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Zinc in PDB 2j1m: P450 BM3 Heme Domain in Complex with Dmso

Enzymatic activity of P450 BM3 Heme Domain in Complex with Dmso

All present enzymatic activity of P450 BM3 Heme Domain in Complex with Dmso:
1.14.14.1;

Protein crystallography data

The structure of P450 BM3 Heme Domain in Complex with Dmso, PDB code: 2j1m was solved by J.Kuper, W.Tuck-Seng, D.Roccatano, M.Wilmanns, U.Schwaneberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.04 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.765, 86.849, 159.408, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.9

Other elements in 2j1m:

The structure of P450 BM3 Heme Domain in Complex with Dmso also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the P450 BM3 Heme Domain in Complex with Dmso (pdb code 2j1m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the P450 BM3 Heme Domain in Complex with Dmso, PDB code: 2j1m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2j1m

Go back to Zinc Binding Sites List in 2j1m
Zinc binding site 1 out of 7 in the P450 BM3 Heme Domain in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P450 BM3 Heme Domain in Complex with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1457

b:34.9
occ:1.00
 OD2 A:ASP338 2.0 30.0 1.0
O A:HOH2500 2.1 33.4 1.0
OD1 B:ASP23 2.1 25.1 1.0
OE1 A:GLU348 2.2 32.0 1.0
OE2 A:GLU348 2.4 35.4 1.0
CD A:GLU348 2.6 31.1 1.0
OD2 B:ASP23 2.7 35.3 1.0
CG B:ASP23 2.7 34.9 1.0
CG A:ASP338 2.8 27.7 1.0
OD1 A:ASP338 2.9 24.7 1.0
O B:HOH2030 3.5 34.5 1.0
CG A:GLU348 4.1 32.0 1.0
CB B:ASP23 4.2 29.2 1.0
CB A:ASP338 4.3 23.5 1.0
O B:HOH2015 4.3 33.1 1.0
CE B:LYS24 4.6 30.0 1.0
CG B:LYS24 4.6 26.3 1.0
O B:HOH2425 4.7 81.1 1.0
N B:ASP23 4.7 29.5 1.0
CD B:LYS24 4.7 27.3 1.0
O A:HOH2368 4.8 59.9 1.0
CB A:GLU348 4.8 28.4 1.0
CA B:ASP23 4.8 31.5 1.0
CA A:GLU348 4.9 26.5 1.0
C B:ASP23 5.0 29.8 1.0

Zinc binding site 2 out of 7 in 2j1m

Go back to Zinc Binding Sites List in 2j1m
Zinc binding site 2 out of 7 in the P450 BM3 Heme Domain in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P450 BM3 Heme Domain in Complex with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1458

b:45.2
occ:1.00
 NE2 A:HIS266 2.3 22.7 1.0
O A:HOH2501 2.6 42.8 1.0
CE1 A:HIS266 3.2 26.4 1.0
CD2 A:HIS266 3.4 26.2 1.0
CG2 A:ILE174 3.7 36.3 1.0
CG2 A:VAL178 4.0 31.4 1.0
CG2 A:THR146 4.0 22.0 1.0
O A:HOH2221 4.2 25.4 1.0
ND1 A:HIS266 4.3 24.4 1.0
CG A:HIS266 4.5 22.8 1.0

Zinc binding site 3 out of 7 in 2j1m

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Zinc binding site 3 out of 7 in the P450 BM3 Heme Domain in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of P450 BM3 Heme Domain in Complex with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1459

b:71.5
occ:1.00
 OE2 A:GLU140 2.4 31.0 1.0
NE2 A:HIS138 2.5 29.3 1.0
O A:HOH2502 3.0 55.3 1.0
CE1 A:HIS138 3.3 30.2 1.0
CD A:GLU140 3.3 25.7 1.0
CG A:GLU140 3.4 20.4 1.0
CD2 A:HIS138 3.6 29.0 1.0
O A:HOH2091 3.9 30.1 1.0
CG1 A:VAL445 4.3 17.8 1.0
ND1 A:HIS138 4.5 31.4 1.0
OE1 A:GLU140 4.5 24.4 1.0
CG A:HIS138 4.7 26.9 1.0
O A:HOH2089 4.8 52.2 1.0
CB A:GLU140 4.9 17.2 1.0

