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Calcium in PDB 2q10: Restriction Endonuclease Bcni (Wild Type)-Cognate Dna Substrate Complex

Protein crystallography data

The structure of Restriction Endonuclease Bcni (Wild Type)-Cognate Dna Substrate Complex, PDB code: 2q10 was solved by M.Sokolowska, M.Kaus-Drobek, H.Czapinska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.354, 87.551, 79.162, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.3

Other elements in 2q10:

The structure of Restriction Endonuclease Bcni (Wild Type)-Cognate Dna Substrate Complex also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Restriction Endonuclease Bcni (Wild Type)-Cognate Dna Substrate Complex (pdb code 2q10). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Restriction Endonuclease Bcni (Wild Type)-Cognate Dna Substrate Complex, PDB code: 2q10:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2q10

Go back to Calcium Binding Sites List in 2q10
Calcium binding site 1 out of 3 in the Restriction Endonuclease Bcni (Wild Type)-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 Bcni (Wild Type)-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:22.1
occ:0.50
O A:HOH745 2.2 9.1 1.0
OD1 A:ASP55 2.2 22.5 1.0
O A:HOH764 2.3 14.7 1.0
OD1 A:ASN49 2.6 22.7 1.0
OP1 C:DC0 2.6 6.9 1.0
O3' C:DC-1 3.1 5.8 1.0
CG A:ASP55 3.2 14.9 1.0
O A:HOH790 3.3 19.8 1.0
O A:HOH878 3.4 23.9 1.0
P C:DC0 3.4 6.2 1.0
CG A:ASN49 3.6 24.6 1.0
OD2 A:ASP55 3.6 14.4 1.0
CA A:ASN49 4.0 25.0 1.0
CB A:ASN49 4.0 25.0 1.0
CA A:CA701 4.0 6.8 1.0
NZ A:LYS152 4.2 20.2 1.0
OP2 C:DC0 4.4 5.3 1.0
C3' C:DC-1 4.4 5.4 1.0
O A:HOH852 4.4 25.7 1.0
OE1 A:GLU60 4.4 12.2 1.0
O C:HOH710 4.4 14.7 1.0
OE2 A:GLU41 4.5 14.4 1.0
CB A:ASP55 4.5 11.9 1.0
C4' C:DC-1 4.6 6.7 1.0
N A:ASN50 4.7 25.0 1.0
O5' C:DC0 4.7 6.4 1.0
O A:HOH707 4.7 8.5 1.0
OE2 A:GLU60 4.7 8.3 1.0
C5' C:DC-1 4.8 7.9 1.0
ND2 A:ASN49 4.8 23.4 1.0
CA A:ASP55 4.8 11.0 1.0
C5' C:DC0 4.8 7.0 1.0
N A:ASN49 4.9 25.5 1.0
C A:ASN49 4.9 25.1 1.0
N A:ASP55 5.0 10.6 1.0

Calcium binding site 2 out of 3 in 2q10

Go back to Calcium Binding Sites List in 2q10
Calcium binding site 2 out of 3 in the Restriction Endonuclease Bcni (Wild Type)-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 Bcni (Wild Type)-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:6.8
occ:1.00
OD2 A:ASP55 2.1 14.4 1.0
O A:HOH707 2.2 8.5 1.0
OP1 C:DC0 2.3 6.9 1.0
OE2 A:GLU60 2.3 8.3 1.0
O A:LEU61 2.3 7.7 1.0
O C:HOH704 2.4 3.8 1.0
CG A:ASP55 3.2 14.9 1.0
CD A:GLU60 3.2 11.1 1.0
C A:LEU61 3.5 8.1 1.0
P C:DC0 3.5 6.2 1.0
OD1 A:ASP55 3.6 22.5 1.0
OE1 A:GLU60 3.6 12.2 1.0
O A:HOH745 3.9 9.1 1.0
N A:LEU61 4.0 7.9 1.0
OP2 C:DC0 4.0 5.3 1.0
CA C:CA703 4.0 22.1 0.5
O5' C:DC0 4.1 6.4 1.0
CA A:LEU61 4.2 8.5 1.0
C5' C:DC0 4.4 7.0 1.0
CB A:ASP55 4.4 11.9 1.0
CB A:LEU61 4.4 8.9 1.0
CG A:GLU60 4.4 9.4 1.0
OE2 A:GLU41 4.4 14.4 1.0
NZ A:LYS62 4.5 7.6 1.0
N A:LYS62 4.6 8.6 1.0
O C:HOH708 4.6 6.6 1.0
CG A:LYS62 4.7 11.2 1.0
O3' C:DC-1 4.8 5.8 1.0
OP2 C:DG1 4.8 5.1 1.0
CA A:LYS62 4.9 8.6 1.0
O3' C:DC0 4.9 4.2 1.0
C A:GLU60 5.0 8.4 1.0

Calcium binding site 3 out of 3 in 2q10

Go back to Calcium Binding Sites List in 2q10
Calcium binding site 3 out of 3 in the Restriction Endonuclease Bcni (Wild Type)-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 Bcni (Wild Type)-Cognate Dna Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:4.9
occ:1.00
OP1 E:DC0 2.3 5.4 1.0
O B:LEU61 2.3 8.6 1.0
OE2 B:GLU60 2.4 11.4 1.0
O B:HOH736 2.4 5.0 1.0
OD2 B:ASP55 2.4 19.2 1.0
O E:HOH80 2.5 3.4 1.0
OD1 B:ASP55 2.8 14.9 1.0
CG B:ASP55 2.9 14.2 1.0
CD B:GLU60 3.3 10.9 1.0
P E:DC0 3.5 5.3 1.0
C B:LEU61 3.5 9.0 1.0
O B:HOH739 3.7 10.3 1.0
OE1 B:GLU60 3.8 12.2 1.0
O5' E:DC0 4.0 3.7 1.0
OP2 E:DC0 4.1 4.0 1.0
N B:LEU61 4.1 8.4 1.0
CA B:LEU61 4.2 8.2 1.0
C5' E:DC0 4.2 3.4 1.0
CB B:ASP55 4.4 12.1 1.0
NZ B:LYS62 4.4 9.5 1.0
CG B:GLU60 4.4 8.7 1.0
CB B:LEU61 4.5 8.2 1.0
N B:LYS62 4.6 9.4 1.0
O E:HOH75 4.6 6.1 1.0
ND2 B:ASN49 4.6 17.6 1.0
CG B:LYS62 4.7 12.3 1.0
O3' E:DC-1 4.7 3.9 1.0
OE1 B:GLU41 4.8 13.2 1.0
CA B:LYS62 4.8 9.3 1.0
O3' E:DC0 4.8 5.6 1.0
OP2 E:DG1 4.8 4.2 1.0

Reference:

M.Sokolowska, M.Kaus-Drobek, H.Czapinska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, M.Bochtler. Monomeric Restriction Endonuclease Bcni in the Apo Form and in An Asymmetric Complex with Target Dna. J.Mol.Biol. V. 369 722 2007.
ISSN: ISSN 0022-2836
PubMed: 17445830
DOI: 10.1016/J.JMB.2007.03.018
Page generated: Sat Dec 12 03:50:43 2020

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