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Chlorine in PDB 5mf2: Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4

Protein crystallography data

The structure of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4, PDB code: 5mf2 was solved by S.Engilberge, F.Riobe, S.Di Pietro, L.Lassalle, C.-A.Arnaud, C.Breyton, D.Madern, N.Coquelle, O.Maury, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.464, 95.502, 71.492, 90.00, 103.46, 90.00
R / Rfree (%) 21 / 23.6

Other elements in 5mf2:

The structure of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 also contains other interesting chemical elements:

Terbium (Tb) 15 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 (pdb code 5mf2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4, PDB code: 5mf2:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5mf2

Go back to Chlorine Binding Sites List in 5mf2
Chlorine binding site 1 out of 4 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:44.4
occ:1.00
HD22 A:ASN112 2.4 49.5 1.0
HD22 C:ASN112 2.5 47.2 1.0
HG21 A:THR99 2.9 47.8 1.0
HG21 C:THR99 2.9 50.5 1.0
HB A:THR99 3.2 47.4 1.0
HB3 A:ASN112 3.2 42.2 1.0
HB3 C:ASN112 3.2 43.9 1.0
ND2 A:ASN112 3.2 41.2 1.0
HB C:THR99 3.2 50.7 1.0
ND2 C:ASN112 3.4 39.3 1.0
HB2 A:ASN112 3.4 42.2 1.0
HB2 C:ASN112 3.4 43.9 1.0
HG22 C:THR99 3.5 50.5 1.0
CG2 A:THR99 3.5 39.8 1.0
CG2 C:THR99 3.5 42.0 1.0
HG22 A:THR99 3.6 47.8 1.0
CB A:ASN112 3.6 35.1 1.0
CB C:ASN112 3.7 36.5 1.0
CB A:THR99 3.8 39.5 1.0
HD21 A:ASN112 3.8 49.5 1.0
HG1 A:THR99 3.8 49.8 1.0
CB C:THR99 3.8 42.2 1.0
HG3 C:PRO101 3.9 45.8 1.0
HG3 A:PRO101 3.9 42.0 1.0
CG A:ASN112 3.9 38.7 1.0
HD21 C:ASN112 3.9 47.2 1.0
HG1 C:THR99 4.0 52.0 1.0
CG C:ASN112 4.0 37.1 1.0
OG1 A:THR99 4.3 41.5 1.0
HG23 A:THR99 4.4 47.8 1.0
HG23 C:THR99 4.4 50.5 1.0
OG1 C:THR99 4.4 43.3 1.0
HD3 A:PRO101 4.5 40.7 1.0
HD3 C:PRO101 4.7 45.3 1.0
CG C:PRO101 4.8 38.1 1.0
CG A:PRO101 4.8 35.0 1.0
HD21 A:ASN114 4.9 52.0 1.0

Chlorine binding site 2 out of 4 in 5mf2

Go back to Chlorine Binding Sites List in 5mf2
Chlorine binding site 2 out of 4 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:84.7
occ:1.00
HD22 A:ASN149 3.5 47.0 1.0
HG A:SER142 3.7 49.2 1.0
HB2 A:ASN149 3.7 42.4 1.0
OG A:SER142 3.9 41.0 1.0
HB2 A:SER142 4.0 48.0 1.0
HB2 A:SER144 4.0 39.2 1.0
HB3 A:ASN149 4.0 42.4 1.0
CB A:ASN149 4.3 35.3 1.0
ND2 A:ASN149 4.3 39.1 1.0
CB A:SER142 4.5 40.0 1.0
HA A:SER143 4.5 42.9 1.0
HB3 A:SER144 4.6 39.2 1.0
C A:SER143 4.6 37.1 1.0
N A:SER143 4.7 33.2 1.0
O A:SER143 4.7 36.9 1.0
HG13 B:VAL23 4.7 52.4 1.0
CB A:SER144 4.7 32.6 1.0
C A:SER142 4.8 39.0 1.0
H A:SER143 4.8 39.9 1.0
HG12 A:VAL147 4.8 33.6 1.0
CA A:SER143 4.8 35.7 1.0
CG A:ASN149 4.9 36.7 1.0
N A:SER144 4.9 31.9 1.0
HG13 C:ILE110 4.9 42.8 1.0
HD21 A:ASN149 5.0 47.0 1.0
O A:SER142 5.0 38.5 1.0
HD11 C:ILE110 5.0 43.4 1.0
HG22 B:VAL23 5.0 59.4 1.0

