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

Go back to Chlorine Binding Sites List in 6tsi
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

Go back to Chlorine Binding Sites List in 6tsi
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

Go back to Chlorine Binding Sites List in 6tsi
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

Go back to Chlorine Binding Sites List in 6tsi
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

Go back to Chlorine Binding Sites List in 6tsi
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: Sat Dec 12 13:46:18 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy