Atomistry » Chlorine » PDB 6vcl-6vke » 6veb
Atomistry »
  Chlorine »
    PDB 6vcl-6vke »
      6veb »

Chlorine in PDB 6veb: Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase

Enzymatic activity of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase

All present enzymatic activity of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase:
1.3.1.76; 2.1.1.107; 4.99.1.4;

Protein crystallography data

The structure of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase, PDB code: 6veb was solved by J.M.Pennington, M.E.Stroupe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.682, 99.489, 146.037, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 24.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase (pdb code 6veb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase, PDB code: 6veb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6veb

Go back to Chlorine Binding Sites List in 6veb
Chlorine binding site 1 out of 7 in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:85.8
occ:1.00
 N A:HIS346 2.7 37.6 1.0
O A:ALA350 2.7 45.9 1.0
O A:HIS346 2.8 51.2 1.0
O A:ARG347 2.9 39.4 0.5
N A:ALA350 3.0 45.5 1.0
C A:HIS346 3.1 51.6 1.0
N A:TYR349 3.3 70.4 1.0
CA A:HIS346 3.4 46.2 1.0
C A:ARG347 3.5 46.9 0.5
CB A:THR345 3.6 32.8 1.0
C A:ALA350 3.6 46.4 1.0
C A:THR345 3.6 35.7 1.0
CA A:THR345 3.6 36.1 1.0
CA A:ASP348 3.7 76.3 1.0
CA A:ALA350 3.7 45.9 1.0
N A:ASP348 4.0 50.5 1.0
C A:TYR349 4.0 53.6 1.0
C A:ASP348 4.0 81.2 1.0
N A:ARG347 4.0 54.0 0.5
CB A:ALA350 4.1 46.7 1.0
N A:ARG347 4.1 54.2 0.5
CA A:TYR349 4.1 53.7 1.0
CG2 A:THR345 4.3 26.2 1.0
C A:ARG347 4.4 50.9 0.5
CB A:TYR349 4.4 44.1 1.0
CA A:ARG347 4.4 51.0 0.5
CL A:CL504 4.6 61.5 1.0
CB A:HIS346 4.6 46.0 1.0
OG1 A:THR345 4.7 40.6 1.0
CA A:ARG347 4.7 52.5 0.5
O A:THR345 4.8 35.5 1.0
N A:GLN351 4.8 50.4 1.0
CB A:ASP348 4.9 94.1 1.0

Chlorine binding site 2 out of 7 in 6veb

Go back to Chlorine Binding Sites List in 6veb
Chlorine binding site 2 out of 7 in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:61.5
occ:1.00
 OG1 A:THR345 3.3 40.6 1.0
O B:HOH633 3.4 46.2 1.0
CA B:PHE307 3.7 28.6 1.0
N B:ARG309 3.7 44.8 1.0
CB A:THR345 3.8 32.8 1.0
N A:HIS346 4.0 37.6 1.0
C B:PHE307 4.0 29.7 1.0
CA B:ARG309 4.0 43.0 1.0
N B:GLY308 4.0 36.8 1.0
O A:ARG347 4.1 39.4 0.5
C A:THR345 4.1 35.7 1.0
CA A:HIS346 4.1 46.2 1.0
N B:PHE307 4.1 35.5 1.0
CG B:ARG309 4.2 50.1 1.0
N A:ARG347 4.2 54.0 0.5
N A:ARG347 4.3 54.2 0.5
O A:THR345 4.4 35.5 1.0
C A:HIS346 4.4 51.6 1.0
O A:HOH639 4.4 34.9 1.0
CL A:CL503 4.6 85.8 1.0
CD1 B:PHE307 4.6 32.9 1.0
CA A:THR345 4.6 36.1 1.0
CB B:ARG309 4.7 48.1 1.0
CA A:ARG347 4.7 51.0 0.5
C B:GLY308 4.8 36.4 1.0
O B:PHE307 4.8 33.4 1.0
CB B:PHE307 4.8 27.0 1.0
C A:ARG347 4.9 46.9 0.5

Chlorine binding site 3 out of 7 in 6veb

Go back to Chlorine Binding Sites List in 6veb
Chlorine binding site 3 out of 7 in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:84.2
occ:1.00
 NZ A:LYS142 3.9 63.4 0.4
NZ A:LYS142 4.0 63.9 0.6
CD A:LYS142 4.2 62.8 0.4
CD A:LYS142 4.2 63.9 0.6
CD2 A:LEU139 4.2 51.6 1.0
OE1 B:GLN241 4.6 70.4 1.0
CE A:LYS142 4.6 63.9 0.4
CE A:LYS142 4.7 64.3 0.6
CD2 B:LEU151 5.0 54.1 1.0

