Calcium in PDB 5c2v: Kuenenia Stuttgartiensis Hydrazine Synthase

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase, PDB code: 5c2v was solved by A.Dietl, C.Ferousi, W.J.Maalcke, A.Menzel, S.De Vries, J.T.Keltjens, M.S.M.Jetten, B.Kartal, T.R.M.Barends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	464.540, 464.540, 145.750, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 27.1

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms
Iron	(Fe)	8 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Kuenenia Stuttgartiensis Hydrazine Synthase (pdb code 5c2v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Kuenenia Stuttgartiensis Hydrazine Synthase, PDB code: 5c2v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:59.3 occ:1.00 O A:ILE797 2.2 68.2 1.0 OD2 A:ASP801 2.4 61.4 1.0 O A:GLY799 2.4 75.8 1.0 OD2 A:ASP795 2.4 77.2 1.0 O A:HOH1041 2.4 63.4 1.0 O A:HOH1004 2.4 68.2 1.0 OD1 A:ASP795 2.5 55.6 1.0 CG A:ASP795 2.6 62.1 1.0 C A:ILE797 3.5 50.9 1.0 C A:GLY799 3.5 78.0 1.0 CG A:ASP801 3.5 73.5 1.0 O A:HOH1119 3.9 60.7 1.0 CB A:ASP795 4.0 58.0 1.0 N A:GLY799 4.0 65.5 1.0 NE2 A:GLN529 4.1 59.4 1.0 C A:PRO798 4.1 53.8 1.0 OD1 A:ASN522 4.2 66.3 1.0 O A:HOH1065 4.2 71.7 1.0 N A:ASP801 4.3 63.8 1.0 OD1 A:ASP801 4.3 73.3 1.0 CA A:GLY799 4.4 64.2 1.0 CA A:ILE797 4.4 53.1 1.0 N A:PRO800 4.4 76.4 1.0 N A:PRO798 4.4 65.3 1.0 CB A:ILE797 4.4 51.3 1.0 O A:PRO798 4.5 53.6 1.0 CA A:PRO800 4.5 68.7 1.0 CB A:ASP801 4.5 62.7 1.0 CA A:PRO798 4.5 48.8 1.0 C A:PRO800 4.6 66.4 1.0 N A:ILE797 4.6 59.4 1.0 NH2 A:ARG674 4.6 63.8 1.0 OE2 A:GLU499 4.7 60.5 1.0 NH1 A:ARG674 4.7 53.2 1.0 CG2 A:ILE797 4.8 45.3 1.0

Calcium binding site 2 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:68.9 occ:1.00 O A:PHE385 2.3 63.5 1.0 OD2 A:ASP403 2.4 87.4 1.0 OD2 A:ASP409 2.4 62.6 1.0 O A:ASP404 2.5 72.7 1.0 OD1 A:ASP403 2.5 94.7 1.0 O A:TRP407 2.6 44.1 1.0 CG A:ASP403 2.6 83.0 1.0 CG A:ASP409 3.3 65.2 1.0 C A:PHE385 3.4 65.2 1.0 OD2 A:ASP384 3.5 73.8 1.0 C A:ASP404 3.6 78.3 1.0 N A:ASP404 3.8 75.7 1.0 C A:TRP407 3.8 56.1 1.0 N A:ASP409 3.9 75.1 1.0 CB A:ASP403 3.9 84.3 1.0 OD1 A:ASP409 4.0 60.4 1.0 CB A:ASP409 4.1 78.3 1.0 CA A:ASP403 4.1 83.0 1.0 CA A:GLY386 4.2 80.2 1.0 N A:GLY386 4.2 81.0 1.0 C A:ASP403 4.3 84.4 1.0 N A:PHE385 4.3 79.2 1.0 CA A:ASN408 4.3 74.3 1.0 CA A:ASP404 4.3 74.4 1.0 CG A:ASP384 4.4 92.6 1.0 CA A:PHE385 4.5 72.6 1.0 C A:ASP384 4.5 77.8 1.0 N A:ASN408 4.5 61.5 1.0 C A:ASN408 4.6 76.9 1.0 N A:PRO405 4.6 81.5 1.0 O A:ASP384 4.6 85.3 1.0 CA A:ASP409 4.6 66.3 1.0 CA A:PRO405 4.8 80.8 1.0 OD1 A:ASN408 4.8 52.5 1.0 CB A:ASP384 4.9 89.4 1.0 CA A:TRP407 4.9 64.2 1.0 N A:TRP407 5.0 75.5 1.0

