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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

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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

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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

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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

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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

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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

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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

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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: Mon Jul 29 16:16:02 2024

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