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Chlorine in PDB 6frm: Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4

Protein crystallography data

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4, PDB code: 6frm was solved by S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, S.Shima, E.Girard, E.Dumont, O.Maury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.170, 147.875, 146.059, 90.00, 90.40, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 6frm:

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 also contains other interesting chemical elements:

Terbium (Tb) 16 atoms
Iron (Fe) 4 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 (pdb code 6frm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 17 binding sites of Chlorine where determined in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4, PDB code: 6frm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 17 in 6frm

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Chlorine binding site 1 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:68.3
occ:1.00
 NH2 A:ARG399 3.7 78.1 1.0
NH1 A:ARG399 3.7 68.4 1.0
CG A:LYS392 4.0 52.7 1.0
ND2 A:ASN395 4.0 54.1 1.0
CB A:ASN395 4.0 50.1 1.0
CZ A:ARG399 4.2 87.3 1.0
O A:HOH763 4.4 75.5 1.0
CA A:LYS392 4.4 48.7 1.0
NZ A:LYS392 4.4 56.8 1.0
CB A:LYS392 4.5 51.6 1.0
CG A:ASN395 4.5 63.8 1.0
CD A:LYS392 4.5 58.4 1.0
O A:LYS392 4.6 52.5 1.0

Chlorine binding site 2 out of 17 in 6frm

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Chlorine binding site 2 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:67.9
occ:1.00
 OG A:SER121 3.4 67.3 1.0
CB A:SER121 3.9 57.1 1.0
O A:HOH760 3.9 66.3 1.0
CB A:PHE119 4.1 51.7 1.0
CA A:PHE119 4.2 50.5 1.0
N A:SER121 4.2 54.3 1.0
CD A:PRO120 4.3 56.0 1.0
N A:PRO120 4.5 54.4 1.0
C A:PHE119 4.5 56.6 1.0
CG A:PRO94 4.5 47.9 1.0
CB A:PRO94 4.5 43.4 1.0
CA A:SER121 4.7 54.2 1.0
CD1 A:PHE119 4.8 55.3 1.0
CG A:PHE119 5.0 52.3 1.0

Chlorine binding site 3 out of 17 in 6frm

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Chlorine binding site 3 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:64.6
occ:1.00
 NH1 B:ARG399 2.7 91.1 1.0
CZ B:ARG399 4.0 93.2 1.0
CG B:LYS392 4.1 45.9 1.0
CB B:ASN395 4.1 52.9 1.0
ND2 B:ASN395 4.1 66.0 1.0
NZ B:LYS392 4.4 74.5 1.0
CA B:LYS392 4.6 49.4 1.0
CD B:LYS392 4.6 52.2 1.0
O B:LYS392 4.7 52.8 1.0
CG B:ASN395 4.7 70.2 1.0
CB B:LYS392 4.7 50.2 1.0
NE B:ARG399 4.8 79.2 1.0
NH2 B:ARG399 4.8 76.7 1.0

Chlorine binding site 4 out of 17 in 6frm

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Chlorine binding site 4 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:59.6
occ:1.00
 O B:HOH751 2.9 64.3 1.0
OG B:SER121 3.4 47.4 1.0
O B:HOH798 3.7 72.3 1.0
CB B:SER121 4.0 41.3 1.0
CA B:PHE119 4.0 40.1 1.0
CB B:PHE119 4.1 41.2 1.0
CD B:PRO120 4.1 43.8 1.0
N B:SER121 4.2 42.7 1.0
N B:PRO120 4.3 43.0 1.0
C B:PHE119 4.3 45.1 1.0
CB B:PRO94 4.5 44.0 1.0
CG B:PRO94 4.5 47.4 1.0
CA B:SER121 4.8 42.1 1.0
CD1 B:PHE119 4.8 45.5 1.0
CG B:PHE119 4.9 42.3 1.0
O B:PHE119 5.0 44.8 1.0

Chlorine binding site 5 out of 17 in 6frm

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Chlorine binding site 5 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl505

b:59.4
occ:1.00
 OG C:SER121 3.4 67.0 1.0
CA C:PHE119 3.8 48.6 1.0
CB C:PHE119 3.9 49.3 1.0
CB C:SER121 3.9 59.6 1.0
CD C:PRO120 4.0 56.1 1.0
N C:SER121 4.0 57.2 1.0
N C:PRO120 4.0 54.2 1.0
C C:PHE119 4.0 54.2 1.0
CG C:PRO94 4.4 53.2 1.0
CB C:PRO94 4.5 50.6 1.0
CA C:SER121 4.6 57.3 1.0
CD1 C:PHE119 4.7 52.0 1.0
O C:PHE119 4.7 53.4 1.0
CG C:PHE119 4.8 49.6 1.0
C C:PRO120 4.9 61.3 1.0
CA C:PRO120 5.0 56.0 1.0