Calcium binding site 3 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:68.6 occ:1.00 OD2 B:ASP111 2.3 78.6 1.0 O B:HOH501 2.4 88.1 1.0 O B:HOH528 2.4 74.8 1.0 O B:HOH559 2.4 70.0 1.0 O B:HOH552 2.4 55.5 1.0 OD1 B:ASP111 2.5 98.6 1.0 OD1 B:ASP131 2.5 85.5 1.0 OD2 B:ASP131 2.5 89.6 1.0 CG B:ASP131 2.6 58.0 1.0 CG B:ASP111 2.7 70.7 1.0 N B:TRP132 3.7 67.9 1.0 CB B:ASP131 3.7 55.1 1.0 CA B:ASP131 3.9 61.4 1.0 CB B:ASP111 4.2 54.2 1.0 C B:ASP131 4.2 63.2 1.0 O B:ALA108 4.3 64.7 1.0 CA B:TRP132 4.6 62.1 1.0 O B:GLU109 4.8 63.3 1.0 CB B:TRP132 4.8 42.3 1.0 CA B:ASP111 4.8 64.6 1.0

Calcium binding site 4 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:54.6 occ:1.00 ND2 C:ASN129 2.1 83.4 1.0 O C:HOH502 2.4 74.9 1.0 O C:HOH568 2.4 57.4 1.0 OD1 C:ASN129 2.6 83.4 1.0 OG C:SER306 2.6 86.7 1.0 CG C:ASN129 2.7 54.1 1.0 O C:THR308 2.9 84.5 1.0 O C:GLY307 2.9 85.1 1.0 O C:HOH504 3.0 52.5 1.0 C C:THR308 3.8 35.6 1.0 CB C:SER306 3.9 65.3 1.0 C C:GLY307 3.9 69.8 1.0 O C:THR130 4.0 53.5 1.0 CB C:ASN129 4.1 64.8 1.0 N C:TYR309 4.4 41.2 1.0 CA C:TYR309 4.4 72.3 1.0 N C:GLY307 4.4 99.7 1.0 C C:SER306 4.4 52.7 1.0 CA C:SER306 4.5 58.5 1.0 N C:THR308 4.6 63.0 1.0 O C:HOH554 4.7 53.0 1.0 CA C:THR308 4.7 51.9 1.0 CA C:GLY307 4.8 69.2 1.0 O C:PHE310 4.8 68.8 1.0 O C:SER306 4.9 53.3 1.0 O2A C:HEC405 5.0 55.2 1.0

Calcium binding site 5 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:59.5 occ:1.00 O C:PRO141 2.3 38.9 1.0 O C:HOH509 2.4 67.7 1.0 OD2 C:ASP296 2.4 70.6 1.0 O C:HOH565 2.4 54.2 1.0 O C:HOH572 2.4 81.8 1.0 O C:LEU139 2.5 76.8 1.0 CG C:ASP296 3.2 60.4 1.0 OD1 C:ASP296 3.3 61.0 1.0 C C:LEU139 3.5 59.5 1.0 C C:PRO141 3.6 55.8 1.0 C C:PRO140 4.0 51.3 1.0 CB C:LEU139 4.1 46.7 1.0 N C:PRO141 4.1 58.1 1.0 CA C:PRO140 4.2 64.9 1.0 N C:PRO140 4.3 74.8 1.0 O C:PRO140 4.3 63.4 1.0 CA C:LEU139 4.4 46.7 1.0 N C:PHE142 4.5 65.3 1.0 O C:THR297 4.5 57.3 1.0 CA C:PHE142 4.5 67.8 1.0 CA C:PRO141 4.5 55.8 1.0 CB C:ASP296 4.6 44.9 1.0 CD C:PRO141 4.7 51.5 1.0 O C:HOH571 4.8 43.7 1.0

