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Calcium in PDB 1fwx: Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans

Enzymatic activity of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans

All present enzymatic activity of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans:
1.7.99.6;

Protein crystallography data

The structure of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans, PDB code: 1fwx was solved by K.Brown, K.Djinovic-Carugo, T.Haltia, I.Cabrito, M.Saraste, J.J.Moura, I.Moura, M.Tegoni, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.595, 105.090, 116.696, 90.00, 110.69, 90.00
R / Rfree (%) 24.1 / 26.4

Other elements in 1fwx:

The structure of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans also contains other interesting chemical elements:

Copper (Cu) 24 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans (pdb code 1fwx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans, PDB code: 1fwx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 1fwx

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Calcium binding site 1 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4903

b:21.4
occ:1.00
O A:HOH5018 2.4 23.3 1.0
O A:TYR204 2.4 21.5 1.0
OD2 A:ASP221 2.5 25.7 1.0
O A:MET215 2.5 26.6 1.0
OD1 A:ASN268 2.5 23.5 1.0
OE2 A:GLU207 2.6 23.8 1.0
OE1 A:GLU207 2.6 23.9 1.0
OD1 A:ASP221 2.6 25.8 1.0
CG A:ASP221 2.9 25.9 1.0
CD A:GLU207 2.9 24.0 1.0
CG A:ASN268 3.4 23.6 1.0
C A:TYR204 3.5 21.6 1.0
C A:MET215 3.6 26.6 1.0
ND2 A:ASN268 3.9 23.3 1.0
CA A:THR216 4.1 27.1 1.0
N A:THR216 4.2 26.8 1.0
CA A:ASN205 4.3 22.2 1.0
N A:ASN205 4.3 21.8 1.0
N A:ASN268 4.4 24.6 1.0
N A:SER206 4.4 22.8 1.0
OD1 A:ASN267 4.4 26.9 1.0
CB A:ASP221 4.4 25.9 1.0
CA A:TYR204 4.4 21.4 1.0
CG A:GLU207 4.4 24.1 1.0
CA A:ASN268 4.5 23.9 1.0
O A:ALA218 4.6 29.4 1.0
CB A:ASN268 4.6 23.7 1.0
CA A:MET215 4.6 26.6 1.0
CB A:ALA218 4.6 29.1 1.0
OG A:SER206 4.7 23.1 1.0
C A:THR216 4.8 27.4 1.0
C A:ASN205 4.9 22.4 1.0
N A:ALA218 4.9 28.8 1.0

Calcium binding site 2 out of 11 in 1fwx

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Calcium binding site 2 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4904

b:74.9
occ:1.00
O A:HOH5504 2.6 35.6 1.0
OD1 A:ASP366 3.0 29.0 1.0
OD2 A:ASP366 3.4 29.0 1.0
O A:MET424 3.6 23.4 1.0
CG A:ASP366 3.6 28.9 1.0
O A:LYS367 3.9 26.6 1.0
CD1 A:LEU368 4.4 25.8 1.0
N A:MET424 4.5 24.4 1.0
CB A:LYS423 4.5 25.7 1.0
C A:MET424 4.6 23.4 1.0
C A:LYS367 4.8 26.8 1.0
O A:HOH5086 5.0 27.4 1.0
CB A:LEU368 5.0 25.9 1.0
CA A:LEU368 5.0 26.1 1.0

Calcium binding site 3 out of 11 in 1fwx

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Calcium binding site 3 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4905

b:17.9
occ:1.00
O B:HOH6542 2.3 15.5 1.0
O A:LYS397 2.3 18.4 1.0
O B:HOH6541 2.3 14.4 1.0
OE1 A:GLU412 2.3 18.3 1.0
O A:HOH5615 2.3 20.5 1.0
O A:HOH4981 2.4 16.8 1.0
CD A:GLU412 3.0 17.8 1.0
OE2 A:GLU412 3.0 18.3 1.0
C A:LYS397 3.4 18.5 1.0
OD1 B:ASP523 4.1 18.5 1.0
CA A:LYS397 4.2 18.6 1.0
CD1 B:TRP563 4.2 14.7 1.0
N A:PHE398 4.3 18.4 1.0
O A:LYS410 4.4 14.2 1.0
O B:HOH5828 4.4 15.8 1.0
CG A:GLU412 4.4 17.4 1.0
CA A:PHE398 4.5 18.3 1.0
O B:HOH5887 4.5 16.2 1.0
CD1 A:PHE398 4.5 18.5 1.0
NE1 B:TRP563 4.5 14.5 1.0
O A:PRO411 4.6 15.2 1.0
CB A:LYS397 4.7 18.6 1.0
OE1 A:GLU435 4.7 21.1 1.0
CA A:GLU412 4.7 16.5 1.0
O B:PHE564 4.8 16.4 1.0
O A:HOH5062 4.8 24.9 1.0
O B:ASP523 5.0 17.9 1.0
CB A:GLU412 5.0 16.8 1.0
C A:PRO411 5.0 15.3 1.0
CG B:ASP523 5.0 18.4 1.0

Calcium binding site 4 out of 11 in 1fwx

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Calcium binding site 4 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4903

b:13.8
occ:1.00
O B:TYR204 2.4 14.8 1.0
O B:MET215 2.4 17.5 1.0
O B:HOH6540 2.4 15.4 1.0
OD1 B:ASN268 2.4 15.8 1.0
OE2 B:GLU207 2.4 18.0 1.0
OD2 B:ASP221 2.5 17.8 1.0
OD1 B:ASP221 2.5 17.7 1.0
OE1 B:GLU207 2.6 18.0 1.0
CG B:ASP221 2.8 18.0 1.0
CD B:GLU207 2.9 18.3 1.0
CG B:ASN268 3.4 16.2 1.0
C B:MET215 3.5 17.9 1.0
C B:TYR204 3.5 14.7 1.0
ND2 B:ASN268 3.9 15.8 1.0
CA B:THR216 4.1 17.8 1.0
N B:THR216 4.2 17.8 1.0
CA B:ASN205 4.3 15.9 1.0
N B:ASN205 4.3 15.3 1.0
CB B:ASP221 4.3 18.4 1.0
N B:ASN268 4.4 17.9 1.0
CG B:GLU207 4.4 18.4 1.0
N B:SER206 4.4 16.9 1.0
CA B:ASN268 4.5 16.8 1.0
CA B:TYR204 4.5 14.4 1.0
CA B:MET215 4.5 18.1 1.0
CB B:ASN268 4.5 16.5 1.0
CB B:ALA218 4.7 20.7 1.0
C B:THR216 4.7 18.2 1.0
OG B:SER206 4.7 17.2 1.0
O B:ALA218 4.8 21.1 1.0
C B:ASN205 4.9 16.3 1.0
N B:ALA218 4.9 20.2 1.0
OD1 B:ASN267 4.9 21.9 1.0
N B:ALA217 5.0 18.7 1.0

Calcium binding site 5 out of 11 in 1fwx

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Calcium binding site 5 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4909

b:67.5
occ:1.00
O B:HOH6537 2.1 21.4 1.0
O B:HOH6539 2.2 24.4 1.0
O B:HOH6538 2.4 27.8 1.0
O B:HOH6536 2.4 27.4 1.0
O B:HOH6494 2.9 50.8 1.0
O B:HOH6417 3.8 43.9 1.0
OD2 B:ASP366 4.2 17.5 1.0
O B:MET424 4.2 16.4 1.0
OD1 B:ASP366 4.3 17.1 1.0
O B:LYS367 4.6 15.8 1.0
CG B:ASP366 4.7 17.2 1.0
O B:HOH5964 4.8 21.2 1.0
CD1 B:LEU368 4.8 16.1 1.0
CB B:LYS423 4.9 19.5 1.0

