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Calcium in PDB 9f8x: Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase

Enzymatic activity of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase

All present enzymatic activity of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase:
1.7.2.4;

Protein crystallography data

The structure of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase, PDB code: 9f8x was solved by O.Einsle, A.Pomowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.50 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.26, 69.375, 153.188, 81.38, 77.92, 88.61
R / Rfree (%) 13 / 15.2

Other elements in 9f8x:

The structure of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase also contains other interesting chemical elements:

Sodium (Na) 3 atoms
Chlorine (Cl) 4 atoms
Copper (Cu) 24 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase (pdb code 9f8x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase, PDB code: 9f8x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 9f8x

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Calcium binding site 1 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:19.4
occ:1.00
 O A:TYR257 2.4 18.1 1.0
O A:THR268 2.4 22.3 1.0
OD1 A:ASN321 2.4 18.6 1.0
O A:HOH820 2.5 22.2 1.0
OD1 A:ASP274 2.5 20.3 1.0
OE1 A:GLU260 2.6 21.4 1.0
OE2 A:GLU260 2.6 22.2 1.0
OD2 A:ASP274 2.7 19.3 1.0
CD A:GLU260 2.9 22.1 1.0
CG A:ASP274 2.9 18.6 1.0
CG A:ASN321 3.4 17.7 1.0
C A:TYR257 3.5 17.5 1.0
C A:THR268 3.5 23.4 1.0
ND2 A:ASN321 3.9 17.9 1.0
CA A:MET269 4.2 26.7 1.0
N A:MET269 4.3 24.5 1.0
N A:ASN258 4.3 18.0 1.0
CA A:ASN258 4.3 19.5 1.0
OG A:SER259 4.4 22.9 1.0
N A:SER259 4.4 20.0 1.0
CA A:TYR257 4.4 16.5 1.0
CG A:GLU260 4.4 21.0 1.0
CB A:ASP274 4.4 17.8 1.0
N A:ASN321 4.5 16.2 1.0
CA A:THR268 4.5 23.0 1.0
CA A:ASN321 4.5 15.3 1.0
CB A:ASN321 4.6 15.8 1.0
C A:MET269 4.7 26.5 1.0
O A:ASN271 4.8 24.4 1.0
C A:ASN258 4.9 20.1 1.0
N A:ARG270 4.9 24.5 1.0
N A:ASN271 4.9 23.7 1.0

Calcium binding site 2 out of 8 in 9f8x

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Calcium binding site 2 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:16.9
occ:1.00
 OE1 A:GLU465 2.2 27.5 1.0
O A:LYS450 2.2 16.7 1.0
O B:HOH921 2.3 15.0 1.0
O B:HOH1135 2.3 16.3 1.0
O A:HOH1132 2.4 15.4 1.0
O A:HOH1246 2.5 20.4 1.0
CD A:GLU465 2.9 25.6 1.0
OE2 A:GLU465 3.0 30.4 1.0
C A:LYS450 3.4 17.2 1.0
OD1 B:ASP576 4.1 17.4 1.0
CA A:LYS450 4.2 16.1 1.0
CD1 B:TRP616 4.3 15.1 1.0
N A:PHE451 4.3 15.6 1.0
CG A:GLU465 4.4 21.1 1.0
CA A:PHE451 4.5 16.0 1.0
O B:HOH949 4.5 16.3 1.0
NE1 B:TRP616 4.5 15.8 1.0
CD1 A:PHE451 4.5 18.5 1.0
O A:HIS463 4.6 16.4 1.0
O B:HOH979 4.6 16.5 1.0
OE1 A:GLU488 4.6 19.6 1.0
O A:PRO464 4.7 14.1 1.0
O B:PHE617 4.7 16.1 1.0
CB A:LYS450 4.8 15.7 1.0
CA A:GLU465 4.9 15.4 1.0
CG B:ASP576 5.0 16.6 1.0
CB A:GLU465 5.0 17.5 1.0
C A:PRO464 5.0 14.2 1.0

