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Calcium in PDB 196d: Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction

Protein crystallography data

The structure of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction, PDB code: 196d was solved by D.S.Goodsell, K.Grzeskowiak, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.230, 24.320, 40.830, 90.00, 126.78, 90.00
R / Rfree (%) n/a / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction (pdb code 196d). 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 C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction, PDB code: 196d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 196d

Go back to Calcium Binding Sites List in 196d
Calcium binding site 1 out of 6 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


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 C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca21

b:16.8
occ:1.00
O A:HOH111 2.4 17.0 1.0
O B:HOH115 2.4 16.6 1.0
O B:HOH110 2.5 19.1 1.0
O A:HOH113 2.5 19.0 1.0
O B:HOH114 2.5 11.9 1.0
O A:HOH112 2.5 10.1 1.0
O B:HOH109 2.5 17.9 1.0
N2 A:DG6 4.4 12.0 1.0
O2 B:DC15 4.5 12.9 1.0
C4' B:DG16 4.6 9.4 1.0
C5' B:DG16 4.6 9.9 1.0
O4' A:DA7 4.7 9.8 1.0
O A:HOH87 4.7 29.7 1.0
O A:HOH28 4.7 15.3 1.0
O B:HOH34 4.7 13.6 1.0
O4' B:DG16 4.7 13.0 1.0
O B:HOH90 4.7 33.4 1.0
O B:HOH27 4.8 13.6 1.0
N3 A:DA7 4.8 9.5 1.0
C5' A:DG8 4.9 14.2 1.0

Calcium binding site 2 out of 6 in 196d

Go back to Calcium Binding Sites List in 196d
Calcium binding site 2 out of 6 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


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 C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca22

b:21.3
occ:1.00
O A:HOH120 2.4 31.2 1.0
O A:HOH116 2.4 23.9 1.0
O A:HOH117 2.4 26.6 1.0
OP2 A:DC5 2.4 13.1 1.0
O A:HOH119 2.5 23.4 1.0
O A:HOH118 2.6 24.5 1.0
P A:DC5 3.4 15.2 1.0
OP1 A:DC5 3.9 15.9 1.0
O3' A:DT4 4.1 14.4 1.0
O A:HOH78 4.3 21.8 1.0
C3' A:DT4 4.5 12.2 1.0
O5' A:DC5 4.8 12.3 1.0

Calcium binding site 3 out of 6 in 196d

Go back to Calcium Binding Sites List in 196d
Calcium binding site 3 out of 6 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


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 C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca24

b:26.5
occ:1.00
O B:HOH125 2.3 22.4 1.0
O A:HOH127 2.4 29.8 1.0
O B:HOH128 2.4 19.2 1.0
O A:HOH126 2.5 28.8 1.0
O A:HOH124 2.5 11.6 1.0
O4' A:DC3 4.4 15.7 1.0
O A:HOH30 4.4 13.6 1.0
O B:HOH29 4.5 15.8 1.0
C4' A:DC3 4.6 19.1 1.0
C1' B:DG20 4.8 13.6 1.0
N3 B:DG20 4.8 12.1 1.0
O2 A:DT2 4.9 15.1 1.0
O4' B:DG20 4.9 12.5 1.0

Calcium binding site 4 out of 6 in 196d

Go back to Calcium Binding Sites List in 196d
Calcium binding site 4 out of 6 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


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 C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca23

b:28.4
occ:1.00
O B:HOH121 2.3 24.5 1.0
O B:HOH122 2.4 21.9 1.0
O B:HOH123 2.5 24.6 1.0
OP1 B:DG16 2.6 19.4 1.0
P B:DG16 3.7 17.0 1.0
O5' B:DG16 4.0 14.8 1.0
C5' B:DG16 4.2 9.9 1.0
OP2 B:DG16 4.5 13.4 1.0
O B:HOH90 4.7 33.4 1.0
O3' B:DC15 4.9 15.9 1.0
OP1 B:DA17 4.9 18.8 1.0
O B:HOH97 4.9 37.6 1.0

Calcium binding site 5 out of 6 in 196d

Go back to Calcium Binding Sites List in 196d
Calcium binding site 5 out of 6 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


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 C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca25

b:35.6
occ:1.00
O B:HOH129 2.4 23.5 1.0
O A:HOH134 2.4 22.5 1.0
O B:HOH133 2.4 20.3 1.0
O B:HOH132 2.4 22.9 1.0
O A:HOH131 2.5 24.1 1.0
O B:HOH130 2.5 16.2 1.0
O B:HOH102 3.4 39.4 1.0
O A:HOH37 4.2 20.1 1.0
O B:HOH80 4.2 30.5 1.0
O A:HOH79 4.5 20.5 1.0
O B:HOH63 4.6 27.6 1.0
O2 A:DT4 4.8 16.4 1.0
N2 B:DG18 4.8 14.4 1.0
O B:HOH107 4.9 27.8 1.0
O B:HOH61 4.9 24.4 1.0
N3 B:DG18 4.9 13.4 1.0

Calcium binding site 6 out of 6 in 196d

Go back to Calcium Binding Sites List in 196d
Calcium binding site 6 out of 6 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


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 C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca26

b:35.2
occ:1.00
O B:HOH136 2.4 29.9 1.0
O B:HOH140 2.4 44.3 1.0
O B:HOH137 2.5 28.8 1.0
O B:HOH138 2.5 16.1 1.0
O B:HOH135 2.5 29.1 1.0
O B:HOH139 2.5 27.3 1.0
O B:HOH99 4.2 27.1 1.0
O B:HOH56 4.3 22.1 1.0
O6 B:DG20 4.5 10.9 1.0
N7 B:DG20 4.9 17.8 1.0
O B:HOH38 5.0 25.4 1.0

Reference:

D.S.Goodsell, K.Grzeskowiak, R.E.Dickerson. Crystal Structure of C-T-C-T-C-G-A-G-A-G. Implications For the Structure of the Holliday Junction. Biochemistry V. 34 1022 1995.
ISSN: ISSN 0006-2960
PubMed: 7827018
DOI: 10.1021/BI00003A037
Page generated: Sat Dec 12 02:47:38 2020

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