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Iron 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:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa, PDB code: 3pm5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 1 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe1001

b:74.3
occ:1.00
 OE1 A:GLU150 2.3 29.8 0.4
ND1 A:HIS153 2.5 33.5 1.0
OE1 A:GLU120 2.5 45.1 1.0
OE2 A:GLU120 2.9 43.4 1.0
CD A:GLU120 3.1 41.6 1.0
OE1 A:GLU240 3.1 65.1 1.0
CE1 A:HIS153 3.3 35.2 1.0
CD A:GLU150 3.5 31.3 0.4
CG A:HIS153 3.5 33.8 1.0
C7B A:BYC1003 3.7 50.5 1.0
FE A:FE1002 3.7 60.0 1.0
CB A:HIS153 3.9 33.0 1.0
CD A:GLU240 3.9 58.6 1.0
C6B A:BYC1003 3.9 51.1 1.0
OE2 A:GLU240 4.0 62.6 1.0
OE2 A:GLU150 4.2 33.4 0.4
NE2 A:HIS153 4.5 38.0 1.0
CG A:GLU120 4.5 35.7 1.0
C2B A:BYC1003 4.6 49.7 1.0
O57 A:BYC1003 4.6 49.3 1.0
CD2 A:HIS153 4.6 35.7 1.0
CA A:GLU150 4.6 32.6 0.4
CG A:GLU150 4.7 31.7 0.4
CB A:GLU150 4.8 31.2 0.4
CA A:GLU150 4.8 32.8 0.6
CE A:MET236 4.8 31.3 1.0
C5B A:BYC1003 5.0 50.0 1.0

Iron binding site 2 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 2 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe1002

b:60.0
occ:1.00
 OE2 A:GLU240 1.8 62.6 1.0
OD2 A:ASP211 2.0 46.0 1.0
ND1 A:HIS243 2.3 33.9 1.0
OE2 A:GLU150 2.3 33.4 0.4
CD A:GLU240 2.7 58.6 1.0
OE1 A:GLU150 2.9 29.8 0.4
CD A:GLU150 2.9 31.3 0.4
OE1 A:GLU240 3.0 65.1 1.0
CG A:ASP211 3.1 37.0 1.0
CE1 A:HIS243 3.2 36.6 1.0
CG A:HIS243 3.3 37.2 1.0
CB A:HIS243 3.6 37.4 1.0
FE A:FE1001 3.7 74.3 1.0
OD1 A:ASP211 3.8 42.7 1.0
CB A:ASP211 4.0 37.0 1.0
O A:HOH568 4.0 45.5 1.0
CG A:GLU240 4.1 50.6 1.0
CG A:GLU150 4.3 31.7 0.4
NE2 A:HIS243 4.4 39.6 1.0
C5B A:BYC1003 4.4 50.0 1.0
CD2 A:HIS243 4.4 38.9 1.0
C6B A:BYC1003 4.5 51.1 1.0
CG A:GLU150 4.7 31.7 0.6
CA A:ASP211 4.8 35.7 1.0
CG1 A:VAL146 4.8 24.4 1.0
C4B A:BYC1003 4.9 53.1 1.0
OE2 A:GLU150 4.9 31.9 0.6
CB A:GLU240 5.0 45.8 1.0

Iron binding site 3 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 3 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
B:Fe1001

b:72.8
occ:1.00
 OE1 B:GLU150 2.3 41.7 0.5
OE1 B:GLU120 2.5 40.4 1.0
ND1 B:HIS153 2.7 33.3 1.0
OE2 B:GLU120 3.1 43.7 1.0
CD B:GLU120 3.2 38.1 1.0
CD B:GLU150 3.4 39.1 0.5
C7B B:BYC1003 3.4 47.5 1.0
C6B B:BYC1003 3.6 49.0 1.0
CE1 B:HIS153 3.6 38.0 1.0
OE1 B:GLU240 3.7 61.8 1.0
OE2 B:GLU240 3.7 56.3 1.0
CG B:HIS153 3.7 36.9 1.0
FE B:FE1002 3.7 63.8 1.0
OE2 B:GLU150 3.8 41.1 0.5
CB B:HIS153 3.9 34.7 1.0
CD B:GLU240 4.0 56.7 1.0
O57 B:BYC1003 4.4 53.1 1.0
C2B B:BYC1003 4.4 49.7 1.0
C5B B:BYC1003 4.6 50.3 1.0
CG B:GLU120 4.7 32.5 1.0
CG B:GLU150 4.7 35.7 0.5
NE2 B:HIS153 4.8 39.3 1.0
CE B:MET236 4.8 36.8 1.0
NE2 B:GLN116 4.8 49.3 1.0
CD2 B:HIS153 4.8 38.2 1.0
CA B:GLU150 4.8 34.9 0.5
C1B B:BYC1003 4.9 51.6 1.0
CB B:GLU150 5.0 34.6 0.5
CA B:GLU150 5.0 34.3 0.5

