Calcium in PDB 6frn: Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride

Protein crystallography data

The structure of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride, PDB code: 6frn was solved by S.Engilberge, F.Riobe, S.Di Pietro, T.Wagner, 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) 25.48 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.660, 144.970, 74.210, 90.00, 91.78, 90.00
R / Rfree (%) 16.4 / 18.9

Other elements in 6frn:

The structure of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride also contains other interesting chemical elements:

Terbium (Tb) 8 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Calcium atom in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride (pdb code 6frn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride, PDB code: 6frn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in 6frn

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Calcium binding site 1 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:35.7
occ:1.00
O B:HOH710 2.3 24.3 1.0
O A:HOH622 2.4 40.8 1.0
O A:HOH760 2.4 45.7 1.0
OD2 A:ASP297 2.5 29.1 1.0
O A:HOH654 2.5 39.8 1.0
O B:HOH702 2.6 43.9 1.0
OD1 A:ASP297 2.6 29.9 1.0
CG A:ASP297 2.9 32.7 1.0
HA B:ASP21 3.5 24.7 1.0
HD2 B:ARG23 3.6 58.8 1.0
HH11 B:ARG23 3.6 48.5 1.0
H A:PHE293 3.7 23.4 1.0
HA A:TYR292 3.9 20.8 1.0
HG2 B:ARG23 3.9 35.7 1.0
HG3 B:ARG23 4.0 38.3 1.0
HB3 A:PHE293 4.1 24.9 1.0
O B:TRP20 4.3 24.5 1.0
CG B:ARG23 4.3 38.0 1.0
CB A:ASP297 4.4 27.6 1.0
CD B:ARG23 4.4 58.1 1.0
O A:MET291 4.4 27.7 1.0
HD1 A:TYR292 4.5 28.6 1.0
HA B:ASN31 4.5 23.6 1.0
O B:ASP21 4.5 27.4 1.0
CA B:ASP21 4.6 25.6 1.0
OD1 A:ASN296 4.6 35.0 1.0
NH1 B:ARG23 4.6 47.6 1.0
N A:PHE293 4.6 22.9 1.0
HB3 A:ASP297 4.7 28.5 1.0
C B:ASP21 4.8 28.7 1.0
OD1 B:ASP21 4.8 38.0 1.0
HB2 A:ASP297 4.9 26.4 1.0
CA A:TYR292 4.9 21.9 1.0
O B:HOH674 4.9 38.1 1.0
CB A:PHE293 4.9 24.4 1.0
HB2 A:PHE293 5.0 24.7 1.0

Calcium binding site 2 out of 15 in 6frn

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Calcium binding site 2 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:65.8
occ:1.00
OD1 A:ASP10 2.1 56.9 1.0
O A:HOH803 2.3 45.5 1.0
O A:HOH711 2.6 59.5 1.0
O A:HOH646 2.8 46.9 1.0
CG A:ASP10 3.2 55.6 1.0
OD2 A:ASP10 3.6 61.6 1.0
H A:GLY11 3.7 36.7 1.0
N A:GLY11 4.2 36.3 1.0
O A:HOH783 4.2 69.5 1.0
HA A:ASP10 4.2 36.9 1.0
CB A:ASP10 4.4 39.7 1.0
HA2 A:GLY11 4.6 36.1 1.0
C A:ASP10 4.7 41.5 1.0
CA A:ASP10 4.7 37.2 1.0
OE2 A:GLU71 4.7 40.0 1.0
OE1 A:GLU71 4.8 49.1 1.0
HA3 A:GLY11 4.8 35.8 1.0
CA A:GLY11 4.8 36.2 1.0
HB3 A:ASP10 4.9 39.2 1.0
HZ2 A:LYS7 4.9 0.1 1.0

Calcium binding site 3 out of 15 in 6frn

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Calcium binding site 3 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:41.6
occ:1.00
OE2 A:GLU113 2.1 93.8 1.0
OE1 A:GLU113 2.4 83.5 1.0
CD A:GLU113 2.5 90.9 1.0
O A:HOH805 2.8 67.0 1.0
CG A:GLU113 4.0 58.4 1.0
HG3 A:GLU113 4.4 59.3 1.0
HG2 A:GLU113 4.5 57.9 1.0
HB3 A:GLU113 4.7 36.3 1.0
HB2 A:GLU113 4.7 38.4 1.0
CB A:GLU113 4.8 38.2 1.0

