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Calcium in PDB 2oaa: Restriction Endonuclease Mvai-Cognate Dna Substrate Complex

Protein crystallography data

The structure of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex, PDB code: 2oaa was solved by M.Kaus-Drobek, H.Czapinska, M.Sokolowska, G.Tamulaitis, R.H.Szczepanowski, K.Urbanke, V.Siksnys, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.848, 81.380, 71.308, 90.00, 90.52, 90.00
R / Rfree (%) 17.6 / 19.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex (pdb code 2oaa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex, PDB code: 2oaa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2oaa

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Calcium binding site 1 out of 7 in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca605

b:6.7
occ:0.50
 OD1 A:ASP50 2.3 12.3 1.0
O A:HOH699 2.3 19.8 1.0
O A:HOH748 2.4 26.0 1.0
O A:HOH608 2.5 16.1 1.0
OP1 C:DT0 2.5 5.3 1.0
O A:HOH773 2.5 26.5 1.0
O3' C:DC-1 2.8 4.3 1.0
P C:DT0 3.3 5.0 1.0
CG A:ASP50 3.4 10.5 1.0
OD2 A:ASP50 4.0 10.5 1.0
CA A:CA601 4.0 8.8 1.0
O A:ALA48 4.1 10.6 1.0
C3' C:DC-1 4.1 3.2 1.0
OE2 A:GLU36 4.3 14.0 0.5
OP2 C:DT0 4.4 5.5 1.0
O5' C:DT0 4.4 3.7 1.0
O A:LEU46 4.4 11.9 1.0
OD1 A:ASP44 4.4 17.1 0.5
NZ A:LYS41 4.4 24.0 1.0
C5' C:DT0 4.4 3.2 1.0
C4' C:DC-1 4.4 3.4 1.0
CE A:LYS41 4.5 23.1 1.0
NZ A:LYS159 4.5 10.7 1.0
OE1 A:GLU55 4.5 12.9 1.0
O A:HOH615 4.6 11.2 1.0
CB A:ASP50 4.6 9.2 1.0
OD2 A:ASP44 4.6 17.9 0.5
CA A:ASP50 4.7 9.0 1.0
O A:HOH637 4.8 13.1 1.0
C5' C:DC-1 4.8 4.7 1.0
N A:ASP50 4.8 9.6 1.0
C2' C:DC-1 4.8 3.5 1.0
CG A:ASP44 4.9 16.0 1.0
OE2 A:GLU55 4.9 10.2 1.0

Calcium binding site 2 out of 7 in 2oaa

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Calcium binding site 2 out of 7 in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca606

b:11.1
occ:0.50
 O B:HOH737 2.2 33.6 1.0
O B:HOH754 2.3 31.9 1.0
OD1 B:ASP50 2.3 15.5 1.0
O B:HOH674 2.4 20.4 1.0
OP1 E:DT0 2.5 8.9 1.0
O3' E:DC-1 2.8 8.2 1.0
P E:DT0 3.3 8.1 1.0
CG B:ASP50 3.4 14.4 1.0
OD2 B:ASP50 3.9 14.6 1.0
O B:ALA48 4.0 15.0 1.0
NZ B:LYS41 4.0 26.8 1.0
CA B:CA602 4.0 11.3 1.0
C3' E:DC-1 4.1 8.1 1.0
OE2 B:GLU36 4.2 15.7 0.5
O B:LEU46 4.3 16.4 1.0
CE B:LYS41 4.3 25.7 1.0
OP2 E:DT0 4.4 8.1 1.0
O5' E:DT0 4.4 7.2 1.0
OD1 B:ASP44 4.4 22.8 1.0
C5' E:DT0 4.4 7.3 1.0
NZ B:LYS159 4.4 10.5 1.0
C4' E:DC-1 4.5 8.3 1.0
OE1 B:GLU55 4.5 15.2 1.0
O B:HOH621 4.6 13.1 1.0
CB B:ASP50 4.7 13.3 1.0
O B:HOH657 4.7 19.8 1.0
C5' E:DC-1 4.8 7.8 1.0
OE2 B:GLU55 4.8 11.2 1.0
C2' E:DC-1 4.9 7.7 1.0
CA B:ASP50 4.9 13.5 1.0
O B:PRO49 5.0 13.7 1.0

