.0
O C:HOH1005 4.9 34.8 1.0

Calcium binding site 8 out of 10 in 1sds

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Calcium binding site 8 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca753

b:29.1
occ:1.00
 O2' F:A205 2.6 27.3 1.0
O4 F:U207 2.7 25.7 1.0
O F:HOH979 2.9 37.5 1.0
O6 F:G208 3.0 28.6 1.0
OP2 F:U206 3.1 24.9 1.0
O F:HOH995 3.1 41.0 1.0
O3' F:A205 3.2 22.6 1.0
O F:HOH893 3.3 33.4 1.0
P F:U206 3.6 25.4 1.0
C4 F:U207 3.7 25.6 1.0
C6 F:G208 3.7 28.4 1.0
C2' F:A205 3.8 24.8 1.0
CA F:CA751 3.9 29.6 1.0
N1 F:G208 3.9 28.8 1.0
C3' F:A205 4.0 25.4 1.0
C5 F:U207 4.0 24.6 1.0
OP1 F:U206 4.1 23.9 1.0
C1' F:A205 4.7 24.7 1.0
C5 F:G208 4.9 26.8 1.0
N3 F:U207 4.9 24.1 1.0

Calcium binding site 9 out of 10 in 1sds

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Calcium binding site 9 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca758

b:31.0
occ:0.90
 O F:HOH1007 2.2 34.4 0.9
OP2 F:A212 2.3 27.9 1.0
O F:HOH1021 2.3 31.9 0.9
O F:HOH885 2.4 24.7 0.9
O F:HOH851 2.4 18.5 0.9
P F:A212 3.7 26.6 1.0
O2' F:G211 4.1 27.4 1.0
O5' F:A212 4.3 25.3 1.0
O F:HOH932 4.3 36.2 1.0
O6 F:G214 4.3 20.7 1.0
O F:HOH1022 4.4 35.2 0.5
OP1 F:A212 4.4 26.8 1.0
N7 F:G213 4.7 20.4 1.0
O3' F:G211 4.8 26.0 1.0
O6 F:G213 4.8 21.9 1.0

Calcium binding site 10 out of 10 in 1sds

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Calcium binding site 10 out of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca760

b:47.8
occ:0.90
 O F:HOH1078 2.2 39.2 0.9
O F:HOH1041 2.2 33.4 0.9
O F:HOH1043 2.3 38.6 0.9
O F:HOH1042 2.6 35.5 0.9
O F:HOH1040 2.7 47.9 0.9
O2 F:U210 4.5 23.1 1.0
O2' F:U210 4.6 22.6 1.0
O F:HOH919 4.7 35.1 1.0
O3' F:U210 5.0 24.8 1.0

Reference:

T.Hamma, A.Ferre-D'amare. Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna at 1.8 A Resolution. Structure V. 12 893 2004.
ISSN: ISSN 0969-2126
PubMed: 15130481
DOI: 10.1016/J.STR.2004.03.015
Page generated: Thu Jul 11 22:36:07 2024

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