Calcium binding site 4 out of 15 in 6frn

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Calcium binding site 4 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:36.9
occ:1.00
O B:HOH675 2.3 38.1 1.0
O B:HOH757 2.4 38.1 1.0
O A:HOH706 2.5 28.1 1.0
OD2 B:ASP297 2.5 28.7 1.0
O A:HOH695 2.5 46.7 1.0
OD1 B:ASP297 2.6 31.6 1.0
CG B:ASP297 2.9 31.1 1.0
HH21 A:ARG23 3.5 42.4 1.0
HD2 A:ARG23 3.6 49.8 1.0
HA A:ASP21 3.6 23.7 1.0
H B:PHE293 3.7 26.0 1.0
HG2 A:ARG23 3.9 31.2 1.0
HA B:TYR292 3.9 20.8 1.0
HG3 A:ARG23 4.0 32.2 1.0
HB3 B:PHE293 4.1 21.5 1.0
CG A:ARG23 4.3 33.1 1.0
O A:TRP20 4.3 26.9 1.0
CB B:ASP297 4.4 27.4 1.0
O B:MET291 4.4 27.9 1.0
CD A:ARG23 4.4 49.1 1.0
HD1 B:TYR292 4.5 27.3 1.0
NH2 A:ARG23 4.5 41.7 1.0
HA A:ASN31 4.5 25.4 1.0
OD1 B:ASN296 4.6 37.9 1.0
O A:ASP21 4.6 27.2 1.0
CA A:ASP21 4.6 25.7 1.0
N B:PHE293 4.6 23.9 1.0
HB3 B:ASP297 4.7 27.1 1.0
C A:ASP21 4.9 30.0 1.0
HB2 B:ASP297 4.9 29.5 1.0
OD1 A:ASP21 4.9 36.4 1.0
O A:HOH682 4.9 41.0 1.0
HH22 A:ARG23 4.9 41.3 1.0
CA B:TYR292 4.9 22.2 1.0
HB3 A:ASN31 5.0 30.6 1.0

Calcium binding site 5 out of 15 in 6frn

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Calcium binding site 5 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:39.5
occ:1.00
OE2 B:GLU113 2.1 83.5 1.0
OE1 B:GLU113 2.3 71.7 1.0
CD B:GLU113 2.5 80.7 1.0
O B:HOH778 2.8 78.8 1.0
CG B:GLU113 4.0 56.8 1.0
HG3 B:GLU113 4.4 57.3 1.0
HG2 B:GLU113 4.5 56.4 1.0
HB3 B:GLU113 4.6 36.0 1.0
HB2 B:GLU113 4.7 36.3 1.0
CB B:GLU113 4.8 36.9 1.0

Calcium binding site 6 out of 15 in 6frn

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Calcium binding site 6 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:35.6
occ:1.00
O D:HOH661 2.2 34.2 1.0
O D:HOH708 2.4 26.3 1.0
O C:HOH773 2.4 43.4 1.0
O C:HOH648 2.4 34.0 1.0
OD2 C:ASP297 2.4 26.3 1.0
O C:HOH732 2.5 41.3 1.0
OD1 C:ASP297 2.5 28.1 1.0
CG C:ASP297 2.8 26.9 1.0
HA D:ASP21 3.5 23.8 1.0
HH21 D:ARG23 3.6 35.7 1.0
H C:PHE293 3.7 23.0 1.0
HD2 D:ARG23 3.7 53.9 1.0
HA C:TYR292 3.8 21.4 1.0
HG2 D:ARG23 4.0 33.0 1.0
HG3 D:ARG23 4.1 34.4 1.0
HB3 C:PHE293 4.1 24.2 1.0
O D:TRP20 4.2 27.0 1.0
CB C:ASP297 4.3 23.6 1.0
HD1 C:TYR292 4.4 26.8 1.0
O C:MET291 4.4 25.9 1.0
CG D:ARG23 4.4 34.5 1.0
CA D:ASP21 4.5 25.0 1.0
HD22 D:ASN31 4.5 62.5 1.0
NH2 D:ARG23 4.6 35.4 1.0
CD D:ARG23 4.6 53.2 1.0
O D:ASP21 4.6 27.3 1.0
N C:PHE293 4.6 22.5 1.0
OD1 C:ASN296 4.6 37.2 1.0
HB3 C:ASP297 4.6 22.2 1.0
HA D:ASN31 4.6 19.2 1.0
O D:HOH796 4.7 58.2 1.0
OD1 D:ASP21 4.7 35.7 1.0
HB2 C:ASP297 4.8 24.4 1.0
C D:ASP21 4.8 27.2 1.0
O D:HOH675 4.8 38.4 1.0
CA C:TYR292 4.9 21.6 1.0
HA C:ASP297 5.0 24.1 1.0
HH22 D:ARG23 5.0 36.0 1.0