Calcium binding site 6 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:48.4 occ:1.00 OD1 C:ASP118 2.3 63.5 1.0 O C:SER126 2.4 38.0 1.0 O C:HOH501 2.4 55.3 1.0 O C:LEU119 2.4 48.2 1.0 O C:GLY123 2.8 60.3 1.0 OG C:SER126 2.8 42.3 1.0 OE2 C:GLU122 2.9 78.1 1.0 CG C:GLU122 2.9 40.8 1.0 N C:LEU119 3.1 45.0 1.0 CD C:GLU122 3.3 61.2 1.0 C C:LEU119 3.4 34.1 1.0 C C:SER126 3.5 55.6 1.0 CG C:ASP118 3.5 40.2 1.0 C C:ASP118 3.7 34.0 1.0 CA C:LEU119 3.7 37.8 1.0 CA C:ASP118 3.8 31.9 1.0 CB C:SER126 3.9 42.1 1.0 C C:GLY123 4.0 53.0 1.0 CA C:SER126 4.1 45.5 1.0 N C:SER126 4.2 54.5 1.0 CB C:ASP118 4.3 31.7 1.0 CB C:GLU122 4.3 55.3 1.0 CB C:LEU119 4.3 51.6 1.0 OD2 C:ASP118 4.4 49.6 1.0 OE1 C:GLU122 4.4 75.6 1.0 N C:GLY123 4.5 52.4 1.0 O C:ASP118 4.6 50.9 1.0 N C:TRP127 4.6 34.4 1.0 C C:GLU122 4.6 35.9 1.0 N C:GLY120 4.6 30.7 1.0 CA C:TRP124 4.8 52.0 1.0 N C:TRP124 4.8 39.2 1.0 CA C:GLU122 4.8 47.2 1.0 CA C:GLY123 4.9 52.0 1.0 N C:GLU122 4.9 53.0 1.0 CA C:TRP127 4.9 38.7 1.0 O C:TRP117 5.0 49.8 1.0

Calcium binding site 7 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:68.5 occ:1.00 O D:ILE797 2.0 72.6 1.0 O D:GLY799 2.3 66.4 1.0 OD2 D:ASP801 2.3 52.6 1.0 OD1 D:ASP795 2.3 70.0 1.0 O D:HOH1025 2.4 57.0 1.0 O D:HOH1001 2.4 62.8 1.0 CG D:ASP795 2.9 75.0 1.0 OD2 D:ASP795 3.0 90.4 1.0 C D:ILE797 3.3 60.6 1.0 C D:GLY799 3.5 56.3 1.0 CG D:ASP801 3.5 73.2 1.0 NE2 D:GLN529 4.0 52.0 1.0 N D:GLY799 4.0 60.7 1.0 O D:HOH1091 4.0 53.2 1.0 C D:PRO798 4.1 55.9 1.0 CA D:ILE797 4.1 45.5 1.0 CB D:ILE797 4.1 55.8 1.0 CB D:ASP795 4.2 70.1 1.0 OD1 D:ASP801 4.2 66.5 1.0 N D:PRO798 4.2 50.1 1.0 CA D:GLY799 4.3 55.5 1.0 N D:ILE797 4.3 75.2 1.0 N D:ASP801 4.3 57.4 1.0 CA D:PRO798 4.4 56.7 1.0 OD1 D:ASN522 4.4 55.2 1.0 N D:PRO800 4.4 54.0 1.0 O D:PRO798 4.4 67.7 1.0 CB D:ASP801 4.5 52.1 1.0 CA D:PRO800 4.5 60.1 1.0 NH2 D:ARG674 4.5 71.0 1.0 C D:PRO800 4.6 48.3 1.0 CG2 D:ILE797 4.6 58.6 1.0 OE2 D:GLU499 4.7 46.1 1.0 NH1 D:ARG674 4.8 71.7 1.0 O D:HOH1043 4.9 66.3 1.0

