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Chlorine in PDB 6tsi: CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1

Enzymatic activity of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1

All present enzymatic activity of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1:
1.7.2.1; 1.7.99.1;

Protein crystallography data

The structure of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1, PDB code: 6tsi was solved by T.Kluenemann, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.61 / 2.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 163.762, 91.093, 112.706, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 28

Other elements in 6tsi:

The structure of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 (pdb code 6tsi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1, PDB code: 6tsi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6tsi

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Chlorine binding site 1 out of 5 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:20.6
occ:1.00
 H B:SER265 2.6 19.2 1.0
H A:MET269 2.6 18.4 1.0
HA3 A:GLY268 3.0 21.8 1.0
HA B:VAL264 3.1 16.6 1.0
HG12 B:VAL264 3.2 15.3 1.0
O A:HOH748 3.2 20.2 1.0
N B:SER265 3.4 15.8 1.0
N A:MET269 3.5 15.2 1.0
HG2 A:MET269 3.6 14.9 1.0
HB3 B:SER265 3.6 19.4 1.0
HA2 A:GLY268 3.7 21.8 1.0
CA A:GLY268 3.7 18.0 1.0
HB2 A:MET269 3.9 20.8 1.0
CA B:VAL264 3.9 13.6 1.0
HZ1 A:LYS303 4.0 27.3 1.0
CG1 B:VAL264 4.1 12.6 1.0
C A:GLY268 4.1 15.1 1.0
C B:VAL264 4.2 15.3 1.0
HB2 B:SER265 4.2 19.4 1.0
CB B:SER265 4.2 16.0 1.0
CG A:MET269 4.3 12.3 1.0
CB A:MET269 4.4 17.2 1.0
HG11 B:VAL264 4.4 15.3 1.0
CA B:SER265 4.4 13.3 1.0
O B:ILE263 4.4 19.0 1.0
HG3 A:MET269 4.4 14.9 1.0
CA A:MET269 4.5 14.4 1.0
CB B:VAL264 4.5 12.6 1.0
HG21 B:VAL264 4.6 14.2 1.0
O B:SER265 4.6 17.9 1.0
HZ3 A:LYS303 4.6 27.3 1.0
NZ A:LYS303 4.7 22.6 1.0
O A:MET269 4.7 17.4 1.0
HG13 B:VAL264 4.7 15.3 1.0
HZ2 A:LYS303 4.8 27.3 1.0
O A:ARG267 4.8 13.1 1.0
HG23 B:VAL264 4.9 14.2 1.0
CG2 B:VAL264 4.9 11.6 1.0
N A:GLY268 5.0 15.0 1.0

Chlorine binding site 2 out of 5 in 6tsi

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Chlorine binding site 2 out of 5 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:40.5
occ:1.00
 HD2 A:PRO292 3.1 20.9 1.0
HH22 A:ARG356 3.2 31.8 1.0
HD21 A:ASN308 3.5 27.3 1.0
HD3 A:PRO292 3.7 20.9 1.0
ND1 A:HIS291 3.7 21.9 1.0
HH21 A:ARG356 3.8 31.8 1.0
CD A:PRO292 3.8 17.3 1.0
NH2 A:ARG356 3.8 26.3 1.0
HB3 A:HIS291 3.9 24.8 1.0
ND2 A:ASN308 4.2 22.6 1.0
HG3 A:PRO292 4.3 21.4 1.0
HD3 A:LYS310 4.3 40.3 1.0
HG2 A:PRO292 4.3 21.4 1.0
CG A:PRO292 4.4 17.6 1.0
HD22 A:ASN308 4.4 27.3 1.0
HA A:HIS291 4.5 22.4 1.0
HD2 A:LYS310 4.5 40.3 1.0
CE1 A:HIS291 4.6 23.2 1.0
CG A:HIS291 4.6 21.0 1.0
CB A:HIS291 4.6 20.5 1.0
HE1 A:HIS291 4.6 28.1 1.0
CD A:LYS310 4.9 33.4 1.0

Chlorine binding site 3 out of 5 in 6tsi

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Chlorine binding site 3 out of 5 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:23.1
occ:1.00
 H B:MET269 2.6 20.2 1.0
HA3 B:GLY268 2.7 22.4 1.0
H A:SER265 2.8 16.0 1.0
O A:HOH715 3.2 19.2 1.0
O B:HOH758 3.3 21.8 1.0
HA A:VAL264 3.3 13.5 1.0
HG12 A:VAL264 3.3 10.4 1.0
N B:MET269 3.4 16.7 1.0
CA B:GLY268 3.5 18.5 1.0
HA2 B:GLY268 3.6 22.4 1.0
HB3 A:SER265 3.7 12.7 1.0
HG2 B:MET269 3.7 16.8 1.0
N A:SER265 3.7 13.1 1.0
O B:HOH757 3.7 26.3 1.0
HB2 B:MET269 3.9 16.4 1.0
C B:GLY268 4.0 13.9 1.0
CA A:VAL264 4.2 11.1 1.0
CG1 A:VAL264 4.3 8.5 1.0
CB A:SER265 4.4 10.4 1.0
CG B:MET269 4.4 13.8 1.0
CB B:MET269 4.4 13.5 1.0
HZ3 B:LYS303 4.4 25.0 1.0
CA B:MET269 4.4 14.0 1.0
C A:VAL264 4.5 13.4 1.0
HZ1 B:LYS303 4.5 25.0 1.0
HB2 A:SER265 4.5 12.7 1.0
HG22 A:VAL264 4.5 12.8 1.0
CA A:SER265 4.6 12.3 1.0
O B:MET269 4.6 19.1 1.0
O A:SER265 4.6 15.2 1.0
O B:ARG267 4.6 14.6 1.0
O A:ILE263 4.7 23.2 1.0
HZ2 B:LYS303 4.7 25.0 1.0
N B:GLY268 4.7 14.9 1.0
CB A:VAL264 4.7 12.2 1.0
HG3 B:MET269 4.7 16.8 1.0
HG11 A:VAL264 4.8 10.4 1.0
NZ B:LYS303 4.8 20.7 1.0
HG13 A:VAL264 4.8 10.4 1.0

Chlorine binding site 4 out of 5 in 6tsi

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Chlorine binding site 4 out of 5 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl606

b:23.0
occ:1.00
 HH22 B:ARG201 3.0 28.3 1.0
HH12 B:ARG201 3.3 28.2 1.0
HZ1 B:LYS214 3.5 29.8 1.0
HZ3 B:LYS214 3.6 29.8 1.0
HZ2 B:LYS214 3.7 29.8 1.0
NH2 B:ARG201 3.8 23.4 1.0
NZ B:LYS214 3.8 24.7 1.0
HB3 B:ASP176 3.9 24.0 1.0
HB2 B:ASP176 4.0 24.0 1.0
NH1 B:ARG201 4.0 23.3 1.0
CZ B:ARG201 4.4 24.7 1.0
HH21 B:ARG201 4.4 28.3 1.0
CB B:ASP176 4.4 19.8 1.0
HH11 B:ARG201 4.8 28.2 1.0

Chlorine binding site 5 out of 5 in 6tsi

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Chlorine binding site 5 out of 5 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:24.3
occ:1.00
 HH12 B:ARG356 3.1 46.0 1.0
HD2 B:PRO292 3.1 19.6 1.0
HD22 B:ASN308 3.2 30.9 1.0
HB3 B:HIS291 3.7 30.6 1.0
NH1 B:ARG356 3.9 38.2 1.0
CD B:PRO292 3.9 16.1 1.0
HD3 B:PRO292 4.0 19.6 1.0
ND2 B:ASN308 4.0 25.5 1.0
ND1 B:HIS291 4.0 25.4 1.0
HH22 B:ARG356 4.1 56.1 1.0
HD21 B:ASN308 4.2 30.9 1.0
HD2 B:LYS310 4.2 38.1 1.0
HG2 B:PRO292 4.3 25.0 1.0
HH11 B:ARG356 4.3 46.0 1.0
HG3 B:PRO292 4.4 25.0 1.0
CG B:PRO292 4.5 20.6 1.0
CB B:HIS291 4.6 25.4 1.0
CG B:HIS291 4.6 25.0 1.0
HA B:HIS291 4.7 26.6 1.0
NH2 B:ARG356 4.7 46.6 1.0
CZ B:ARG356 4.8 38.4 1.0
HZ3 B:LYS310 4.9 48.2 1.0
CE1 B:HIS291 4.9 31.0 1.0

Reference:

T.Klunemann, W.Blankenfeldt. Structure of Heme D 1 -Free Cd 1 Nitrite Reductase Nirs. Acta Crystallogr.,Sect.F V. 76 250 2020.
ISSN: ESSN 2053-230X
PubMed: 32510465
DOI: 10.1107/S2053230X20006676
Page generated: Mon Jul 29 15:34:57 2024

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