Chlorine binding site 6 out of 17 in 6frm

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Chlorine binding site 6 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl506

b:80.0
occ:1.00
 NZ C:LYS338 3.1 96.8 1.0
NE C:ARG341 3.5 70.2 1.0
ND2 C:ASN340 3.6 73.0 1.0
NH2 C:ARG341 3.7 59.5 1.0
O C:HOH681 4.0 67.8 1.0
CZ C:ARG341 4.0 81.2 1.0
CE C:LYS338 4.4 82.8 1.0
CD C:ARG341 4.5 64.9 1.0
CD C:LYS338 4.5 64.4 1.0
CG C:ARG341 4.5 64.9 1.0
CG C:ASN340 4.7 80.1 1.0
OD1 C:ASN340 5.0 78.4 1.0

Chlorine binding site 7 out of 17 in 6frm

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Chlorine binding site 7 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl506

b:89.4
occ:1.00
 NE D:ARG341 3.4 89.5 1.0
NH1 D:ARG341 3.5 83.9 1.0
ND2 D:ASN340 3.9 77.5 1.0
CZ D:ARG341 3.9 93.3 1.0
CD D:ARG341 4.5 88.0 1.0
CG D:ARG341 4.6 80.6 1.0
CD D:LYS338 4.6 74.9 1.0
CG D:LYS338 4.9 62.3 1.0
CG D:ASN340 5.0 86.1 1.0

Chlorine binding site 8 out of 17 in 6frm

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Chlorine binding site 8 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl507

b:74.8
occ:1.00
 O D:HOH1646 3.0 74.0 1.0
OG D:SER121 3.3 72.6 1.0
CB D:SER121 3.8 65.1 1.0
CB D:PHE119 3.9 58.5 1.0
CA D:PHE119 3.9 57.0 1.0
N D:SER121 4.0 62.6 1.0
CD D:PRO120 4.0 63.7 1.0
C D:PHE119 4.1 63.6 1.0
N D:PRO120 4.1 62.1 1.0
O D:HOH1655 4.2 74.2 1.0
CG D:PRO94 4.4 61.2 1.0
CB D:PRO94 4.4 57.6 1.0
CA D:SER121 4.6 62.9 1.0
CD1 D:PHE119 4.7 60.8 1.0
O D:PHE119 4.8 63.7 1.0
CG D:PHE119 4.8 59.2 1.0
O D:HOH1638 4.9 60.2 1.0

Chlorine binding site 9 out of 17 in 6frm

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Chlorine binding site 9 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl503

b:94.5
occ:1.00
 ND2 E:ASN340 3.4 64.6 1.0
NE E:ARG341 3.4 85.8 1.0
NH1 E:ARG341 3.7 78.2 1.0
CZ E:ARG341 3.9 92.2 1.0
CD E:LYS338 4.1 46.1 1.0
CG E:ARG341 4.2 72.7 1.0
CD E:ARG341 4.3 80.4 1.0
CG E:ASN340 4.4 81.4 1.0
CG E:LYS338 4.5 45.0 1.0
OD1 E:ASN340 4.5 80.5 1.0
CB E:LYS338 4.6 41.3 1.0

Chlorine binding site 10 out of 17 in 6frm

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Chlorine binding site 10 out of 17 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra) Co-Crystallized with 10 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl504

b:65.3
occ:1.00
 NH2 E:ARG399 3.6 46.9 1.0
NH1 E:ARG399 3.8 54.2 1.0
CG E:LYS392 4.1 50.9 1.0
ND2 E:ASN395 4.1 44.9 1.0
CB E:ASN395 4.2 39.5 1.0
CZ E:ARG399 4.2 66.0 1.0
CE E:LYS392 4.2 75.7 1.0
NZ E:LYS392 4.6 74.2 1.0
CA E:LYS392 4.6 38.2 1.0
CD E:LYS392 4.7 61.6 1.0
CG E:ASN395 4.7 55.7 1.0
CB E:LYS392 4.7 39.5 1.0
O E:LYS392 4.7 43.5 1.0

Reference:

S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, C.Breyton, B.Franzetti, S.Shima, E.Girard, E.Dumont, O.Maury. Unveiling the Binding Modes of the Crystallophore, A Terbium-Based Nucleating and Phasing Molecular Agent For Protein Crystallography. Chemistry V. 24 9739 2018.
ISSN: ISSN 1521-3765
PubMed: 29806881
DOI: 10.1002/CHEM.201802172
Page generated: Sat Jul 27 23:29:05 2024

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