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Calcium in PDB 3odh: Structure of Okrai/Dna Complex

Protein crystallography data

The structure of Structure of Okrai/Dna Complex, PDB code: 3odh was solved by E.S.Vanamee, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.982, 83.075, 119.670, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 23.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Okrai/Dna Complex (pdb code 3odh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Okrai/Dna Complex, PDB code: 3odh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3odh

Go back to Calcium Binding Sites List in 3odh
Calcium binding site 1 out of 6 in the Structure of Okrai/Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Okrai/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca195

b:10.9
occ:1.00
 OP1 D:DG5 2.2 8.8 1.0
O A:TRP100 2.3 7.7 1.0
OD2 A:ASP86 2.4 18.5 1.0
O A:HOH640 2.4 8.1 1.0
O D:HOH254 2.4 2.5 1.0
O A:HOH262 2.6 2.0 1.0
OD1 A:ASP86 3.0 11.8 1.0
CG A:ASP86 3.1 13.1 1.0
P D:DG5 3.2 9.0 1.0
O A:HOH228 3.3 26.1 1.0
OP2 D:DG5 3.5 7.9 1.0
C A:TRP100 3.5 7.3 1.0
CA A:CA196 3.8 30.5 1.0
O D:HOH13 4.0 2.0 1.0
N A:TRP100 4.0 8.4 1.0
O5' D:DG5 4.2 9.6 1.0
O D:HOH258 4.2 16.4 1.0
OE2 A:GLU101 4.2 9.7 1.0
OE1 A:GLU99 4.2 9.8 1.0
CA A:TRP100 4.3 7.8 1.0
O A:HOH257 4.4 6.5 1.0
O3' D:DG4 4.4 11.5 1.0
CD A:GLU101 4.5 11.5 1.0
N A:GLU101 4.5 7.7 1.0
CB A:ASP86 4.6 10.4 1.0
CD A:GLU99 4.6 7.3 1.0
CA A:GLU101 4.7 6.9 1.0
CB A:TRP100 4.7 7.3 1.0
OE2 A:GLU99 4.7 9.4 1.0
CG A:GLU101 4.8 7.5 1.0
C5' D:DG5 4.8 6.6 1.0
C A:GLU99 4.9 8.4 1.0
CD1 A:TRP100 4.9 8.6 1.0

Calcium binding site 2 out of 6 in 3odh

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Calcium binding site 2 out of 6 in the Structure of Okrai/Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Okrai/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca196

b:30.5
occ:1.00
 OD1 A:ASP86 2.3 11.8 1.0
O A:HOH200 2.3 12.7 1.0
O A:HOH343 2.3 25.7 1.0
OP1 D:DG5 2.5 8.8 1.0
O A:HOH228 2.6 26.1 1.0
O3' D:DG4 2.9 11.5 1.0
O D:HOH258 3.0 16.4 1.0
OE2 A:GLU71 3.1 18.2 1.0
P D:DG5 3.3 9.0 1.0
CG A:ASP86 3.4 13.1 1.0
CA A:CA195 3.8 10.9 1.0
OE1 A:GLU71 3.8 19.9 1.0
CD A:GLU71 3.9 18.6 1.0
C3' D:DG4 4.0 10.6 1.0
O A:HOH262 4.1 2.0 1.0
OD2 A:ASP86 4.1 18.5 1.0
OP2 D:DG5 4.3 7.9 1.0
C4' D:DG4 4.3 9.6 1.0
CA A:ASP86 4.4 10.4 1.0
O5' D:DG5 4.4 9.6 1.0
CB A:ASP86 4.5 10.4 1.0
C5' D:DG5 4.5 6.6 1.0
N A:ASP86 4.6 9.5 1.0
O A:PRO84 4.7 8.9 1.0
O A:HOH391 4.8 19.2 1.0
O A:HOH383 4.8 9.8 1.0
OE2 A:GLU99 5.0 9.4 1.0

Calcium binding site 3 out of 6 in 3odh

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Calcium binding site 3 out of 6 in the Structure of Okrai/Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Okrai/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca195

b:15.2
occ:1.00
 O C:HOH256 2.4 17.9 1.0
OP1 C:DG5 2.4 9.8 1.0
O B:HOH655 2.4 2.6 1.0
OD1 B:ASP86 2.4 14.4 1.0
O B:HOH196 2.5 13.0 1.0
OE2 B:GLU99 2.5 17.6 1.0
OE1 B:GLU99 2.8 18.1 1.0
CD B:GLU99 3.0 17.3 1.0
CG B:ASP86 3.3 11.2 1.0
OD2 B:ASP86 3.5 9.7 1.0
P C:DG5 3.6 10.0 1.0
O3' C:DG4 3.9 10.7 1.0
O B:HOH227 3.9 14.5 1.0
NZ B:LYS56 4.0 17.3 1.0
O B:HOH288 4.1 10.8 1.0
O B:HOH649 4.3 13.3 1.0
O C:HOH227 4.4 17.9 1.0
N B:ASP86 4.4 12.3 1.0
CG B:GLU99 4.5 15.6 1.0
CB B:ASP86 4.5 11.8 1.0
OP2 C:DG5 4.6 9.7 1.0
O5' C:DG5 4.7 11.4 1.0
O B:TRP100 4.7 14.0 1.0
O C:HOH106 4.8 2.0 1.0
O B:PRO84 4.8 15.7 1.0
CA B:ASP86 4.8 12.9 1.0
O B:HOH224 4.8 14.3 1.0
OG1 B:THR102 4.9 12.9 1.0
C5' C:DG5 4.9 12.3 1.0

