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Calcium in PDB 1dmu: Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence

Enzymatic activity of Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence

All present enzymatic activity of Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence:
3.1.21.4;

Protein crystallography data

The structure of Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence, PDB code: 1dmu was solved by M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, S.E.V.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.480, 81.600, 117.060, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence (pdb code 1dmu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence, PDB code: 1dmu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1dmu

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Calcium binding site 1 out of 4 in the Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence


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 the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca9

b:22.7
occ:1.00
 OD1 A:ASP116 2.3 15.6 1.0
O A:HOH307 2.4 16.1 1.0
O F:HOH11 2.4 21.9 1.0
OP1 F:DA2 2.5 16.0 0.5
O A:HOH306 2.6 5.9 1.0
O A:HOH305 2.6 16.8 1.0
O3' F:DT1 2.8 13.9 0.5
P F:DA2 3.3 12.8 0.5
CG A:ASP116 3.5 10.8 1.0
C3' F:DT1 3.9 14.7 0.5
OE2 A:GLU87 4.1 24.3 1.0
C4' F:DT1 4.2 14.5 0.5
CA A:CA300 4.2 17.5 1.0
OD2 A:ASP116 4.3 11.7 1.0
O A:HOH320 4.3 31.3 1.0
O A:HOH418 4.3 23.9 1.0
O5' F:DA2 4.4 14.8 0.5
OP2 F:DA2 4.4 12.4 0.5
C5' F:DA2 4.4 15.5 0.5
CA A:ASP116 4.4 9.4 1.0
O A:HOH416 4.5 9.9 1.0
OD2 A:ASP142 4.5 9.6 1.0
CB A:ASP116 4.6 8.7 1.0
N A:ASP116 4.6 8.8 1.0
O A:HOH304 4.9 13.2 1.0
O A:HOH329 4.9 10.3 1.0
C5' F:DT1 5.0 15.3 0.5

Calcium binding site 2 out of 4 in 1dmu

Go back to Calcium Binding Sites List in 1dmu
Calcium binding site 2 out of 4 in the Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence


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 the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca300

b:17.5
occ:1.00
 OD2 A:ASP116 2.3 11.7 1.0
OP1 F:DA2 2.3 16.0 0.5
O A:ILE143 2.4 12.6 1.0
OD1 A:ASP142 2.5 9.1 1.0
O A:HOH304 2.5 13.2 1.0
O F:HOH10 2.8 14.1 1.0
CG A:ASP116 3.0 10.8 1.0
OD1 A:ASP116 3.2 15.6 1.0
CG A:ASP142 3.3 9.4 1.0
C A:ILE143 3.4 11.5 1.0
P F:DA2 3.5 12.8 0.5
OD2 A:ASP142 3.6 9.6 1.0
N A:ILE143 3.6 8.9 1.0
O5' F:DA2 4.0 14.8 0.5
CA A:ILE143 4.0 9.6 1.0
OE2 A:GLU87 4.0 24.3 1.0
OP2 F:DA2 4.1 12.4 0.5
CA F:CA9 4.2 22.7 1.0
NZ A:LYS144 4.3 14.6 1.0
CB A:ILE143 4.4 11.4 1.0
O A:HOH306 4.4 5.9 1.0
C A:ASP142 4.4 9.6 1.0
CD A:LYS144 4.4 15.9 1.0
CB A:ASP116 4.4 8.7 1.0
CB A:ASP142 4.4 10.9 1.0
C5' F:DA2 4.5 15.5 0.5
N A:LYS144 4.6 11.1 1.0
CA A:ASP142 4.6 12.4 1.0
CE A:LYS144 4.7 15.6 1.0
O3' F:DT1 4.8 13.9 0.5
OP2 F:DG3 4.8 12.4 0.5
O A:HOH308 4.8 10.7 1.0
CG A:GLU87 4.9 17.3 1.0
CA A:LYS144 4.9 12.5 1.0
CD A:GLU87 4.9 19.1 1.0

Calcium binding site 3 out of 4 in 1dmu

Go back to Calcium Binding Sites List in 1dmu
Calcium binding site 3 out of 4 in the Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence


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 the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:33.5
occ:1.00
 O A:HOH386 2.4 24.8 1.0
O A:GLY77 2.5 17.9 1.0
O A:HOH384 2.6 25.2 1.0
O A:HOH385 2.6 21.7 1.0
O A:HOH383 2.6 34.9 1.0
O A:HOH382 2.6 15.3 1.0
O A:HOH374 2.6 35.5 1.0
C A:GLY77 3.5 14.7 1.0
CA A:GLY77 4.2 15.2 1.0
N A:ASP78 4.4 13.8 1.0
OD1 A:ASP70 4.6 17.0 1.0
CA A:ASP78 4.6 13.7 1.0
OD2 A:ASP70 4.9 17.7 1.0
O A:GLN79 4.9 12.0 1.0

Calcium binding site 4 out of 4 in 1dmu

Go back to Calcium Binding Sites List in 1dmu
Calcium binding site 4 out of 4 in the Crystal Structure of the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence


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 the Restriction Endonuclease Bgli (E.C.3.1.21.4) Bound to Its Dna Recognition Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:46.4
occ:1.00
 O A:ARG101 2.2 18.3 1.0
O A:ILE104 2.4 15.9 1.0
O A:SER99 2.4 14.8 1.0
O A:HOH397 2.5 39.6 1.0
O A:HOH426 2.6 25.1 1.0
O A:HOH425 2.7 27.6 1.0
C A:ARG101 3.4 19.3 1.0
C A:ILE104 3.5 16.1 1.0
C A:SER99 3.5 12.8 1.0
O A:GLU102 3.7 28.6 1.0
C A:GLN100 3.8 14.0 1.0
N A:ILE104 3.8 17.4 1.0
N A:ARG101 3.9 16.7 1.0
C A:GLU102 4.0 26.0 1.0
CA A:ILE104 4.1 16.3 1.0
O A:HOH424 4.2 18.2 1.0
O A:GLN100 4.2 14.3 1.0
CA A:GLN100 4.2 13.1 1.0
N A:GLU102 4.2 21.9 1.0
O A:HOH525 4.3 48.4 1.0
N A:GLN100 4.3 12.3 1.0
O A:HOH409 4.3 16.9 1.0
CA A:ARG101 4.3 18.3 1.0
CA A:GLU102 4.3 24.6 1.0
CA A:SER99 4.6 12.2 1.0
CB A:ILE104 4.6 15.3 1.0
N A:THR105 4.7 15.3 1.0
N A:ASP103 4.7 23.9 1.0
C A:ASP103 4.9 21.1 1.0
O A:VAL98 4.9 12.0 1.0
CA A:THR105 5.0 15.3 1.0

Reference:

M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, S.E.Phillips. Crystal Structure of Restriction Endonuclease Bgli Bound to Its Interrupted Dna Recognition Sequence. Embo J. V. 17 5466 1998.
ISSN: ISSN 0261-4189
PubMed: 9736624
DOI: 10.1093/EMBOJ/17.18.5466
Page generated: Thu Jul 11 07:35:49 2024

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