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Calcium in PDB 1en7: Endonuclease VII (Endovii) From Phage T4

Enzymatic activity of Endonuclease VII (Endovii) From Phage T4

All present enzymatic activity of Endonuclease VII (Endovii) From Phage T4:
3.1.22.4;

Protein crystallography data

The structure of Endonuclease VII (Endovii) From Phage T4, PDB code: 1en7 was solved by H.Raaijmakers, O.Vix, I.Toro, D.Suck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 144.990, 39.450, 75.750, 90.00, 106.20, 90.00
R / Rfree (%) 23.9 / 30.8

Other elements in 1en7:

The structure of Endonuclease VII (Endovii) From Phage T4 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Endonuclease VII (Endovii) From Phage T4 (pdb code 1en7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Endonuclease VII (Endovii) From Phage T4, PDB code: 1en7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1en7

Go back to Calcium Binding Sites List in 1en7
Calcium binding site 1 out of 3 in the Endonuclease VII (Endovii) From Phage T4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Endonuclease VII (Endovii) From Phage T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:40.7
occ:1.00
OD1 A:ASP40 2.3 38.0 1.0
OD1 A:ASN62 2.4 37.1 1.0
O A:HOH447 2.5 38.3 1.0
O A:HOH450 2.6 32.9 1.0
CE1 A:HIS38 3.0 38.7 1.0
CG A:ASP40 3.4 36.7 1.0
CG A:ASN62 3.6 34.7 1.0
ND1 A:HIS38 3.8 41.0 1.0
NE2 A:HIS38 3.9 38.6 1.0
CB A:ASP40 3.9 38.4 1.0
ND2 A:ASN62 4.1 33.6 1.0
CA A:ASP40 4.2 38.4 1.0
N A:HIS41 4.2 34.3 1.0
O A:HIS41 4.3 36.9 1.0
OD2 A:ASP40 4.4 36.0 1.0
NE2 A:HIS43 4.5 36.0 1.0
NH2 A:ARG54 4.5 32.2 1.0
OE1 A:GLU65 4.7 31.0 1.0
C A:ASP40 4.7 37.6 1.0
CB A:ASN62 4.8 35.0 1.0
O A:ASN62 4.8 38.2 1.0
CE1 A:HIS43 4.8 36.0 1.0

Calcium binding site 2 out of 3 in 1en7

Go back to Calcium Binding Sites List in 1en7
Calcium binding site 2 out of 3 in the Endonuclease VII (Endovii) From Phage T4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Endonuclease VII (Endovii) From Phage T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:41.4
occ:1.00
OD1 B:ASN62 2.3 34.7 1.0
OD1 B:ASP40 2.4 35.1 1.0
O B:HOH444 2.5 41.5 1.0
CG B:ASN62 3.4 30.1 1.0
CG B:ASP40 3.6 29.9 1.0
NE2 B:HIS38 3.7 27.3 1.0
ND2 B:ASN62 3.8 26.5 1.0
CE1 B:HIS43 4.1 38.0 1.0
OD2 B:ASP40 4.3 29.0 1.0
CD2 B:HIS38 4.4 27.1 1.0
O B:HOH429 4.5 29.7 1.0
N B:HIS41 4.5 28.7 1.0
CB B:ASP40 4.5 31.5 1.0
CA B:ASP40 4.6 31.4 1.0
O B:ASN62 4.6 17.9 1.0
O B:HIS41 4.6 27.1 1.0
CB B:ASN62 4.7 27.2 1.0
NE2 B:HIS43 4.7 36.8 1.0
CE1 B:HIS38 4.8 26.2 1.0
OE1 B:GLU65 4.8 29.1 1.0
NH2 B:ARG54 4.9 28.3 1.0

Calcium binding site 3 out of 3 in 1en7

Go back to Calcium Binding Sites List in 1en7
Calcium binding site 3 out of 3 in the Endonuclease VII (Endovii) From Phage T4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Endonuclease VII (Endovii) From Phage T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:45.0
occ:1.00
O B:GLY81 2.4 36.0 1.0
O B:HOH448 2.6 35.8 1.0
OE2 B:GLU86 2.6 40.6 1.0
OE1 B:GLU86 2.7 36.6 1.0
CD B:GLU86 3.0 36.9 1.0
C B:GLY81 3.7 36.8 1.0
CA B:VAL82 4.4 36.2 1.0
N B:VAL82 4.4 34.0 1.0
N B:ASP83 4.5 39.3 1.0
CG B:GLU86 4.5 35.8 1.0
CA B:GLY81 4.7 35.8 1.0
C B:VAL82 4.9 38.3 1.0
O B:HOH443 5.0 41.1 1.0

Reference:

H.Raaijmakers, O.Vix, I.Toro, S.Golz, B.Kemper, D.Suck. X-Ray Structure of T4 Endonuclease VII: A Dna Junction Resolvase with A Novel Fold and Unusual Domain-Swapped Dimer Architecture. Embo J. V. 18 1447 1999.
ISSN: ISSN 0261-4189
PubMed: 10075917
DOI: 10.1093/EMBOJ/18.6.1447
Page generated: Sat Dec 12 02:54:25 2020

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