Calcium binding site 3 out of 8 in 9f8x

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Calcium binding site 3 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:13.6
occ:1.00
 O B:TYR257 2.4 14.3 1.0
O B:HOH870 2.4 16.2 1.0
O B:THR268 2.4 15.3 1.0
OD1 B:ASN321 2.4 15.2 1.0
OD1 B:ASP274 2.5 14.4 1.0
OE2 B:GLU260 2.5 15.4 1.0
OE1 B:GLU260 2.5 15.6 1.0
OD2 B:ASP274 2.6 15.2 1.0
CD B:GLU260 2.9 15.4 1.0
CG B:ASP274 2.9 14.4 1.0
CG B:ASN321 3.4 14.0 1.0
C B:TYR257 3.5 13.1 1.0
C B:THR268 3.5 14.6 1.0
ND2 B:ASN321 3.9 13.9 1.0
N B:ASN258 4.3 13.4 1.0
N B:MET269 4.3 15.2 1.0
CA B:MET269 4.3 16.2 1.0
OG B:SER259 4.3 16.2 1.0
CA B:ASN258 4.3 13.9 1.0
N B:SER259 4.4 13.3 1.0
CG B:GLU260 4.4 15.1 1.0
CA B:TYR257 4.4 12.5 1.0
CB B:ASP274 4.4 13.2 1.0
CA B:THR268 4.5 15.2 1.0
N B:ASN321 4.5 13.3 1.0
CB B:ASN321 4.6 13.8 1.0
CA B:ASN321 4.6 13.5 1.0
O B:ASN271 4.7 16.3 1.0
C B:MET269 4.7 16.8 1.0
N B:ASN271 4.8 17.5 1.0
N B:ARG270 4.8 16.6 1.0
C B:ASN258 4.9 13.8 1.0
CB B:ASN271 5.0 16.6 1.0

Calcium binding site 4 out of 8 in 9f8x

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Calcium binding site 4 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:16.2
occ:1.00
 O B:LYS450 2.2 17.7 1.0
OE1 B:GLU465 2.2 27.9 1.0
O B:HOH1186 2.3 17.0 1.0
O A:HOH933 2.3 15.4 1.0
O A:HOH1034 2.4 17.4 1.0
O B:HOH1328 2.5 19.4 1.0
CD B:GLU465 3.1 23.8 1.0
OE2 B:GLU465 3.3 27.7 1.0
C B:LYS450 3.4 17.0 1.0
OD1 A:ASP576 4.1 17.2 1.0
CA B:LYS450 4.2 16.1 1.0
N B:PHE451 4.3 17.4 1.0
CA B:PHE451 4.4 17.2 1.0
O A:HOH988 4.4 15.7 1.0
CD1 A:TRP616 4.4 14.4 1.0
CG B:GLU465 4.5 20.0 1.0
O A:HOH1009 4.6 16.3 1.0
O B:HIS463 4.6 14.7 1.0
NE1 A:TRP616 4.6 14.6 1.0
O A:PHE617 4.6 15.8 1.0
OE1 B:GLU488 4.7 20.2 1.0
O B:PRO464 4.7 14.9 1.0
CB B:LYS450 4.7 16.8 1.0
CA B:GLU465 4.9 15.6 1.0
CD2 B:PHE451 4.9 24.4 1.0
CB B:GLU465 4.9 17.1 1.0
C B:PRO464 5.0 15.0 1.0
N B:GLU465 5.0 14.1 1.0

Calcium binding site 5 out of 8 in 9f8x

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Calcium binding site 5 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:12.5
occ:1.00
 O C:THR268 2.3 13.6 1.0
O C:TYR257 2.4 13.1 1.0
O C:HOH880 2.4 15.4 1.0
OD1 C:ASN321 2.4 13.7 1.0
OD1 C:ASP274 2.5 12.9 1.0
OE2 C:GLU260 2.5 14.2 1.0
OE1 C:GLU260 2.5 13.8 1.0
OD2 C:ASP274 2.7 13.9 1.0
CD C:GLU260 2.9 15.2 1.0
CG C:ASP274 2.9 13.6 1.0
CG C:ASN321 3.4 12.9 1.0
C C:THR268 3.5 14.0 1.0
C C:TYR257 3.5 12.4 1.0
ND2 C:ASN321 3.9 13.5 1.0
N C:MET269 4.3 14.1 1.0
N C:ASN258 4.3 13.1 1.0
CA C:MET269 4.3 15.8 1.0
CG C:GLU260 4.4 14.8 1.0
CA C:ASN258 4.4 13.4 1.0
OG C:SER259 4.4 14.8 1.0
CA C:TYR257 4.4 12.3 1.0
CB C:ASP274 4.4 13.2 1.0
CA C:THR268 4.4 14.5 1.0
N C:SER259 4.4 13.2 1.0
N C:ASN321 4.6 12.8 1.0
CB C:ASN321 4.6 11.9 1.0
CA C:ASN321 4.6 12.4 1.0
C C:MET269 4.7 15.2 1.0
O C:ASN271 4.7 16.1 1.0
N C:ARG270 4.8 15.3 1.0
N C:ASN271 4.9 14.8 1.0
C C:ASN258 4.9 13.3 1.0