Calcium binding site 3 out of 7 in 2oaa

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Calcium binding site 3 out of 7 in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:8.8
occ:1.00
 OP1 C:DT0 2.3 5.3 1.0
O A:ILE56 2.3 7.2 1.0
OD2 A:ASP50 2.3 10.5 1.0
O C:HOH76 2.4 11.0 1.0
O A:HOH615 2.4 11.2 1.0
OE2 A:GLU55 2.4 10.2 1.0
CG A:ASP50 3.1 10.5 1.0
CD A:GLU55 3.2 11.6 1.0
OD1 A:ASP50 3.3 12.3 1.0
C A:ILE56 3.5 6.8 1.0
P C:DT0 3.5 5.0 1.0
OE1 A:GLU55 3.7 12.9 1.0
N A:ILE56 3.9 6.4 1.0
O5' C:DT0 4.0 3.7 1.0
CA C:CA605 4.0 6.7 0.5
O A:HOH608 4.1 16.1 1.0
OP2 C:DT0 4.1 5.5 1.0
C5' C:DT0 4.1 3.2 1.0
CA A:ILE56 4.2 7.1 1.0
CG A:GLU55 4.3 7.9 1.0
CG A:LYS57 4.4 9.1 1.0
N A:LYS57 4.5 6.0 1.0
CB A:ASP50 4.5 9.2 1.0
OE2 A:GLU36 4.5 14.0 0.5
CA A:LYS57 4.6 6.4 1.0
NZ A:LYS57 4.6 9.4 1.0
OP2 C:DG1 4.6 5.0 1.0
CB A:ILE56 4.7 7.8 1.0
O3' C:DC-1 4.7 4.3 1.0
O C:HOH121 4.9 14.2 1.0
O A:HOH652 4.9 13.2 1.0
O3' C:DT0 4.9 4.0 1.0
C A:GLU55 5.0 6.3 1.0

Calcium binding site 4 out of 7 in 2oaa

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Calcium binding site 4 out of 7 in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:9.8
occ:0.50
 O A:ILE122 2.3 7.6 1.0
O A:HOH774 2.3 27.5 1.0
O A:HOH759 2.5 23.7 1.0
O A:HOH667 2.5 20.6 1.0
O A:HOH805 2.5 29.4 1.0
OD1 A:ASP121 2.6 17.0 1.0
O A:HOH655 2.6 16.4 1.0
C A:ILE122 3.4 7.2 1.0
CG A:ASP121 3.7 12.8 1.0
OD2 A:ASP121 4.0 19.4 1.0
N A:ILE122 4.2 7.0 1.0
OE2 A:GLU200 4.2 19.3 1.0
N A:ASP123 4.3 6.5 1.0
CA A:ASP123 4.3 7.1 1.0
CA A:ILE122 4.4 7.2 1.0
CD1 A:TRP124 4.6 5.9 1.0
O A:HOH753 4.6 19.9 1.0
O A:HOH679 4.7 20.4 1.0
N A:TRP124 4.8 6.2 1.0
CB A:ILE122 4.8 7.4 1.0
C A:ASP121 4.9 7.2 1.0
O A:HOH750 4.9 26.3 1.0
CB A:ASP121 5.0 8.7 1.0

