Chlorine 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:

Calcium (Ca) 8 atoms
Sodium (Na) 3 atoms
Copper (Cu) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase, PDB code: 9f8x:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 9f8x

Go back to Chlorine Binding Sites List in 9f8x
Chlorine binding site 1 out of 4 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl704

b:14.7
occ:1.00
 O A:HOH1185 3.1 17.4 1.0
ND1 A:HIS378 3.2 13.2 1.0
NH1 A:ARG184 3.2 15.2 1.0
ND2 A:ASN326 3.3 13.7 1.0
N A:LEU325 3.4 14.2 1.0
CA A:GLY324 3.5 14.4 1.0
NH2 A:ARG184 3.5 17.9 1.0
CE1 A:HIS378 3.5 13.9 1.0
O A:HOH1006 3.7 21.1 1.0
CB A:ASN242 3.7 13.8 1.0
O A:LEU325 3.8 14.8 1.0
CZ A:ARG184 3.8 15.9 1.0
CG A:ASN242 3.8 16.3 1.0
C A:GLY324 3.9 14.0 1.0
CE1 A:HIS429 4.1 14.9 1.0
CG A:ASN326 4.2 14.8 1.0
C A:LEU325 4.2 13.9 1.0
OD1 A:ASN242 4.2 18.6 1.0
ND2 A:ASN242 4.3 18.0 1.0
OD1 A:ASN326 4.3 14.9 1.0
CA A:LEU325 4.4 13.6 1.0
CG A:HIS378 4.4 14.8 1.0
ND1 A:HIS429 4.6 14.4 1.0
O A:HOH1230 4.7 15.6 1.0
N A:GLY324 4.8 14.3 1.0
NE2 A:HIS378 4.8 12.8 1.0

Chlorine binding site 2 out of 4 in 9f8x

Go back to Chlorine Binding Sites List in 9f8x
Chlorine binding site 2 out of 4 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl704

b:14.5
occ:1.00
 O B:HOH1143 3.1 15.9 1.0
ND1 B:HIS378 3.2 13.5 1.0
NH1 B:ARG184 3.2 14.5 1.0
N B:LEU325 3.4 12.7 1.0
ND2 B:ASN326 3.4 15.2 1.0
NH2 B:ARG184 3.4 16.9 1.0
CA B:GLY324 3.5 12.9 1.0
CE1 B:HIS378 3.5 14.1 1.0
O B:LEU325 3.7 13.7 1.0
CB B:ASN242 3.7 13.3 1.0
O B:HOH1083 3.7 21.2 1.0
CZ B:ARG184 3.8 15.8 1.0
CG B:ASN242 3.9 16.0 1.0
C B:GLY324 3.9 12.4 1.0
C B:LEU325 4.2 14.1 1.0
CE1 B:HIS429 4.2 14.8 1.0
CG B:ASN326 4.2 15.4 1.0
OD1 B:ASN242 4.2 17.2 1.0
ND2 B:ASN242 4.2 15.8 1.0
OD1 B:ASN326 4.3 14.6 1.0
CA B:LEU325 4.4 13.3 1.0
CG B:HIS378 4.5 14.6 1.0
ND1 B:HIS429 4.6 15.3 1.0
O B:HOH1293 4.7 14.1 1.0
N B:GLY324 4.8 12.8 1.0
NE2 B:HIS378 4.8 13.8 1.0

Chlorine binding site 3 out of 4 in 9f8x

Go back to Chlorine Binding Sites List in 9f8x
Chlorine binding site 3 out of 4 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl704

b:13.8
occ:1.00
 O C:HOH1197 3.1 15.1 1.0
ND1 C:HIS378 3.1 13.1 1.0
NH1 C:ARG184 3.2 12.8 1.0
N C:LEU325 3.3 12.8 1.0
ND2 C:ASN326 3.4 14.2 1.0
NH2 C:ARG184 3.5 16.8 1.0
CA C:GLY324 3.5 12.9 1.0
CE1 C:HIS378 3.5 13.7 1.0
O C:HOH1031 3.7 19.6 1.0
CB C:ASN242 3.7 12.7 1.0
O C:LEU325 3.7 13.4 1.0
CZ C:ARG184 3.8 16.0 1.0
CG C:ASN242 3.9 15.4 1.0
C C:GLY324 3.9 12.2 1.0
CE1 C:HIS429 4.2 12.3 1.0
CG C:ASN326 4.2 13.1 1.0
C C:LEU325 4.2 13.1 1.0
ND2 C:ASN242 4.2 15.3 1.0
OD1 C:ASN242 4.2 16.9 1.0
OD1 C:ASN326 4.3 13.1 1.0
CA C:LEU325 4.4 13.8 1.0
CG C:HIS378 4.4 12.7 1.0
ND1 C:HIS429 4.6 13.9 1.0
O C:HOH1311 4.7 13.4 1.0
N C:GLY324 4.8 12.1 1.0
NE2 C:HIS378 4.8 11.6 1.0

Chlorine binding site 4 out of 4 in 9f8x

Go back to Chlorine Binding Sites List in 9f8x
Chlorine binding site 4 out of 4 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
D:Cl704

b:14.1
occ:1.00
 O D:HOH1231 3.1 17.1 1.0
ND1 D:HIS378 3.2 13.4 1.0
NH1 D:ARG184 3.2 14.9 1.0
ND2 D:ASN326 3.3 13.6 1.0
N D:LEU325 3.4 12.7 1.0
NH2 D:ARG184 3.5 16.6 1.0
CA D:GLY324 3.5 12.6 1.0
CE1 D:HIS378 3.6 13.2 1.0
CB D:ASN242 3.7 12.3 1.0
O D:LEU325 3.7 14.0 1.0
O D:HOH938 3.8 20.8 1.0
CZ D:ARG184 3.8 14.9 1.0
CG D:ASN242 3.8 16.4 1.0
C D:GLY324 4.0 13.2 1.0
CG D:ASN326 4.2 13.5 1.0
CE1 D:HIS429 4.2 13.5 1.0
C D:LEU325 4.2 13.2 1.0
OD1 D:ASN242 4.2 17.2 1.0
ND2 D:ASN242 4.3 16.5 1.0
OD1 D:ASN326 4.3 14.6 1.0
CA D:LEU325 4.4 13.2 1.0
CG D:HIS378 4.5 13.3 1.0
ND1 D:HIS429 4.6 14.3 1.0
O D:HOH1247 4.7 15.2 1.0
N D:GLY324 4.8 12.6 1.0
NE2 D:HIS378 4.9 12.6 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: Tue Jul 30 14:02:25 2024

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