Calcium binding site 6 out of 11 in 1fwx

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Calcium binding site 6 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4905

b:14.6
occ:1.00
O B:HOH6535 2.2 11.0 1.0
O B:LYS397 2.2 12.1 1.0
O B:HOH6534 2.3 14.6 1.0
OE1 B:GLU412 2.3 15.4 1.0
O A:HOH5613 2.3 7.5 1.0
O A:HOH4910 2.3 11.8 1.0
OE2 B:GLU412 2.8 15.2 1.0
CD B:GLU412 2.8 14.6 1.0
C B:LYS397 3.4 12.5 1.0
OD1 A:ASP523 4.2 13.5 1.0
CD1 A:TRP563 4.2 10.4 1.0
CA B:LYS397 4.2 12.6 1.0
N B:PHE398 4.3 12.4 1.0
CG B:GLU412 4.3 13.8 1.0
O A:HOH4907 4.4 10.7 1.0
NE1 A:TRP563 4.4 10.4 1.0
CA B:PHE398 4.4 12.5 1.0
O B:LYS410 4.5 12.0 1.0
O A:HOH4909 4.5 12.9 1.0
CD1 B:PHE398 4.5 12.1 1.0
OE1 B:GLU435 4.6 15.9 1.0
CB B:LYS397 4.7 12.4 1.0
O B:PRO411 4.7 12.1 1.0
O A:PHE564 4.7 11.1 1.0
O B:HOH5973 4.7 20.2 1.0
CA B:GLU412 4.8 12.7 1.0
CB B:GLU412 5.0 13.0 1.0

Calcium binding site 7 out of 11 in 1fwx

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Calcium binding site 7 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4903

b:17.4
occ:1.00
OE1 C:GLU207 2.3 22.8 1.0
O C:TYR204 2.3 20.0 1.0
O C:HOH7448 2.4 22.6 1.0
O C:MET215 2.5 21.5 1.0
OD1 C:ASP221 2.5 23.9 1.0
OD1 C:ASN268 2.5 21.9 1.0
OD2 C:ASP221 2.6 23.9 1.0
OE2 C:GLU207 2.8 22.9 1.0
CD C:GLU207 2.9 23.0 1.0
CG C:ASP221 2.9 24.1 1.0
CG C:ASN268 3.4 22.1 1.0
C C:TYR204 3.5 20.1 1.0
C C:MET215 3.5 22.1 1.0
ND2 C:ASN268 3.9 22.0 1.0
CA C:THR216 4.0 22.2 1.0
N C:THR216 4.2 22.1 1.0
O C:HOH7337 4.3 47.6 1.0
CA C:ASN205 4.3 20.5 1.0
N C:ASN205 4.3 20.3 1.0
CG C:GLU207 4.4 22.7 1.0
N C:ASN268 4.4 23.1 1.0
CB C:ASP221 4.4 24.1 1.0
CA C:TYR204 4.4 19.8 1.0
N C:SER206 4.4 21.1 1.0
CA C:ASN268 4.5 22.6 1.0
CA C:MET215 4.5 22.0 1.0
CB C:ASN268 4.6 22.4 1.0
CB C:ALA218 4.6 25.3 1.0
C C:THR216 4.7 22.6 1.0
O C:ALA218 4.7 25.8 1.0
OG C:SER206 4.8 21.6 1.0
N C:ALA218 4.8 24.6 1.0
OD1 C:ASN267 4.9 25.6 1.0
C C:ASN205 4.9 20.8 1.0
N C:ALA217 5.0 23.0 1.0

Calcium binding site 8 out of 11 in 1fwx

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Calcium binding site 8 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4910

b:66.7
occ:1.00
O C:MET424 2.6 29.5 1.0
OD1 C:ASP366 3.3 32.4 1.0
O C:HOH7238 3.5 37.9 1.0
CD1 C:LEU368 3.6 30.5 1.0
C C:MET424 3.6 29.5 1.0
N C:MET424 3.8 30.0 1.0
OD2 C:ASP366 4.1 32.3 1.0
CG C:ASP366 4.1 32.4 1.0
CA C:MET424 4.1 29.7 1.0
CB C:LEU368 4.3 30.4 1.0
O C:LYS367 4.3 30.9 1.0
CB C:LYS423 4.3 30.9 1.0
C C:LYS423 4.3 30.4 1.0
CB C:MET424 4.3 29.6 1.0
O C:HOH7441 4.4 42.7 1.0
CG C:LEU368 4.5 30.3 1.0
CA C:LYS423 4.7 30.6 1.0
CA C:LEU368 4.7 30.3 1.0
N C:VAL425 4.8 29.1 1.0
CD2 C:LEU368 4.9 30.4 1.0
C C:LYS367 5.0 30.9 1.0