Calcium binding site 5 out of 7 in 2oaa

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Calcium binding site 5 out of 7 in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:11.3
occ:1.00
 OP1 E:DT0 2.2 8.9 1.0
O B:ILE56 2.3 9.6 1.0
OD2 B:ASP50 2.3 14.6 1.0
O B:HOH621 2.4 13.1 1.0
O E:HOH148 2.4 14.3 1.0
OE2 B:GLU55 2.4 11.2 1.0
CG B:ASP50 3.2 14.4 1.0
CD B:GLU55 3.3 13.0 1.0
C B:ILE56 3.4 9.7 1.0
P E:DT0 3.5 8.1 1.0
OD1 B:ASP50 3.5 15.5 1.0
OE1 B:GLU55 3.7 15.2 1.0
O5' E:DT0 3.9 7.2 1.0
N B:ILE56 3.9 9.3 1.0
CA E:CA606 4.0 11.1 0.5
C5' E:DT0 4.1 7.3 1.0
OP2 E:DT0 4.1 8.1 1.0
O B:HOH674 4.2 20.4 1.0
CA B:ILE56 4.2 10.1 1.0
CG B:GLU55 4.3 11.1 1.0
CG B:LYS57 4.4 12.3 1.0
N B:LYS57 4.5 9.3 1.0
NZ B:LYS57 4.5 12.9 1.0
OE2 B:GLU36 4.5 15.7 0.5
CB B:ASP50 4.5 13.3 1.0
OP2 E:DG1 4.6 7.3 1.0
CA B:LYS57 4.6 9.9 1.0
CB B:ILE56 4.7 10.8 1.0
O3' E:DC-1 4.7 8.2 1.0
O E:HOH63 4.8 15.2 1.0
O3' E:DT0 4.8 6.8 1.0
O B:HOH666 4.9 17.6 1.0
C B:GLU55 5.0 9.3 1.0

Calcium binding site 6 out of 7 in 2oaa

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Calcium binding site 6 out of 7 in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:10.1
occ:0.50
 O B:LYS64 2.3 9.9 1.0
O B:HOH714 2.3 18.4 1.0
O B:HOH647 2.4 20.6 1.0
O F:HOH280 2.5 18.9 1.0
O B:HOH726 2.5 24.1 1.0
O B:HOH661 2.5 16.0 1.0
C B:LYS64 3.5 9.4 1.0
CB B:LYS64 3.9 10.7 1.0
CA B:LYS64 4.3 10.2 1.0
O F:HOH94 4.4 14.3 1.0
O B:HOH665 4.5 17.1 1.0
O F:HOH369 4.5 23.3 1.0
N B:SER65 4.5 8.9 1.0
N6 F:DA-4 4.5 12.3 1.0
CA B:SER65 4.6 8.2 1.0
O B:HOH625 4.6 12.5 1.0
O E:HOH327 4.6 24.7 1.0
O B:HOH700 4.7 19.3 1.0
C B:SER65 4.8 7.7 1.0
N7 F:DA-4 4.8 11.1 1.0

Calcium binding site 7 out of 7 in 2oaa

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Calcium binding site 7 out of 7 in the Restriction Endonuclease Mvai-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Restriction Endonuclease Mvai-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:10.8
occ:0.50
 O B:HOH751 2.3 23.3 1.0
O B:ILE122 2.3 10.0 1.0
OD1 B:ASP121 2.5 16.4 1.0
O B:HOH690 2.6 23.3 1.0
O B:HOH687 2.6 20.1 1.0
O B:HOH779 2.7 26.1 1.0
C B:ILE122 3.5 8.9 1.0
CG B:ASP121 3.6 12.0 1.0
OD2 B:ASP121 3.9 18.7 1.0
OE2 B:GLU200 4.0 19.8 1.0
N B:ILE122 4.1 8.4 1.0
N B:ASP123 4.3 8.6 1.0
CA B:ASP123 4.4 8.9 1.0
CA B:ILE122 4.4 8.7 1.0
CD1 B:TRP124 4.6 7.7 1.0
O B:HOH749 4.7 25.0 1.0
C B:ASP121 4.9 8.7 1.0
CB B:ILE122 4.9 8.7 1.0
N B:TRP124 4.9 8.2 1.0
CB B:ASP121 4.9 10.3 1.0

Reference:

M.Kaus-Drobek, H.Czapinska, M.Sokolowska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, M.Bochtler. Restriction Endonuclease Mvai Is A Monomer That Recognizes Its Target Sequence Asymmetrically. Nucleic Acids Res. V. 35 2035 2007.
ISSN: ISSN 0305-1048
PubMed: 17344322
DOI: 10.1093/NAR/GKM064
Page generated: Sat Dec 12 03:48:28 2020

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