Zinc binding site 4 out of 7 in 2j1m

Go back to Zinc Binding Sites List in 2j1m
Zinc binding site 4 out of 7 in the P450 BM3 Heme Domain in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of P450 BM3 Heme Domain in Complex with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1460

b:57.9
occ:1.00
 O A:HOH2504 2.1 38.3 1.0
O A:HOH2503 2.1 30.8 1.0
OE2 A:GLU373 2.2 38.9 1.0
OE1 A:GLU373 2.8 38.9 1.0
CD A:GLU373 2.8 38.5 1.0
CG A:GLU373 4.3 28.9 1.0

Zinc binding site 5 out of 7 in 2j1m

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Zinc binding site 5 out of 7 in the P450 BM3 Heme Domain in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of P450 BM3 Heme Domain in Complex with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1461

b:98.6
occ:1.00
 O A:HOH2505 2.2 46.4 1.0
NE2 A:HIS236 2.3 35.3 1.0
OD2 A:ASP231 2.5 59.4 1.0
OD1 A:ASP231 2.9 61.9 1.0
CG A:ASP231 2.9 59.1 1.0
CE1 A:HIS236 3.2 38.9 1.0
CD2 A:HIS236 3.3 32.6 1.0
CB A:ASP231 4.3 54.0 1.0
ND1 A:HIS236 4.3 37.7 1.0
CG A:HIS236 4.4 29.7 1.0
CA A:ASP231 4.6 47.9 1.0
C A:ASP231 4.8 42.4 1.0
O A:ASP231 4.9 48.2 1.0

Zinc binding site 6 out of 7 in 2j1m

Go back to Zinc Binding Sites List in 2j1m
Zinc binding site 6 out of 7 in the P450 BM3 Heme Domain in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of P450 BM3 Heme Domain in Complex with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1457

b:23.7
occ:1.00
 OD1 B:ASP338 1.9 17.8 1.0
OE1 B:GLU348 1.9 20.7 1.0
O B:HOH2450 2.1 22.2 1.0
OD2 B:ASP338 2.4 17.0 1.0
CG B:ASP338 2.5 23.3 1.0
CD B:GLU348 2.8 21.2 1.0
OE2 B:GLU348 3.0 22.6 1.0
CB B:ASP338 4.0 20.0 1.0
CG B:GLU348 4.1 20.1 1.0
O B:HOH2350 4.3 37.8 1.0
O B:HOH2149 4.3 48.7 1.0
CB B:GLU348 4.5 20.6 1.0
N B:LYS349 4.7 18.1 1.0
O B:HOH2338 4.7 32.9 1.0
CA B:GLU348 4.7 17.6 1.0
O B:HOH2156 5.0 57.8 1.0
CA B:ASP338 5.0 20.0 1.0

Zinc binding site 7 out of 7 in 2j1m

Go back to Zinc Binding Sites List in 2j1m
Zinc binding site 7 out of 7 in the P450 BM3 Heme Domain in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of P450 BM3 Heme Domain in Complex with Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1458

b:58.7
occ:1.00
 OD1 B:ASP231 2.0 20.2 1.0
OD2 B:ASP231 2.2 53.2 1.0
NE2 B:HIS236 2.3 38.0 1.0
CG B:ASP231 2.3 42.0 1.0
CE1 B:HIS236 3.0 39.5 1.0
CD2 B:HIS236 3.4 35.4 1.0
CB B:ASP231 3.8 42.7 1.0
ND1 B:HIS236 4.2 34.6 1.0
CG B:HIS236 4.5 33.1 1.0
CA B:ASP231 4.9 40.8 1.0

Reference:

J.Kuper, T.S.Wong, D.Roccatano, M.Wilmanns, U.Schwaneberg. Understanding A Mechanism of Organic Cosolvent Inactivation in Heme Monooxygenase P450 Bm-3. J.Am.Chem.Soc. V. 129 5786 2007.
ISSN: ISSN 0002-7863
PubMed: 17429965
DOI: 10.1021/JA067036X
Page generated: Thu Oct 17 01:03:19 2024

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