Calcium binding site 7 out of 15 in 6frn

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Calcium binding site 7 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:38.0
occ:1.00
O C:ASP44 2.3 38.1 1.0
O27 C:7MT508 2.3 28.8 1.0
O C:HOH602 2.4 41.3 1.0
O2 C:GOL512 2.4 32.5 1.0
O1 C:GOL512 2.6 34.5 1.0
C18 C:7MT508 3.3 31.7 1.0
C2 C:GOL512 3.4 35.9 1.0
C C:ASP44 3.5 38.7 1.0
C1 C:GOL512 3.5 34.5 1.0
H31 C:GOL512 3.6 40.5 1.0
O28 C:7MT508 3.6 29.7 1.0
HA C:ASP44 3.6 38.6 1.0
H11 C:GOL512 3.7 35.1 1.0
HA C:LYS45 3.9 29.8 1.0
C3 C:GOL512 3.9 40.4 1.0
O C:HOH814 4.0 46.9 1.0
H32 C:GOL512 4.1 40.5 1.0
CA C:ASP44 4.1 37.1 1.0
HB3 C:ASP44 4.2 39.4 1.0
HE2 C:LYS76 4.3 63.7 1.0
H2 C:GOL512 4.3 35.8 1.0
OD2 C:ASP78 4.4 39.0 1.0
HG2 C:LYS45 4.4 34.5 1.0
H12 C:GOL512 4.5 32.5 1.0
HD3 C:LYS76 4.5 48.1 1.0
N C:LYS45 4.5 33.2 1.0
OD1 C:ASP78 4.5 44.8 1.0
CA C:LYS45 4.7 30.4 1.0
C16 C:7MT508 4.7 29.2 1.0
CB C:ASP44 4.7 39.0 1.0
HG3 C:LYS45 4.8 35.2 1.0
CG C:ASP78 4.8 39.7 1.0
H151 C:7MT508 4.8 33.3 1.0

Calcium binding site 8 out of 15 in 6frn

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Calcium binding site 8 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:35.3
occ:1.00
OD1 C:ASP321 2.6 34.0 1.0
OD2 C:ASP321 2.7 50.3 1.0
CG C:ASP321 2.9 41.6 1.0
O C:HOH700 3.3 64.1 1.0
HD22 C:ASN357 3.4 60.7 1.0
O C:HOH647 3.5 60.8 1.0
ND2 C:ASN357 4.3 60.7 1.0
CB C:ASP321 4.3 34.2 1.0
HB2 C:ASN357 4.4 43.8 1.0
HB3 C:ASP321 4.4 34.2 1.0
O C:HOH632 4.6 36.3 1.0
HD21 C:ASN357 4.7 61.0 1.0
HB2 C:ASP321 4.8 33.4 1.0

Calcium binding site 9 out of 15 in 6frn

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Calcium binding site 9 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca505

b:26.1
occ:1.00
OE2 C:GLU378 2.3 45.6 1.0
O C:HOH786 2.4 47.6 1.0
O C:HOH783 2.9 60.7 1.0
CD C:GLU378 3.1 62.2 1.0
HZ1 C:LYS369 3.4 71.7 1.0
OE1 C:GLU378 3.5 68.8 1.0
O C:HOH766 3.8 46.2 1.0
HG3 C:GLU378 4.1 43.5 1.0
CG C:GLU378 4.2 43.3 1.0
HB1 C:ALA365 4.3 28.0 1.0
NZ C:LYS369 4.4 71.5 1.0
HZ2 C:LYS362 4.4 99.3 1.0
HB2 C:GLU378 4.5 36.0 1.0
HB3 C:ALA365 4.6 29.2 1.0
HG3 C:LYS362 4.6 49.0 1.0
HZ3 C:LYS369 4.6 71.1 1.0
CB C:ALA365 4.8 29.0 1.0
HB2 C:ALA365 4.9 29.4 1.0
HZ2 C:LYS369 4.9 72.0 1.0
HG2 C:GLU378 5.0 42.6 1.0

Calcium binding site 10 out of 15 in 6frn

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Calcium binding site 10 out of 15 in the Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of F420H2 Oxidase (Fpra) Co-Crystallized with 10MM Tb-XO4 and Calcium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca506

b:53.8
occ:1.00
OE1 C:GLU217 2.7 79.6 1.0
OE2 C:GLU217 3.2 88.6 1.0
CD C:GLU217 3.3 92.3 1.0
HD12 C:LEU151 4.2 54.2 1.0
O C:HOH670 4.5 68.2 1.0
HE3 C:LYS213 4.7 89.4 1.0
HD3 C:LYS214 4.7 84.2 1.0
HZ2 C:LYS213 4.8 0.8 1.0
CG C:GLU217 4.8 69.5 1.0
HD11 C:LEU151 4.9 54.9 1.0
HZ1 C:LYS213 4.9 0.1 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 Dec 12 06:07:31 2020

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