Iron binding site 4 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 4 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
B:Fe1002

b:63.8
occ:1.00
 OE2 B:GLU150 1.9 41.1 0.5
OD2 B:ASP211 2.1 48.0 1.0
ND1 B:HIS243 2.3 41.4 1.0
OE2 B:GLU240 2.4 56.3 1.0
CD B:GLU150 2.9 39.1 0.5
CD B:GLU240 3.0 56.7 1.0
OE1 B:GLU240 3.1 61.8 1.0
CE1 B:HIS243 3.2 42.5 1.0
CG B:ASP211 3.2 39.0 1.0
OE1 B:GLU150 3.2 41.7 0.5
CG B:HIS243 3.3 40.9 1.0
CB B:HIS243 3.6 39.5 1.0
FE B:FE1001 3.7 72.8 1.0
CB B:ASP211 4.0 36.9 1.0
C5B B:BYC1003 4.0 50.3 1.0
OD1 B:ASP211 4.1 44.3 1.0
CG B:GLU150 4.2 35.7 0.5
C6B B:BYC1003 4.3 49.0 1.0
O B:HOH635 4.3 41.9 1.0
NE2 B:HIS243 4.3 41.7 1.0
CG B:GLU240 4.3 51.5 1.0
CD2 B:HIS243 4.4 42.3 1.0
C4B B:BYC1003 4.6 51.6 1.0
CG B:GLU150 4.7 33.5 0.5
CA B:ASP211 4.8 35.7 1.0
CG1 B:VAL146 4.9 31.7 1.0
C7B B:BYC1003 4.9 47.5 1.0

Iron binding site 5 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 5 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 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:Fe1001

b:86.8
occ:1.00
 OE1 C:GLU150 2.5 28.8 0.4
OE1 C:GLU120 2.6 45.5 1.0
ND1 C:HIS153 2.7 34.2 1.0
OE1 C:GLU240 2.8 65.5 1.0
OE2 C:GLU120 3.1 40.8 1.0
CD C:GLU120 3.3 38.7 1.0
FE C:FE1002 3.3 63.7 1.0
CE1 C:HIS153 3.4 36.7 1.0
C7B C:BYC1003 3.4 44.6 1.0
C6B C:BYC1003 3.6 46.4 1.0
CD C:GLU150 3.6 27.2 0.4
CD C:GLU240 3.7 59.4 1.0
CG C:HIS153 3.9 34.0 1.0
OE2 C:GLU240 3.9 60.7 1.0
OE2 C:GLU150 4.1 28.6 0.4
CB C:HIS153 4.3 33.3 1.0
C2B C:BYC1003 4.4 46.1 1.0
O57 C:BYC1003 4.5 46.9 1.0
NE2 C:HIS153 4.6 37.2 1.0
C5B C:BYC1003 4.7 46.8 1.0
CG C:GLU120 4.8 37.0 1.0
CD2 C:HIS153 4.9 38.0 1.0
CG C:GLU150 4.9 29.1 0.4
CA C:GLU150 4.9 31.0 0.4
C1B C:BYC1003 4.9 45.5 1.0
ND1 C:HIS243 5.0 37.9 1.0
CG C:GLU150 5.0 30.4 0.6
CA C:GLU150 5.0 31.2 0.6

Iron binding site 6 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 6 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 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:Fe1002