Calcium binding site 8 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:65.9 occ:1.00 O D:TRP407 2.2 53.0 1.0 O D:ASP404 2.3 67.2 1.0 O D:PHE385 2.4 75.4 1.0 OD2 D:ASP403 2.4 67.0 1.0 OD2 D:ASP409 2.4 66.7 1.0 OD2 D:ASP384 3.2 84.9 1.0 OD1 D:ASP384 3.2 82.1 1.0 C D:ASP404 3.3 86.4 1.0 CG D:ASP409 3.3 65.8 1.0 CG D:ASP384 3.4 80.1 1.0 C D:TRP407 3.4 67.2 1.0 N D:ASP404 3.5 72.0 1.0 C D:PHE385 3.5 82.0 1.0 CG D:ASP403 3.6 75.9 1.0 CA D:ASP404 4.0 79.1 1.0 N D:ASP409 4.0 78.0 1.0 OD1 D:ASP409 4.1 81.5 1.0 CB D:ASP409 4.2 63.3 1.0 C D:ASP403 4.2 79.7 1.0 N D:PHE385 4.3 58.4 1.0 CA D:GLY386 4.3 77.5 1.0 N D:GLY386 4.3 81.2 1.0 CA D:ASN408 4.3 74.4 1.0 CA D:ASP403 4.3 81.2 1.0 N D:ASN408 4.3 68.4 1.0 N D:TRP407 4.4 71.3 1.0 N D:PRO405 4.4 86.3 1.0 CA D:TRP407 4.4 64.4 1.0 OD1 D:ASP403 4.4 71.0 1.0 CA D:PHE385 4.5 83.8 1.0 C D:ASP384 4.5 72.6 1.0 C D:ASN408 4.5 73.4 1.0 CB D:ASP404 4.6 74.4 1.0 CB D:ASP403 4.6 88.3 1.0 CB D:ASP384 4.6 88.4 1.0 CA D:PRO405 4.7 71.5 1.0 CA D:ASP409 4.7 72.0 1.0 O D:ASP384 4.8 75.2 1.0 CB D:TRP407 4.9 77.3 1.0 C D:PRO405 5.0 72.7 1.0 CA D:ASP384 5.0 92.4 1.0

Calcium binding site 9 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca402 b:76.4 occ:1.00 OD1 E:ASP131 2.3 96.1 1.0 OD2 E:ASP111 2.4 67.3 1.0 O E:HOH522 2.4 73.8 1.0 O E:HOH504 2.4 59.5 1.0 CG E:ASP131 2.4 87.5 1.0 O E:HOH509 2.4 81.3 1.0 O E:HOH505 2.4 71.1 1.0 OD2 E:ASP131 2.4 99.2 1.0 OD1 E:ASP111 2.4 77.9 1.0 CG E:ASP111 2.7 76.0 1.0 CB E:ASP131 3.5 66.3 1.0 CA E:ASP131 3.7 75.5 1.0 N E:TRP132 3.8 84.4 1.0 CB E:ASP111 4.2 54.0 1.0 C E:ASP131 4.3 81.2 1.0 O E:ALA108 4.4 61.1 1.0 O E:GLU109 4.7 71.5 1.0 CA E:TRP132 4.8 81.5 1.0 CB F:PRO199 4.9 80.9 1.0 N E:ASP131 5.0 73.7 1.0

Calcium binding site 10 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Kuenenia Stuttgartiensis Hydrazine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:79.9 occ:1.00 ND2 F:ASN129 1.9 85.8 1.0 O F:HOH512 2.4 78.8 1.0 O F:THR308 2.4 81.1 1.0 OG F:SER306 2.5 88.7 1.0 CG F:ASN129 2.6 78.2 1.0 OD1 F:ASN129 2.6 97.4 1.0 O F:HOH501 3.0 56.1 1.0 C F:THR308 3.6 63.7 1.0 O F:THR130 3.9 79.2 1.0 CB F:SER306 3.9 79.5 1.0 N F:THR308 3.9 70.8 1.0 CB F:ASN129 4.0 73.8 1.0 O F:HOH506 4.2 79.9 1.0 N F:GLY307 4.2 0.4 1.0 CA F:THR308 4.4 74.9 1.0 C F:SER306 4.4 75.4 1.0 CA F:SER306 4.5 84.7 1.0 N F:TYR309 4.6 58.6 1.0 CA F:TYR309 4.7 72.3 1.0 O F:HOH531 4.8 61.5 1.0 C F:GLY307 4.9 74.8 1.0 C F:THR130 4.9 77.8 1.0 O F:PHE310 4.9 72.7 1.0 CA F:GLY307 5.0 72.6 1.0

A.Dietl, C.Ferousi, W.J.Maalcke, A.Menzel, S.De Vries, J.T.Keltjens, M.S.Jetten, B.Kartal, T.R.Barends. The Inner Workings of the Hydrazine Synthase Multiprotein Complex. Nature V. 527 394 2015.
ISSN: ESSN 1476-4687
PubMed: 26479033
DOI: 10.1038/NATURE15517