Calcium binding site 4 out of 6 in 3odh

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Calcium binding site 4 out of 6 in the Structure of Okrai/Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Okrai/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca195

b:9.1
occ:1.00
 OP1 H:DG5 2.3 8.0 1.0
O E:TRP100 2.3 7.0 1.0
OD2 E:ASP86 2.4 12.0 1.0
O E:HOH665 2.5 3.7 1.0
O H:HOH35 2.5 2.0 1.0
O E:HOH197 2.7 6.3 1.0
OD1 E:ASP86 3.0 8.9 1.0
CG E:ASP86 3.0 8.6 1.0
P H:DG5 3.4 8.5 1.0
C E:TRP100 3.5 7.7 1.0
OP2 H:DG5 3.8 5.6 1.0
CA H:CA13 3.9 39.1 1.0
O H:HOH17 3.9 2.0 1.0
O E:HOH706 4.0 24.4 1.0
N E:TRP100 4.1 8.1 1.0
OE2 E:GLU101 4.2 8.2 1.0
O H:HOH292 4.3 6.4 1.0
O H:HOH379 4.3 9.0 1.0
O5' H:DG5 4.3 8.3 1.0
CA E:TRP100 4.3 7.9 1.0
OE1 E:GLU99 4.3 10.0 1.0
CD E:GLU101 4.5 6.9 1.0
CB E:ASP86 4.5 8.9 1.0
CB E:TRP100 4.5 8.5 1.0
N E:GLU101 4.6 6.7 1.0
CG E:GLU101 4.6 7.8 1.0
O3' H:DG4 4.6 8.3 1.0
CA E:GLU101 4.7 6.2 1.0
C5' H:DG5 4.7 7.0 1.0
CD1 E:TRP100 4.7 6.0 1.0
CD E:GLU99 4.8 9.4 1.0
C E:GLU99 4.8 7.8 1.0
OE2 E:GLU99 5.0 11.2 1.0
CA E:GLU99 5.0 7.4 1.0

Calcium binding site 5 out of 6 in 3odh

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Calcium binding site 5 out of 6 in the Structure of Okrai/Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Okrai/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca195

b:12.6
occ:1.00
 OD1 F:ASP86 2.3 9.9 1.0
O F:HOH613 2.3 5.1 1.0
O F:HOH612 2.3 5.3 1.0
OE2 F:GLU99 2.4 10.4 1.0
OP1 G:DG5 2.5 9.4 1.0
O F:HOH634 2.7 4.5 1.0
OE1 F:GLU99 2.7 12.9 1.0
CD F:GLU99 2.9 11.9 1.0
CG F:ASP86 3.3 12.6 1.0
OD2 F:ASP86 3.6 8.5 1.0
P G:DG5 3.7 10.4 1.0
O3' G:DG4 3.9 12.0 1.0
O F:HOH200 4.1 8.3 1.0
NZ F:LYS56 4.1 11.6 1.0
O G:HOH266 4.1 9.9 1.0
N F:ASP86 4.3 12.2 1.0
O F:HOH276 4.3 4.6 1.0
CG F:GLU99 4.4 10.2 1.0
O F:HOH196 4.5 17.9 1.0
OP2 G:DG5 4.6 11.5 1.0
CB F:ASP86 4.6 12.4 1.0
O G:HOH680 4.7 9.2 1.0
O F:PRO84 4.7 9.6 1.0
O F:TRP100 4.7 7.3 1.0
OG1 F:THR102 4.8 7.1 1.0
O5' G:DG5 4.8 9.2 1.0
C5' G:DG5 4.9 6.4 1.0
O F:HOH647 4.9 6.8 1.0
CA F:ASP86 5.0 13.9 1.0

Calcium binding site 6 out of 6 in 3odh

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Calcium binding site 6 out of 6 in the Structure of Okrai/Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Okrai/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca13

b:39.1
occ:1.00
 O E:HOH705 2.2 5.8 1.0
OD1 E:ASP86 2.4 8.9 1.0
O E:HOH706 2.5 24.4 1.0
O E:HOH220 2.6 10.1 1.0
OP1 H:DG5 2.6 8.0 1.0
O3' H:DG4 2.8 8.3 1.0
P H:DG5 3.2 8.5 1.0
O H:HOH292 3.5 6.4 1.0
OE2 E:GLU71 3.5 17.0 1.0
CG E:ASP86 3.6 8.6 1.0
C3' H:DG4 3.8 5.9 1.0
O E:HOH382 3.8 36.7 1.0
CA E:CA195 3.9 9.1 1.0
C4' H:DG4 4.1 6.2 1.0
OE1 E:GLU71 4.1 16.9 1.0
OP2 H:DG5 4.2 5.6 1.0
N E:ASP86 4.2 7.9 1.0
CD E:GLU71 4.2 15.6 1.0
CA E:ASP86 4.3 8.5 1.0
OD2 E:ASP86 4.3 12.0 1.0
O5' H:DG5 4.4 8.3 1.0
O E:PRO84 4.4 10.5 1.0
C5' H:DG5 4.5 7.0 1.0
CB E:ASP86 4.5 8.9 1.0
O H:HOH35 4.5 2.0 1.0
C5' H:DG4 4.8 7.3 1.0
OE2 E:GLU99 4.9 11.2 1.0
C E:LEU85 4.9 8.8 1.0

Reference:

E.S.Vanamee, H.Viadiu, S.H.Chan, A.Ummat, A.M.Hartline, S.Y.Xu, A.K.Aggarwal. Asymmetric Dna Recognition By the Okrai Endonuclease, An Isoschizomer of Bamhi. Nucleic Acids Res. V. 39 712 2011.
ISSN: ISSN 0305-1048
PubMed: 20833632
DOI: 10.1093/NAR/GKQ779
Page generated: Sat Jul 13 15:16:35 2024

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