b:63.7
occ:1.00
 OD2 C:ASP211 2.0 48.2 1.0
OE2 C:GLU240 2.2 60.7 1.0
ND1 C:HIS243 2.4 37.9 1.0
OE2 C:GLU150 2.5 28.6 0.4
OE1 C:GLU150 2.8 28.8 0.4
CD C:GLU150 3.0 27.2 0.4
CD C:GLU240 3.1 59.4 1.0
CG C:ASP211 3.2 39.8 1.0
OE1 C:GLU240 3.3 65.5 1.0
CE1 C:HIS243 3.3 39.9 1.0
FE C:FE1001 3.3 86.8 1.0
CG C:HIS243 3.5 36.9 1.0
CB C:HIS243 3.8 37.3 1.0
CB C:ASP211 4.0 34.3 1.0
O C:HOH508 4.0 49.1 1.0
OD1 C:ASP211 4.0 45.1 1.0
C5B C:BYC1003 4.1 46.8 1.0
C6B C:BYC1003 4.1 46.4 1.0
CG C:GLU150 4.3 29.1 0.4
CG C:GLU150 4.5 30.4 0.6
NE2 C:HIS243 4.5 37.5 1.0
CG C:GLU240 4.5 52.4 1.0
CD2 C:HIS243 4.6 35.9 1.0
CA C:ASP211 4.8 34.4 1.0
C7B C:BYC1003 4.8 44.6 1.0
C4B C:BYC1003 4.8 47.6 1.0
OE1 C:GLU150 4.8 30.6 0.6
CG1 C:VAL146 4.8 26.6 1.0

Iron binding site 7 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 7 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 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:Fe1001

b:74.0
occ:1.00
 OE1 D:GLU150 2.1 36.0 0.5
OE1 D:GLU120 2.4 52.4 1.0
ND1 D:HIS153 2.6 44.0 1.0
CD D:GLU120 3.1 46.5 1.0
OE2 D:GLU120 3.1 50.6 1.0
CD D:GLU150 3.2 34.7 0.5
C7B D:BYC1003 3.3 49.9 1.0
CE1 D:HIS153 3.4 45.8 1.0
OE2 D:GLU240 3.5 64.1 1.0
C6B D:BYC1003 3.5 51.2 1.0
OE1 D:GLU240 3.6 63.5 1.0
FE D:FE1002 3.6 73.1 1.0
OE2 D:GLU150 3.7 34.4 0.5
CG D:HIS153 3.7 41.6 1.0
CD D:GLU240 3.9 63.1 1.0
CB D:HIS153 4.1 39.7 1.0
C2B D:BYC1003 4.4 51.2 1.0
O57 D:BYC1003 4.5 51.1 1.0
CG D:GLU150 4.5 36.6 0.5
CG D:GLU120 4.5 42.9 1.0
NE2 D:HIS153 4.6 43.7 1.0
C5B D:BYC1003 4.6 51.5 1.0
CA D:GLU150 4.7 37.9 0.5
CD2 D:HIS153 4.7 40.3 1.0
CB D:GLU150 4.8 37.3 0.5
CE D:MET236 4.9 40.7 1.0
CA D:GLU150 4.9 37.7 0.5
C1B D:BYC1003 4.9 50.6 1.0
NE2 D:GLN116 5.0 48.4 1.0

Iron binding site 8 out of 8 in 3pm5

Go back to Iron Binding Sites List in 3pm5
Iron binding site 8 out of 8 in the Crystal Structure of Boxb in Mixed Valent State with Bound Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 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:Fe1002

b:73.1
occ:1.00
 OE2 D:GLU150 2.1 34.4 0.5
OE2 D:GLU240 2.1 64.1 1.0
OD2 D:ASP211 2.2 49.7 1.0
ND1 D:HIS243 2.4 45.7 1.0
CD D:GLU150 3.0 34.7 0.5
CD D:GLU240 3.0 63.1 1.0
CG D:ASP211 3.2 44.6 1.0
OE1 D:GLU150 3.3 36.0 0.5
CE1 D:HIS243 3.3 47.5 1.0
CG D:HIS243 3.4 45.9 1.0
OE1 D:GLU240 3.5 63.5 1.0
FE D:FE1001 3.6 74.0 1.0
CB D:HIS243 3.6 45.2 1.0
CB D:ASP211 3.7 41.5 1.0
C5B D:BYC1003 4.1 51.5 1.0
C6B D:BYC1003 4.1 51.2 1.0
OD1 D:ASP211 4.2 49.8 1.0
CG D:GLU240 4.2 57.4 1.0
O D:HOH581 4.3 54.4 1.0
CG D:GLU150 4.3 36.6 0.5
NE2 D:HIS243 4.4 48.9 1.0
CD2 D:HIS243 4.5 48.7 1.0
CA D:ASP211 4.7 40.3 1.0
C4B D:BYC1003 4.7 52.2 1.0
C7B D:BYC1003 4.7 49.9 1.0
CG D:GLU150 4.9 36.1 0.5
CG1 D:VAL146 5.0 37.9 1.0
CA D:GLU240 5.0 54.6 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 Aug 4 18:04:37 2024

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