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Chlorine in PDB 1e7d: Endonuclease VII (Endovii) Ffrom Phage T4

Enzymatic activity of Endonuclease VII (Endovii) Ffrom Phage T4

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

Protein crystallography data

The structure of Endonuclease VII (Endovii) Ffrom Phage T4, PDB code: 1e7d was solved by H.C.A.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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.900, 37.400, 74.000, 90.00, 108.20, 90.00
R / Rfree (%) 24.5 / 31.5

Other elements in 1e7d:

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

Calcium (Ca) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Endonuclease VII (Endovii) Ffrom Phage T4 (pdb code 1e7d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Endonuclease VII (Endovii) Ffrom Phage T4, PDB code: 1e7d:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 1e7d

Go back to Chlorine Binding Sites List in 1e7d
Chlorine binding site 1 out of 3 in the Endonuclease VII (Endovii) Ffrom Phage T4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Endonuclease VII (Endovii) Ffrom Phage T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1160

b:37.2
occ:1.00
OH A:TYR8 3.1 52.1 1.0
N A:LEU39 3.1 30.2 1.0
NZ A:LYS12 3.2 25.4 1.0
CE A:LYS12 3.3 25.0 1.0
CA A:HIS38 3.4 37.7 1.0
O A:ASN37 3.6 26.6 1.0
C A:HIS38 3.8 33.6 1.0
CZ A:TYR8 4.1 54.3 1.0
CA A:LEU39 4.2 28.5 1.0
CB A:HIS38 4.2 44.1 1.0
CB A:LEU39 4.2 29.2 1.0
CE2 A:TYR8 4.3 54.1 1.0
C A:ASN37 4.4 31.0 1.0
N A:HIS38 4.4 35.4 1.0
ND1 A:HIS38 4.4 51.4 1.0
CG A:HIS38 4.7 50.0 1.0
O A:LEU39 4.7 26.7 1.0
CD A:LYS12 4.8 26.6 1.0
C A:LEU39 4.8 26.7 1.0
O A:HIS38 5.0 31.4 1.0

Chlorine binding site 2 out of 3 in 1e7d

Go back to Chlorine Binding Sites List in 1e7d
Chlorine binding site 2 out of 3 in the Endonuclease VII (Endovii) Ffrom Phage T4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Endonuclease VII (Endovii) Ffrom Phage T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1160

b:34.3
occ:1.00
NH2 B:ARG74 3.3 40.0 1.0
NZ B:LYS71 3.4 25.2 1.0
CE B:LYS71 3.8 25.0 1.0
NZ A:LYS71 4.0 11.1 1.0
CD2 B:HIS70 4.0 18.9 1.0
CZ B:ARG74 4.3 41.2 1.0
NE2 B:HIS70 4.3 21.2 1.0
NH1 B:ARG74 4.4 40.4 1.0
CE A:LYS71 4.6 13.4 1.0
CD B:LYS71 4.6 25.4 1.0

Chlorine binding site 3 out of 3 in 1e7d

Go back to Chlorine Binding Sites List in 1e7d
Chlorine binding site 3 out of 3 in the Endonuclease VII (Endovii) Ffrom Phage T4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Endonuclease VII (Endovii) Ffrom Phage T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1161

b:45.0
occ:1.00
NZ B:LYS12 2.8 26.4 1.0
OH B:TYR8 2.8 43.3 1.0
N B:LEU39 3.2 11.6 1.0
CD2 B:HIS38 3.8 19.4 1.0
CA B:HIS38 3.9 17.6 1.0
CB B:LEU39 4.0 9.2 1.0
CZ B:TYR8 4.0 43.1 1.0
C B:HIS38 4.0 13.6 1.0
CA B:LEU39 4.1 12.5 1.0
O B:ASN37 4.1 13.1 1.0
CE B:LYS12 4.1 23.8 1.0
O B:LEU39 4.2 12.9 1.0
CG B:HIS38 4.2 20.8 1.0
NE2 B:HIS38 4.3 18.9 1.0
C B:LEU39 4.5 14.7 1.0
CB B:HIS38 4.6 20.6 1.0
NE2 A:HIS105 4.7 15.3 1.0
CE2 B:TYR8 4.7 43.6 1.0
CE1 B:TYR8 4.9 42.1 1.0
N B:HIS38 4.9 19.5 1.0
ND1 B:HIS38 4.9 18.8 1.0
CE1 B:HIS38 4.9 19.4 1.0
C B:ASN37 5.0 17.9 1.0

Reference:

H.C.A.Raaijmakers, I.Toro, R.Birkenbihl, B.Kemper, D.Suck. Conformational Flexibility in T4 Endonuclease VII Revealed By Crystallography: Implications For Substrate Binding and Cleavage J.Mol.Biol. V. 308 311 2001.
ISSN: ISSN 0022-2836
PubMed: 11327769
DOI: 10.1006/JMBI.2001.4592
Page generated: Sat Dec 12 08:34:32 2020

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