Calcium binding site 6 out of 8 in 9f8x

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Calcium binding site 6 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca705

b:14.7
occ:1.00
 OE1 C:GLU465 2.2 24.3 1.0
O D:HOH1187 2.3 15.9 1.0
O C:LYS450 2.3 17.2 1.0
O D:HOH1005 2.3 13.3 1.0
O D:HOH1015 2.4 15.7 1.0
O D:HOH1307 2.4 18.2 1.0
CD C:GLU465 3.1 23.8 1.0
OE2 C:GLU465 3.3 28.2 1.0
C C:LYS450 3.5 15.8 1.0
OD1 D:ASP576 4.1 15.2 1.0
CA C:LYS450 4.3 15.3 1.0
CD1 D:TRP616 4.4 14.2 1.0
N C:PHE451 4.4 16.1 1.0
O D:HOH953 4.4 14.2 1.0
CA C:PHE451 4.4 15.4 1.0
CG C:GLU465 4.5 19.3 1.0
O D:HOH935 4.5 15.0 1.0
NE1 D:TRP616 4.5 13.8 1.0
O C:HIS463 4.6 14.8 1.0
O D:PHE617 4.6 14.2 1.0
O C:PRO464 4.7 14.1 1.0
OE1 C:GLU488 4.7 19.8 1.0
CB C:LYS450 4.8 15.2 1.0
CD1 C:PHE451 4.8 20.1 1.0
CA C:GLU465 4.9 14.6 1.0
CB C:GLU465 5.0 15.6 1.0
C C:PRO464 5.0 13.8 1.0

Calcium binding site 7 out of 8 in 9f8x

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Calcium binding site 7 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:16.8
occ:1.00
 O D:TYR257 2.4 15.9 1.0
O D:THR268 2.4 17.9 1.0
O D:HOH843 2.4 18.9 1.0
OD1 D:ASP274 2.5 17.6 1.0
OD1 D:ASN321 2.5 15.9 1.0
OE2 D:GLU260 2.5 19.3 1.0
OE1 D:GLU260 2.6 19.3 1.0
OD2 D:ASP274 2.7 16.9 1.0
CD D:GLU260 2.9 19.5 1.0
CG D:ASP274 2.9 17.2 1.0
CG D:ASN321 3.4 15.0 1.0
C D:TYR257 3.5 15.2 1.0
C D:THR268 3.5 20.4 1.0
ND2 D:ASN321 3.9 15.4 1.0
CA D:MET269 4.2 23.4 1.0
N D:ASN258 4.3 16.8 1.0
N D:MET269 4.3 22.5 1.0
CA D:ASN258 4.4 16.9 1.0
N D:SER259 4.4 17.8 1.0
OG D:SER259 4.4 18.9 1.0
CG D:GLU260 4.4 19.9 1.0
CA D:TYR257 4.4 15.3 1.0
CB D:ASP274 4.4 15.6 1.0
CA D:THR268 4.5 19.3 1.0
N D:ASN321 4.5 13.9 1.0
CA D:ASN321 4.6 14.9 1.0
CB D:ASN321 4.6 14.1 1.0
C D:MET269 4.7 26.0 1.0
O D:ASN271 4.8 22.6 1.0
N D:ARG270 4.8 22.2 1.0
N D:ASN271 4.9 21.9 1.0
C D:ASN258 4.9 17.9 1.0

Calcium binding site 8 out of 8 in 9f8x

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Calcium binding site 8 out of 8 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca705

b:15.3
occ:1.00
 OE1 D:GLU465 2.3 24.9 1.0
O D:LYS450 2.3 15.8 1.0
O D:HOH1139 2.3 14.8 1.0
O C:HOH1165 2.3 16.1 1.0
O C:HOH958 2.4 14.0 1.0
O D:HOH1242 2.5 19.2 1.0
CD D:GLU465 3.0 23.7 1.0
OE2 D:GLU465 3.1 32.0 1.0
C D:LYS450 3.4 17.0 1.0
OD1 C:ASP576 4.1 15.9 1.0
CD1 C:TRP616 4.2 14.7 1.0
CA D:LYS450 4.2 14.8 1.0
O C:HOH997 4.4 15.6 1.0
N D:PHE451 4.4 14.8 1.0
CG D:GLU465 4.5 18.9 1.0
CA D:PHE451 4.5 15.9 1.0
NE1 C:TRP616 4.5 14.3 1.0
CD1 D:PHE451 4.6 19.7 1.0
O D:HIS463 4.6 13.8 1.0
O C:HOH1008 4.6 16.0 1.0
OE1 D:GLU488 4.6 19.8 1.0
O D:PRO464 4.7 14.2 1.0
O C:PHE617 4.7 14.8 1.0
CB D:LYS450 4.7 14.8 1.0
CA D:GLU465 5.0 14.7 1.0

Reference:

A.Pomowski, S.Dell'acqua, A.Wust, S.R.Pauleta, I.Moura, O.Einsle. Revisiting the Metal Sites of Nitrous Oxide Reductase in A Low-Dose Structure From Marinobacter Nauticus. J.Biol.Inorg.Chem. V. 29 279 2024.
ISSN: ESSN 1432-1327
PubMed: 38720157
DOI: 10.1007/S00775-024-02056-Y
Page generated: Thu Jul 10 09:38:54 2025

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