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Calcium in PDB 5c2w: Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon

Protein crystallography data

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon, PDB code: 5c2w 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) 48.50 / 3.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 464.120, 464.120, 145.450, 90.00, 90.00, 120.00
R / Rfree (%) 23.1 / 26.7

Other elements in 5c2w:

The structure of Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Xenon (Xe) 4 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 8 atoms
Chlorine (Cl) 3 atoms

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon (pdb code 5c2w). 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 Pressurized with 20 Bar Xenon, PDB code: 5c2w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 5c2w

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Calcium binding site 1 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:75.3
occ:1.00
O A:GLY799 2.3 84.7 1.0
O A:ILE797 2.3 66.5 1.0
OD2 A:ASP801 2.3 65.5 1.0
O A:HOH1016 2.4 81.0 1.0
OD2 A:ASP795 2.4 79.5 1.0
O A:HOH1046 2.4 65.2 1.0
OD1 A:ASP795 2.5 75.5 1.0
CG A:ASP795 2.6 70.6 1.0
C A:GLY799 3.5 79.2 1.0
CG A:ASP801 3.5 69.8 1.0
C A:ILE797 3.6 63.0 1.0
CB A:ASP795 4.0 68.4 1.0
O A:HOH1113 4.0 70.3 1.0
N A:GLY799 4.0 66.8 1.0
O A:HOH1084 4.1 80.0 1.0
NE2 A:GLN529 4.1 60.0 1.0
C A:PRO798 4.2 63.6 1.0
OD1 A:ASN522 4.2 58.0 1.0
N A:ASP801 4.3 67.7 1.0
OD1 A:ASP801 4.3 78.4 1.0
CA A:GLY799 4.3 70.2 1.0
N A:PRO800 4.3 72.8 1.0
CA A:PRO800 4.4 65.5 1.0
CB A:ASP801 4.5 68.0 1.0
CA A:ILE797 4.5 57.1 1.0
N A:PRO798 4.5 70.1 1.0
CB A:ILE797 4.5 49.3 1.0
O A:PRO798 4.5 60.0 1.0
CA A:PRO798 4.6 55.5 1.0
C A:PRO800 4.6 66.5 1.0
NH2 A:ARG674 4.6 72.9 1.0
N A:ILE797 4.7 59.4 1.0
NH1 A:ARG674 4.7 64.8 1.0
OE2 A:GLU499 4.7 72.8 1.0
CG2 A:ILE797 4.9 54.3 1.0

Calcium binding site 2 out of 12 in 5c2w

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Calcium binding site 2 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:80.4
occ:1.00
O A:PHE385 2.4 81.9 1.0
OD2 A:ASP403 2.4 98.8 1.0
OD2 A:ASP409 2.4 84.7 1.0
O A:ASP404 2.5 74.5 1.0
OD1 A:ASP403 2.5 95.7 1.0
O A:TRP407 2.6 51.6 1.0
CG A:ASP403 2.6 94.9 1.0
CG A:ASP409 3.3 79.1 1.0
C A:PHE385 3.6 83.5 1.0
C A:ASP404 3.6 76.8 1.0
C A:TRP407 3.8 65.5 1.0
N A:ASP404 3.8 98.5 1.0
N A:ASP409 3.9 73.6 1.0
CB A:ASP403 3.9 88.3 1.0
OD1 A:ASP409 4.0 69.5 1.0
CB A:ASP409 4.1 79.8 1.0
CA A:ASP403 4.2 93.2 1.0
CA A:GLY386 4.2 86.0 1.0
OD2 A:ASP384 4.3 84.7 1.0
CA A:ASN408 4.3 78.7 1.0
N A:GLY386 4.3 84.8 1.0
C A:ASP403 4.3 95.1 1.0
CA A:ASP404 4.3 83.3 1.0
N A:PHE385 4.4 81.5 1.0
N A:ASN408 4.5 76.3 1.0
C A:ASN408 4.6 81.7 1.0
CB A:ASP384 4.6 97.3 1.0
N A:PRO405 4.6 92.0 1.0
C A:ASP384 4.6 90.9 1.0
CA A:PHE385 4.6 81.3 1.0
CA A:ASP409 4.7 71.7 1.0
CG A:ASP384 4.7 0.7 1.0
CA A:PRO405 4.8 86.9 1.0
O A:ASP384 4.8 95.3 1.0
OD1 A:ASN408 4.8 75.2 1.0
CA A:TRP407 4.8 69.5 1.0
N A:TRP407 4.9 74.4 1.0

Calcium binding site 3 out of 12 in 5c2w

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Calcium binding site 3 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:68.8
occ:1.00
OD2 B:ASP111 2.3 84.6 1.0
O B:HOH501 2.3 85.0 1.0
O B:HOH548 2.4 72.8 1.0
O B:HOH559 2.4 83.1 1.0
O B:HOH553 2.4 58.9 1.0
OD1 B:ASP111 2.5 98.5 1.0
OD1 B:ASP131 2.5 94.2 1.0
OD2 B:ASP131 2.5 89.0 1.0
CG B:ASP131 2.6 83.0 1.0
CG B:ASP111 2.7 76.7 1.0
CB B:ASP131 3.7 69.0 1.0
N B:TRP132 3.7 71.1 1.0
CA B:ASP131 3.9 71.5 1.0
CB B:ASP111 4.2 69.9 1.0
O B:ALA108 4.2 82.6 1.0
C B:ASP131 4.3 69.9 1.0
CA B:TRP132 4.6 70.9 1.0
CB B:TRP132 4.8 63.1 1.0
CA B:ASP111 4.8 69.3 1.0
O B:GLU109 4.9 79.4 1.0

Calcium binding site 4 out of 12 in 5c2w

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Calcium binding site 4 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:57.0
occ:1.00
O C:HOH553 2.4 64.1 1.0
O C:HOH501 2.4 77.9 1.0
ND2 C:ASN129 2.4 67.2 1.0
OD1 C:ASN129 2.5 97.3 1.0
OG C:SER306 2.5 78.7 1.0
O C:THR308 2.7 77.2 1.0
CG C:ASN129 2.7 78.3 1.0
O C:HOH505 2.9 58.9 1.0
O C:GLY307 2.9 70.9 1.0
C C:THR308 3.7 65.5 1.0
CB C:SER306 3.8 62.2 1.0
C C:GLY307 4.0 80.1 1.0
O C:THR130 4.0 65.3 1.0
CB C:ASN129 4.2 62.8 1.0
CA C:TYR309 4.3 74.0 1.0
N C:TYR309 4.3 60.0 1.0
N C:GLY307 4.4 95.4 1.0
CA C:SER306 4.4 65.7 1.0
C C:SER306 4.5 79.1 1.0
CA C:THR308 4.6 68.8 1.0
O C:HOH561 4.6 62.2 1.0
N C:THR308 4.7 84.3 1.0
O C:PHE310 4.9 73.7 1.0
CA C:GLY307 4.9 92.8 1.0
CB C:THR308 4.9 75.0 1.0
C C:TYR309 4.9 67.7 1.0

Calcium binding site 5 out of 12 in 5c2w

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Calcium binding site 5 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:70.1
occ:1.00
O C:PRO141 2.3 59.1 1.0
O C:HOH576 2.4 75.6 1.0
OD2 C:ASP296 2.4 72.5 1.0
O C:HOH507 2.4 70.7 1.0
O C:HOH559 2.4 60.1 1.0
O C:LEU139 2.5 78.2 1.0
CG C:ASP296 3.1 66.9 1.0
OD1 C:ASP296 3.2 76.2 1.0
C C:PRO141 3.5 72.2 1.0
C C:LEU139 3.5 65.4 1.0
C C:PRO140 4.0 64.0 1.0
N C:PRO141 4.1 63.6 1.0
CB C:LEU139 4.1 56.7 1.0
CA C:PRO140 4.2 62.4 1.0
N C:PRO140 4.3 70.9 1.0
O C:PRO140 4.3 76.7 1.0
CA C:PRO141 4.4 61.6 1.0
N C:PHE142 4.4 71.0 1.0
CA C:PHE142 4.5 77.6 1.0
CA C:LEU139 4.5 57.1 1.0
O C:THR297 4.5 67.3 1.0
CB C:ASP296 4.5 48.4 1.0
CD C:PRO141 4.7 64.4 1.0
O C:HOH570 4.8 51.8 1.0

Calcium binding site 6 out of 12 in 5c2w

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Calcium binding site 6 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:54.1
occ:1.00
OD1 C:ASP118 2.3 54.9 1.0
O C:SER126 2.4 33.1 1.0
O C:LEU119 2.4 39.2 1.0
O C:HOH502 2.4 73.8 1.0
O C:GLY123 2.6 58.4 1.0
OG C:SER126 2.7 46.0 1.0
OE2 C:GLU122 2.9 86.6 1.0
CG C:GLU122 2.9 47.5 1.0
N C:LEU119 3.1 46.8 1.0
CD C:GLU122 3.3 76.3 1.0
C C:LEU119 3.4 42.8 1.0
C C:SER126 3.5 44.1 1.0
CG C:ASP118 3.5 40.8 1.0
C C:ASP118 3.7 40.2 1.0
CA C:LEU119 3.7 44.4 1.0
C C:GLY123 3.8 61.8 1.0
CB C:SER126 3.9 53.8 1.0
CA C:ASP118 3.9 46.1 1.0
CA C:SER126 4.1 42.8 1.0
N C:SER126 4.2 43.6 1.0
CB C:ASP118 4.3 45.6 1.0
CB C:LEU119 4.3 50.2 1.0
CB C:GLU122 4.3 44.5 1.0
N C:GLY123 4.4 57.0 1.0
OD2 C:ASP118 4.4 41.0 1.0
OE1 C:GLU122 4.5 82.8 1.0
C C:GLU122 4.5 43.7 1.0
O C:ASP118 4.6 41.9 1.0
N C:GLY120 4.6 36.1 1.0
N C:TRP127 4.6 53.0 1.0
CA C:GLY123 4.7 56.0 1.0
N C:TRP124 4.7 49.5 1.0
CA C:TRP124 4.7 51.2 1.0
CA C:GLU122 4.8 52.0 1.0
N C:GLU122 4.9 37.7 1.0
O C:GLU122 4.9 39.2 1.0
CA C:TRP127 5.0 48.4 1.0

Calcium binding site 7 out of 12 in 5c2w

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Calcium binding site 7 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca904

b:70.8
occ:1.00
O D:ILE797 2.0 73.8 1.0
O D:GLY799 2.3 72.3 1.0
OD2 D:ASP801 2.3 64.9 1.0
OD1 D:ASP795 2.4 70.6 1.0
O D:HOH1001 2.4 81.5 1.0
O D:HOH1022 2.4 58.8 1.0
CG D:ASP795 2.9 80.1 1.0
OD2 D:ASP795 3.0 93.0 1.0
C D:ILE797 3.2 60.0 1.0
C D:GLY799 3.5 66.4 1.0
CG D:ASP801 3.5 69.4 1.0
NE2 D:GLN529 3.9 58.2 1.0
N D:GLY799 4.0 58.8 1.0
O D:HOH1086 4.0 48.4 1.0
C D:PRO798 4.0 65.9 1.0
CA D:ILE797 4.1 61.2 1.0
CB D:ILE797 4.1 61.1 1.0
OD1 D:ASP801 4.2 70.6 1.0
N D:PRO798 4.2 60.9 1.0
CB D:ASP795 4.3 74.2 1.0
N D:ILE797 4.3 80.7 1.0
CA D:GLY799 4.3 55.6 1.0
N D:ASP801 4.4 68.4 1.0
O D:PRO798 4.4 70.5 1.0
CA D:PRO798 4.4 66.8 1.0
N D:PRO800 4.4 64.2 1.0
OD1 D:ASN522 4.5 65.5 1.0
CB D:ASP801 4.5 63.5 1.0
NH2 D:ARG674 4.5 64.5 1.0
CA D:PRO800 4.5 63.0 1.0
C D:PRO800 4.6 57.4 1.0
CG2 D:ILE797 4.7 65.0 1.0
OE2 D:GLU499 4.8 57.6 1.0
NH1 D:ARG674 4.8 69.5 1.0
O D:HOH1045 4.9 75.1 1.0

Calcium binding site 8 out of 12 in 5c2w

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Calcium binding site 8 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca905