Chlorine binding site 3 out of 4 in 5mf2

Go back to Chlorine Binding Sites List in 5mf2
Chlorine binding site 3 out of 4 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl306

b:42.1
occ:1.00
HD22 B:ASN112 2.5 42.9 1.0
HD22 D:ASN112 2.5 46.1 1.0
HG21 D:THR99 2.8 52.5 1.0
HG21 B:THR99 2.8 44.5 1.0
O B:HOH416 2.9 59.2 1.0
HB D:THR99 3.1 51.0 1.0
HB3 B:ASN112 3.1 39.2 1.0
HB3 D:ASN112 3.1 41.7 1.0
HB B:THR99 3.1 44.4 1.0
HB2 B:ASN112 3.3 39.2 1.0
ND2 B:ASN112 3.3 35.7 1.0
HB2 D:ASN112 3.4 41.7 1.0
ND2 D:ASN112 3.4 38.6 1.0
CG2 D:THR99 3.4 43.7 1.0
CG2 B:THR99 3.5 37.1 1.0
HG22 D:THR99 3.5 52.5 1.0
HG22 B:THR99 3.5 44.5 1.0
CB B:ASN112 3.6 32.6 1.0
CB D:ASN112 3.6 34.9 1.0
CB D:THR99 3.7 42.5 1.0
CB B:THR99 3.7 37.0 1.0
HG1 D:THR99 3.8 55.2 1.0
HG1 B:THR99 3.8 47.4 1.0
HG3 B:PRO101 3.8 37.1 1.0
HG3 D:PRO101 3.9 47.7 1.0
HD21 B:ASN112 3.9 42.9 1.0
CG B:ASN112 4.0 34.3 1.0
HD21 D:ASN112 4.0 46.1 1.0
CG D:ASN112 4.0 36.8 1.0
OG1 D:THR99 4.2 46.0 1.0
OG1 B:THR99 4.3 39.5 1.0
HG23 D:THR99 4.3 52.5 1.0
O D:HOH461 4.3 56.5 1.0
HG23 B:THR99 4.3 44.5 1.0
HD3 B:PRO101 4.5 35.7 1.0
HD3 D:PRO101 4.5 46.8 1.0
CG B:PRO101 4.8 30.9 1.0
CG D:PRO101 4.8 39.7 1.0
HD21 D:ASN114 4.9 49.9 1.0
H B:ASN112 4.9 36.5 1.0
H D:ASN112 4.9 38.0 1.0
CA B:ASN112 5.0 31.4 1.0
O D:THR99 5.0 35.4 1.0

Chlorine binding site 4 out of 4 in 5mf2

Go back to Chlorine Binding Sites List in 5mf2
Chlorine binding site 4 out of 4 in the Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bacteriophage T5 Distal Tail Protein PB9 Co-Crystallized with Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl304

b:75.8
occ:1.00
HD22 D:ASN149 3.3 50.7 1.0
HG D:SER142 3.4 55.4 1.0
HB2 D:ASN149 3.5 46.0 1.0
OG D:SER142 3.7 46.2 1.0
HB3 D:ASN149 3.9 46.0 1.0
CB D:ASN149 4.1 38.3 1.0
ND2 D:ASN149 4.2 42.2 1.0
HB2 D:SER144 4.2 46.0 1.0
HB2 D:SER142 4.2 56.1 1.0
CB D:SER142 4.5 46.7 1.0
HB3 D:SER144 4.6 46.0 1.0
O B:HOH426 4.6 48.1 1.0
HA D:SER143 4.7 51.9 1.0
CG D:ASN149 4.7 40.5 1.0
HD21 D:ASN149 4.8 50.7 1.0
HG12 D:VAL147 4.8 42.5 1.0
CB D:SER144 4.8 38.3 1.0
C D:SER143 4.9 44.8 1.0
C D:SER142 4.9 44.3 1.0
N D:SER143 4.9 43.6 1.0
O D:SER142 5.0 42.6 1.0

Reference:

S.Engilberge, F.Riobe, S.Di Pietro, L.Lassalle, N.Coquelle, C.A.Arnaud, D.Pitrat, J.C.Mulatier, D.Madern, C.Breyton, O.Maury, E.Girard. Crystallophore: A Versatile Lanthanide Complex For Protein Crystallography Combining Nucleating Effects, Phasing Properties, and Luminescence. Chem Sci V. 8 5909 2017.
ISSN: ISSN 2041-6520
PubMed: 29619195
DOI: 10.1039/C7SC00758B
Page generated: Sat Dec 12 12:05:58 2020

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