Calcium binding site 9 out of 11 in 1fwx

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Calcium binding site 9 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4905

b:22.1
occ:1.00
O C:HOH7170 2.2 18.8 1.0
OE1 C:GLU412 2.2 22.4 1.0
O C:LYS397 2.2 21.9 1.0
O D:HOH8295 2.2 16.7 1.0
O D:HOH8294 2.4 18.5 1.0
O C:HOH7174 2.4 18.7 1.0
OE2 C:GLU412 2.8 22.9 1.0
CD C:GLU412 2.8 22.3 1.0
C C:LYS397 3.3 22.1 1.0
O D:HOH7809 4.0 23.3 1.0
OD1 D:ASP523 4.1 22.2 1.0
CA C:LYS397 4.2 21.9 1.0
N C:PHE398 4.3 22.4 1.0
CD1 D:TRP563 4.3 17.6 1.0
CG C:GLU412 4.3 22.0 1.0
O D:HOH7803 4.3 18.7 1.0
CA C:PHE398 4.4 22.7 1.0
O C:LYS410 4.4 20.5 1.0
CD1 C:PHE398 4.5 22.7 1.0
CB C:LYS397 4.6 21.8 1.0
NE1 D:TRP563 4.6 17.7 1.0
O C:PRO411 4.7 20.8 1.0
CA C:GLU412 4.7 21.4 1.0
O D:PHE564 4.8 18.7 1.0
OE1 C:GLU435 4.8 22.9 1.0
CB C:GLU412 4.9 21.5 1.0
CG D:ASP523 5.0 22.4 1.0
O D:ASP523 5.0 22.0 1.0
O C:HOH6915 5.0 27.6 1.0
CE1 C:PHE398 5.0 22.7 1.0
C C:PRO411 5.0 21.0 1.0

Calcium binding site 10 out of 11 in 1fwx

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Calcium binding site 10 out of 11 in the Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Nitrous Oxide Reductase From P. Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca4903

b:36.6
occ:1.00
O D:TYR204 2.3 32.1 0.8
O D:MET215 2.4 36.7 1.1
OE1 D:GLU207 2.5 32.8 0.5
OD1 D:ASN268 2.5 35.6 1.3
OE2 D:GLU207 2.5 32.7 0.8
OD1 D:ASP221 2.5 37.1 1.1
OD2 D:ASP221 2.5 37.1 0.7
CD D:GLU207 2.8 32.8 1.1
CG D:ASP221 2.9 37.1 1.2
C D:TYR204 3.4 32.2 1.0
CG D:ASN268 3.4 35.6 0.4
C D:MET215 3.5 36.7 0.8
ND2 D:ASN268 3.9 35.6 0.5
CA D:THR216 4.2 36.8 1.0
CA D:ASN205 4.2 32.5 0.5
N D:ASN205 4.2 32.3 0.4
N D:ASN268 4.2 35.9 0.9
N D:THR216 4.2 36.7 1.6
CG D:GLU207 4.3 33.0 0.8
CA D:TYR204 4.4 32.1 1.0
N D:SER206 4.4 32.8 1.3
CB D:ASP221 4.4 37.2 0.8
CA D:ASN268 4.5 35.6 0.7
CA D:MET215 4.5 36.6 0.7
CB D:ASN268 4.5 35.6 0.6
CB D:ALA218 4.6 37.1 1.0
OG D:SER206 4.7 32.6 0.9
O D:ALA218 4.7 37.1 0.5
C D:ASN205 4.8 32.6 0.8
C D:THR216 4.9 36.8 0.9
N D:ALA218 5.0 37.0 0.6

Reference:

K.Brown, K.Djinovic-Carugo, T.Haltia, I.Cabrito, M.Saraste, J.J.Moura, I.Moura, M.Tegoni, C.Cambillau. Revisiting the Catalytic Cuz Cluster of Nitrous Oxide (N2O) Reductase. Evidence of A Bridging Inorganic Sulfur J.Biol.Chem. V. 275 41133 2000.
ISSN: ISSN 0021-9258
PubMed: 11024061
DOI: 10.1074/JBC.M008617200
Page generated: Sat Dec 12 02:56:19 2020

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