Atomistry » Calcium » PDB 3nur-3ojn » 3odh
Atomistry »
  Calcium »
    PDB 3nur-3ojn »
      3odh »

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

Go back to Calcium Binding Sites List in 3odh
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

Go back to Calcium Binding Sites List in 3odh
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

Go back to Calcium Binding Sites List in 3odh
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

Go back to Calcium Binding Sites List in 3odh
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

Go back to Calcium Binding Sites List in 3odh
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 Dec 12 04:23:05 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy