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Chlorine in PDB 3pm5: Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa

Enzymatic activity of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa

All present enzymatic activity of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa:
1.14.12.21;

Protein crystallography data

The structure of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa, PDB code: 3pm5 was solved by T.Weinert, L.Rather, G.Fuchs, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.40 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.180, 76.650, 148.200, 90.00, 108.34, 90.00
R / Rfree (%) 17.4 / 22.4

Other elements in 3pm5:

The structure of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa (pdb code 3pm5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa, PDB code: 3pm5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3pm5

Go back to Chlorine Binding Sites List in 3pm5
Chlorine binding site 1 out of 4 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl485

b:40.6
occ:1.00
 O A:HOH534 2.8 30.4 1.0
NE A:ARG110 3.3 36.4 1.0
N B:GLU416 3.3 37.0 1.0
OE2 A:GLU172 3.6 36.8 1.0
CB B:GLU416 3.9 38.9 1.0
CA B:SER415 3.9 37.1 1.0
CB B:SER415 4.0 38.1 1.0
CA A:ARG111 4.0 35.9 1.0
NH2 A:ARG110 4.0 37.8 1.0
CG A:ARG110 4.0 39.5 1.0
CD A:ARG110 4.1 38.9 1.0
CZ A:ARG110 4.1 40.3 1.0
C B:SER415 4.1 36.4 1.0
CB A:ARG111 4.2 35.8 1.0
N A:ARG111 4.2 36.2 1.0
CA B:GLU416 4.2 38.4 1.0
CD A:GLU172 4.2 36.9 1.0
CG2 A:VAL114 4.4 30.1 1.0
C A:ARG110 4.4 36.8 1.0
OE1 A:GLU172 4.5 36.9 1.0
O A:ARG110 4.6 36.6 1.0
CB A:ARG110 4.6 38.5 1.0
CG A:ARG111 4.8 39.7 1.0
CB A:VAL114 4.8 33.7 1.0
O A:SER107 4.9 41.7 1.0
O B:HOH582 4.9 37.4 1.0
OD2 A:ASP168 4.9 35.2 1.0
OG B:SER415 5.0 38.8 1.0

Chlorine binding site 2 out of 4 in 3pm5

Go back to Chlorine Binding Sites List in 3pm5
Chlorine binding site 2 out of 4 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl486

b:40.0
occ:1.00
 O B:HOH624 2.8 43.1 1.0
N A:GLU416 3.2 37.7 1.0
NE B:ARG110 3.4 37.7 1.0
CB A:GLU416 3.8 38.7 1.0
CA A:SER415 3.8 38.1 1.0
CB A:SER415 3.9 39.3 1.0
OE2 B:GLU172 3.9 40.5 1.0
CA B:ARG111 3.9 37.1 1.0
N B:ARG111 4.0 37.5 1.0
C A:SER415 4.0 37.6 1.0
NH2 B:ARG110 4.0 40.9 1.0
CA A:GLU416 4.1 38.7 1.0
CZ B:ARG110 4.2 40.8 1.0
CB B:ARG111 4.2 37.3 1.0
CG B:ARG110 4.3 40.9 1.0
CD B:ARG110 4.3 39.5 1.0
CD B:GLU172 4.4 39.0 1.0
C B:ARG110 4.4 37.7 1.0
CB B:ARG110 4.5 40.6 1.0
CG2 B:VAL114 4.6 34.0 1.0
OE1 B:GLU172 4.6 35.8 1.0
CG B:ARG111 4.7 40.0 1.0
CB B:VAL114 4.8 36.1 1.0
O B:ARG110 4.8 36.4 1.0
OG A:SER415 4.9 38.4 1.0
O A:HOH562 4.9 50.1 1.0
O B:SER107 5.0 39.4 1.0

Chlorine binding site 3 out of 4 in 3pm5

Go back to Chlorine Binding Sites List in 3pm5
Chlorine binding site 3 out of 4 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl485

b:44.6
occ:1.00
 O D:HOH566 2.9 40.0 1.0
N C:GLU416 3.2 37.5 1.0
NE D:ARG110 3.4 40.6 1.0
OE2 D:GLU172 3.7 46.6 1.0
CB C:GLU416 3.8 39.5 1.0
CA C:SER415 3.9 37.6 1.0
CA D:ARG111 3.9 40.6 1.0
C C:SER415 4.0 36.7 1.0
NH2 D:ARG110 4.0 46.8 1.0
CB C:SER415 4.0 38.1 1.0
CA C:GLU416 4.1 38.1 1.0
N D:ARG111 4.1 40.9 1.0
CB D:ARG111 4.2 41.9 1.0
CZ D:ARG110 4.2 45.5 1.0
CG D:ARG110 4.2 40.6 1.0
CD D:ARG110 4.3 42.1 1.0
CD D:GLU172 4.3 46.6 1.0
OE1 D:GLU172 4.4 45.1 1.0
C D:ARG110 4.5 40.0 1.0
CG2 D:VAL114 4.5 37.1 1.0
CB D:ARG110 4.6 41.6 1.0
O D:ARG110 4.6 37.4 1.0
CG D:ARG111 4.7 43.9 1.0
CB D:VAL114 4.8 38.2 1.0
O D:HOH570 4.9 55.9 1.0
O D:SER107 5.0 45.9 1.0

Chlorine binding site 4 out of 4 in 3pm5

Go back to Chlorine Binding Sites List in 3pm5
Chlorine binding site 4 out of 4 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl483

b:42.6
occ:1.00
 O D:HOH534 2.9 46.5 1.0
N D:GLU416 3.3 37.7 1.0
NE C:ARG110 3.6 39.6 1.0
CA C:ARG111 3.8 37.9 1.0
CA D:SER415 3.8 37.5 1.0
CB D:GLU416 3.8 38.7 1.0
CB D:SER415 3.9 37.0 1.0
OE2 C:GLU172 3.9 43.0 1.0
CB C:ARG111 4.0 39.5 1.0
N C:ARG111 4.0 37.3 1.0
C D:SER415 4.0 37.7 1.0
NH2 C:ARG110 4.2 43.0 1.0
CA D:GLU416 4.2 38.4 1.0
CG C:ARG110 4.2 39.5 1.0
CZ C:ARG110 4.3 42.0 1.0
CG2 C:VAL114 4.4 35.3 1.0
CD C:ARG110 4.4 40.1 1.0
C C:ARG110 4.4 36.5 1.0
CD C:GLU172 4.4 40.5 1.0
CG C:ARG111 4.6 43.2 1.0
O D:HOH515 4.6 42.6 1.0
O C:ARG110 4.7 33.0 1.0
CB C:ARG110 4.7 39.2 1.0
CB C:VAL114 4.7 33.7 1.0
OE1 C:GLU172 4.7 38.3 1.0
O C:SER107 4.9 43.3 1.0
OG D:SER415 4.9 37.9 1.0

Reference:

L.J.Rather, T.Weinert, U.Demmer, E.Bill, W.Ismail, G.Fuchs, U.Ermler. Structure and Mechanism of the Diiron Benzoyl-Coenzyme A Epoxidase Boxb. J.Biol.Chem. V. 286 29241 2011.
ISSN: ISSN 0021-9258
PubMed: 21632537
DOI: 10.1074/JBC.M111.236893
Page generated: Sun Jul 21 02:29:18 2024

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