Chlorine binding site 4 out of 7 in 6veb

Go back to Chlorine Binding Sites List in 6veb
Chlorine binding site 4 out of 7 in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:77.8
occ:1.00
 N A:GLY130 3.2 65.9 1.0
CB A:ALA128 3.3 37.9 1.0
CA A:GLY130 3.4 65.1 1.0
O A:HOH605 3.5 45.1 1.0
N A:ALA128 3.5 32.0 1.0
N A:PRO133 3.6 81.3 1.0
CA A:PRO133 3.6 79.3 1.0
C A:SER132 3.6 71.7 1.0
O A:SER132 3.7 62.5 1.0
CA A:ALA128 3.8 44.8 1.0
C A:GLY130 3.8 71.2 1.0
C A:ALA128 3.9 62.9 1.0
N A:SER132 3.9 65.6 1.0
N A:GLY129 4.0 64.0 1.0
CG A:PRO133 4.0 86.4 1.0
CD A:PRO133 4.1 85.4 1.0
N A:THR131 4.1 72.3 1.0
CB A:PRO133 4.3 84.8 1.0
CB A:ALA136 4.3 50.0 1.0
C A:GLY129 4.4 70.2 1.0
CA A:SER132 4.4 73.1 1.0
OG A:SER127 4.4 48.4 1.0
O A:GLY130 4.4 71.2 1.0
O A:ALA128 4.5 67.8 1.0
C A:SER127 4.7 34.0 1.0
CA A:GLY129 4.8 65.4 1.0
C A:PRO133 4.8 65.6 1.0
C A:THR131 4.9 73.7 1.0
CA A:SER127 5.0 36.4 1.0

Chlorine binding site 5 out of 7 in 6veb

Go back to Chlorine Binding Sites List in 6veb
Chlorine binding site 5 out of 7 in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:58.6
occ:1.00
 O A:HOH668 3.0 46.5 1.0
N A:ARG309 3.1 37.0 1.0
CA A:ARG309 3.4 37.5 1.0
OG1 B:THR345 3.4 41.9 1.0
CA A:PHE307 3.7 38.7 1.0
CG A:ARG309 3.7 56.3 1.0
N A:GLY308 3.8 50.9 1.0
C A:PHE307 3.9 45.8 1.0
N A:PHE307 4.1 30.4 1.0
CB B:THR345 4.1 30.0 1.0
CB A:ARG309 4.1 40.6 1.0
N B:HIS346 4.2 34.4 1.0
CA B:HIS346 4.2 27.0 1.0
C B:THR345 4.2 32.0 1.0
O B:THR345 4.2 38.0 1.0
C A:GLY308 4.3 32.9 1.0
N B:ARG347 4.3 47.3 1.0
OE1 A:GLU312 4.6 62.0 1.0
C B:HIS346 4.6 40.2 1.0
C A:ARG309 4.7 45.0 1.0
CA A:GLY308 4.7 32.1 1.0
CD A:ARG309 4.8 71.5 1.0
O A:PHE307 4.8 37.5 1.0
CB A:PHE307 4.9 34.2 1.0
CA B:THR345 4.9 29.2 1.0
CD1 A:PHE307 4.9 34.9 1.0

Chlorine binding site 6 out of 7 in 6veb

Go back to Chlorine Binding Sites List in 6veb
Chlorine binding site 6 out of 7 in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:60.8
occ:1.00
 N B:LYS375 3.3 46.0 1.0
O B:HOH685 3.4 40.0 1.0
CG B:ARG443 4.0 30.4 1.0
CE B:MET403 4.0 51.4 1.0
CA B:LYS375 4.1 42.6 1.0
CB B:GLU374 4.1 44.0 1.0
CA B:GLU374 4.1 37.3 1.0
C B:GLU374 4.2 42.0 1.0
NE B:ARG443 4.4 71.0 1.0
OE1 B:GLU374 4.5 85.1 1.0
CG B:GLU374 4.6 59.2 1.0
CD B:ARG443 4.7 64.1 1.0
O B:TYR349 4.7 33.0 1.0
SD B:MET403 4.7 50.5 1.0
CD B:GLU374 4.8 77.5 1.0
N B:GLN376 4.9 34.5 1.0
O B:HOH668 5.0 40.9 1.0

Chlorine binding site 7 out of 7 in 6veb

Go back to Chlorine Binding Sites List in 6veb
Chlorine binding site 7 out of 7 in the Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Precorrin-2-Bound S128A S. Typhimurium Siroheme Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:66.9
occ:1.00
 O B:HOH655 3.3 26.2 1.0
N B:LEU384 3.3 53.1 1.0
CB B:LEU384 3.5 55.3 1.0
C B:MET382 3.5 40.8 1.0
O B:MET382 3.6 40.7 1.0
CA B:MET382 3.8 43.8 1.0
N B:GLY383 3.9 36.5 1.0
CA B:LEU384 3.9 56.8 1.0
N B:ASN385 4.1 72.2 1.0
C B:GLY383 4.3 48.3 1.0
C B:LEU384 4.5 67.4 1.0
O3' B:SAH501 4.5 47.7 1.0
CB B:MET382 4.5 50.8 1.0
CA B:GLY383 4.5 41.4 1.0
CB B:SER435 4.6 41.4 1.0
OG B:SER435 4.7 51.9 1.0
CG B:LEU384 4.8 55.3 1.0
OD1 B:ASN385 4.8 0.3 1.0
N B:MET382 4.9 26.4 1.0
CD2 B:LEU384 5.0 43.6 1.0

Reference:

J.M.Pennington, M.Kemp, L.Mcgarry, Y.Chen, M.E.Stroupe. Siroheme Synthase Orients Substrates For Dehydrogenase and Chelatase Activities in A Common Active Site. Nat Commun V. 11 864 2020.
ISSN: ESSN 2041-1723
PubMed: 32054833
DOI: 10.1038/S41467-020-14722-1
Page generated: Sat Jul 12 20:52:11 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy