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Calcium in PDB 2f03: Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form)

Enzymatic activity of Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form)

All present enzymatic activity of Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form):
3.1.21.4;

Protein crystallography data

The structure of Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form), PDB code: 2f03 was solved by A.K.Aggarwal, E.S.Vanamee, H Viadiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.600, 85.600, 418.700, 90.00, 90.00, 120.00
R / Rfree (%) 24.1 / 29.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form) (pdb code 2f03). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form), PDB code: 2f03:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2f03

Go back to Calcium Binding Sites List in 2f03
Calcium binding site 1 out of 2 in the Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form)


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 Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:35.5
occ:0.50
OD2 A:ASP79 2.6 31.4 0.5
O A:ALA101 2.7 23.1 0.5
OD1 A:ASP100 3.1 31.6 0.5
OP1 F:DT13 3.4 68.5 0.5
CG A:ASP79 3.5 32.6 0.5
OD2 A:ASP100 3.5 34.9 0.5
CG A:ASP100 3.6 31.8 0.5
OD1 A:ASP79 3.7 34.9 0.5
C A:ALA101 3.9 25.5 0.5
N A:ALA101 4.1 26.3 0.5
CA A:ALA101 4.5 25.6 0.5
CD A:LYS102 4.6 37.3 0.5
P F:DT13 4.6 67.9 0.5
O5' F:DT13 4.6 65.0 0.5
C5' F:DT13 4.7 58.9 0.5
NZ A:LYS102 4.8 39.4 0.5
C3' F:DT13 4.8 52.9 0.5
C A:ASP100 4.8 26.3 0.5
OE2 A:GLU55 4.8 32.2 0.5
CB A:ASP79 4.9 31.8 0.5
O3' F:DT13 4.9 51.7 0.5
CB A:ASP100 4.9 29.3 0.5
N A:LYS102 5.0 27.2 0.5
CE A:LYS102 5.0 38.1 0.5

Calcium binding site 2 out of 2 in 2f03

Go back to Calcium Binding Sites List in 2f03
Calcium binding site 2 out of 2 in the Crystal Structure of Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form)


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 Tetrameric Restriction Endonuclease Sfii in Complex with Cognate Dna (Partial Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:61.5
occ:0.50
OD1 C:ASP100 2.7 36.9 0.5
O C:ALA101 2.8 32.8 0.5
CD C:LYS102 3.1 40.1 0.5
NZ C:LYS102 3.2 45.0 0.5
CE C:LYS102 3.4 41.7 0.5
OD2 C:ASP79 3.7 47.9 0.5
CG C:ASP100 3.8 36.7 0.5
C C:ALA101 4.0 33.2 0.5
CG C:LYS102 4.2 37.5 0.5
OD2 C:ASP100 4.3 38.3 0.5
NE2 C:GLN116 4.4 35.8 0.5
CA C:LYS102 4.5 32.7 0.5
N C:LYS102 4.7 33.1 0.5
CG C:ASP79 4.8 47.1 0.5
CB C:LYS102 4.8 34.8 0.5
N C:ALA101 4.9 33.4 0.5
OD1 C:ASP79 4.9 49.5 0.5
CB C:ASP100 5.0 34.2 0.5
OE2 C:GLU55 5.0 45.4 0.5

Reference:

E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, A.K.Aggarwal. A View of Consecutive Binding Events From Structures of Tetrameric Endonuclease Sfii Bound to Dna. Embo J. V. 24 4198 2005.
ISSN: ISSN 0261-4189
PubMed: 16308566
DOI: 10.1038/SJ.EMBOJ.7600880
Page generated: Fri Jul 12 10:20:43 2024

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