b:84.4
occ:1.00
O D:TRP407 2.2 78.6 1.0
O D:ASP404 2.3 90.0 1.0
O D:PHE385 2.3 95.9 1.0
OD2 D:ASP403 2.4 81.1 1.0
OD2 D:ASP409 2.5 93.6 1.0
OD1 D:ASP384 3.3 90.6 1.0
C D:ASP404 3.3 97.0 1.0
CG D:ASP409 3.4 94.4 1.0
OD2 D:ASP384 3.4 99.7 1.0
C D:PHE385 3.4 98.7 1.0
C D:TRP407 3.4 86.4 1.0
N D:ASP404 3.5 82.5 1.0
CG D:ASP384 3.6 92.3 1.0
CG D:ASP403 3.6 88.1 1.0
CA D:ASP404 3.9 89.7 1.0
N D:ASP409 4.0 94.7 1.0
OD1 D:ASP409 4.1 93.9 1.0
C D:ASP403 4.2 95.2 1.0
CB D:ASP409 4.2 88.4 1.0
CA D:GLY386 4.2 85.9 1.0
N D:GLY386 4.2 92.9 1.0
N D:PHE385 4.2 79.1 1.0
CA D:ASN408 4.3 93.0 1.0
N D:ASN408 4.3 91.1 1.0
CA D:ASP403 4.3 0.8 1.0
N D:PRO405 4.4 96.3 1.0
N D:TRP407 4.4 85.6 1.0
CA D:TRP407 4.4 88.9 1.0
CA D:PHE385 4.4 89.1 1.0
OD1 D:ASP403 4.4 95.2 1.0
C D:ASP384 4.5 89.0 1.0
CB D:ASP404 4.5 86.9 1.0
C D:ASN408 4.5 87.4 1.0
CB D:ASP403 4.6 0.1 1.0
CA D:PRO405 4.7 86.7 1.0
O D:ASP384 4.7 82.6 1.0
CA D:ASP409 4.8 90.2 1.0
CB D:ASP384 4.8 98.0 1.0
CB D:TRP407 4.9 91.7 1.0
C D:PRO405 4.9 87.8 1.0

Calcium binding site 9 out of 12 in 5c2w

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Calcium binding site 9 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:90.1
occ:1.00
OD1 E:ASP131 2.3 1.0 1.0
OD2 E:ASP111 2.4 79.9 1.0
CG E:ASP131 2.4 1.0 1.0
O E:HOH511 2.4 60.9 1.0
O E:HOH502 2.4 93.8 1.0
OD2 E:ASP131 2.4 0.2 1.0
O E:HOH510 2.4 72.3 1.0
O E:HOH504 2.4 95.3 1.0
OD1 E:ASP111 2.4 91.1 1.0
CG E:ASP111 2.7 90.5 1.0
CB E:ASP131 3.4 86.7 1.0
CA E:ASP131 3.7 90.3 1.0
N E:TRP132 3.9 91.4 1.0
CB E:ASP111 4.2 89.6 1.0
C E:ASP131 4.4 87.9 1.0
O E:GLU109 4.4 90.7 1.0
O E:ALA108 4.5 88.6 1.0
CB F:PRO199 4.7 0.7 1.0
CA E:GLU109 4.8 0.2 1.0
C E:GLU109 4.9 94.9 1.0
CA E:TRP132 4.9 92.2 1.0
N E:ASP131 5.0 89.6 1.0

Calcium binding site 10 out of 12 in 5c2w

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Calcium binding site 10 out of 12 in the Kuenenia Stuttgartiensis Hydrazine Synthase Pressurized with 20 Bar Xenon


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 Pressurized with 20 Bar Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:91.7
occ:1.00
O F:THR308 2.3 97.3 1.0
O F:HOH519 2.4 0.5 1.0
OG F:SER306 2.4 93.6 1.0
OD1 F:ASN129 2.5 0.8 1.0
ND2 F:ASN129 2.6 85.4 1.0
CG F:ASN129 2.8 98.9 1.0
O F:HOH507 2.9 71.6 1.0
C F:THR308 3.5 97.7 1.0
N F:THR308 3.7 86.7 1.0
CB F:SER306 3.8 81.5 1.0
O F:THR130 3.8 93.2 1.0
N F:GLY307 4.0 0.2 1.0
CA F:THR308 4.2 99.1 1.0
O F:HOH506 4.2 93.2 1.0
CB F:ASN129 4.2 85.0 1.0
CA F:SER306 4.3 83.9 1.0
C F:SER306 4.3 0.1 1.0
N F:TYR309 4.5 91.5 1.0
CG2 F:THR112 4.6 76.6 1.0
C F:GLY307 4.6 97.4 1.0
CA F:TYR309 4.7 91.7 1.0
OG1 F:THR112 4.7 73.0 1.0
CA F:GLY307 4.7 93.3 1.0
O F:HOH539 4.8 80.3 1.0
C F:THR130 4.9 91.3 1.0
CB F:THR308 5.0 93.7 1.0

Reference:

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
Page generated: Sat Dec 12 05:19:11 2020

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