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Iron in PDB 9jp5: Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1

Protein crystallography data

The structure of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1, PDB code: 9jp5 was solved by K.A.Kumar, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.46 / 2.88
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 194.599, 194.599, 157.287, 90, 90, 120
R / Rfree (%) 24.7 / 30.6

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 (pdb code 9jp5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1, PDB code: 9jp5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 9jp5

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Iron binding site 1 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:18.5
occ:1.00
 FE1 A:FES501 0.0 18.5 1.0
S2 A:FES501 2.2 17.9 1.0
S1 A:FES501 2.2 18.3 1.0
SG A:CYS94 2.2 22.7 1.0
SG A:CYS74 2.4 21.3 1.0
FE2 A:FES501 2.6 18.6 1.0
CB A:CYS94 3.1 24.8 1.0
CB A:CYS74 3.2 20.1 1.0
CB A:TYR96 4.2 27.6 1.0
CB A:HIS76 4.3 21.4 1.0
N A:HIS97 4.4 23.4 1.0
ND1 A:HIS97 4.4 22.2 1.0
CA A:CYS94 4.5 25.7 1.0
ND1 A:HIS76 4.5 22.1 1.0
CB A:MET79 4.5 20.9 1.0
CA A:CYS74 4.7 19.3 1.0
C A:CYS94 4.8 24.8 1.0
N A:ARG77 4.8 29.3 1.0
O A:CYS94 4.8 25.6 1.0
CG A:HIS76 4.9 22.0 1.0
N A:TYR96 4.9 24.8 1.0
CB A:TRP99 4.9 27.3 1.0
N A:MET79 5.0 25.4 1.0
CA A:TYR96 5.0 25.7 1.0
CB A:HIS97 5.0 22.4 1.0

Iron binding site 2 out of 12 in 9jp5

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Iron binding site 2 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:18.6
occ:1.00
 FE2 A:FES501 0.0 18.6 1.0
ND1 A:HIS97 2.2 22.2 1.0
ND1 A:HIS76 2.2 22.1 1.0
S2 A:FES501 2.2 17.9 1.0
S1 A:FES501 2.2 18.3 1.0
FE1 A:FES501 2.6 18.5 1.0
CG A:HIS97 3.0 22.2 1.0
CG A:HIS76 3.1 22.0 1.0
CE1 A:HIS76 3.2 22.4 1.0
CB A:HIS97 3.2 22.4 1.0
CE1 A:HIS97 3.2 20.9 1.0
CB A:HIS76 3.4 21.4 1.0
N A:HIS97 3.8 23.4 1.0
CB A:TYR96 4.0 27.6 1.0
CA A:HIS97 4.1 24.0 1.0
N A:ARG77 4.2 29.3 1.0
CD2 A:HIS97 4.2 22.0 1.0
SG A:CYS74 4.2 21.3 1.0
NE2 A:HIS97 4.2 20.1 1.0
CD2 A:HIS76 4.3 22.5 1.0
NE2 A:HIS76 4.3 23.7 1.0
SG A:CYS94 4.4 22.7 1.0
CG A:TYR96 4.5 27.0 1.0
C A:TYR96 4.5 24.0 1.0
CA A:HIS76 4.6 22.3 1.0
CD2 A:TYR96 4.6 26.8 1.0
CB A:ARG77 4.7 37.9 1.0
CG A:ARG77 4.8 48.9 1.0
C A:HIS76 4.8 25.9 1.0
CD1 A:TRP99 4.8 28.8 1.0
CA A:TYR96 4.9 25.7 1.0
C A:HIS97 4.9 24.8 1.0
NE1 A:TRP99 4.9 26.9 1.0
CA A:ARG77 5.0 30.9 1.0

Iron binding site 3 out of 12 in 9jp5

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Iron binding site 3 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:2.1
occ:1.00
 OD1 A:ASP363 2.0 11.5 1.0
NE2 A:HIS203 2.0 21.1 1.0
NE2 A:HIS208 2.2 19.8 1.0
O A:HOH695 2.2 0.5 1.0
CG A:ASP363 2.6 11.5 1.0
OD2 A:ASP363 2.6 12.0 1.0
CE1 A:HIS203 2.9 21.3 1.0
CE1 A:HIS208 3.1 21.0 1.0
CD2 A:HIS203 3.1 20.1 1.0
CD2 A:HIS208 3.2 21.8 1.0
ND2 A:ASN196 4.0 16.8 1.0
ND1 A:HIS203 4.1 20.6 1.0
CB A:ASP363 4.1 11.2 1.0
CG A:HIS203 4.2 19.9 1.0
ND1 A:HIS208 4.2 20.7 1.0
CG A:HIS208 4.3 21.1 1.0
O A:HOH675 4.3 10.2 1.0
CD2 A:PHE359 4.7 18.4 1.0
OG1 A:THR204 4.9 17.1 1.0
CZ A:PHE353 4.9 14.8 1.0
CE1 A:PHE353 4.9 14.4 1.0

Iron binding site 4 out of 12 in 9jp5

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Iron binding site 4 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:13.5
occ:1.00
 FE1 C:FES501 0.0 13.5 1.0
S2 C:FES501 2.2 13.4 1.0
SG C:CYS94 2.2 22.0 1.0
S1 C:FES501 2.2 14.8 1.0
SG C:CYS74 2.4 10.1 1.0
FE2 C:FES501 2.8 13.3 1.0
CB C:CYS94 3.1 22.3 1.0
CB C:CYS74 3.1 11.3 1.0
CB C:HIS76 4.3 21.8 1.0
CB C:TYR96 4.3 15.6 1.0
N C:HIS97 4.4 17.0 1.0
CA C:CYS94 4.5 22.4 1.0
CB C:MET79 4.6 18.5 1.0
ND1 C:HIS76 4.6 22.2 1.0
CA C:CYS74 4.6 12.1 1.0
CB C:TRP99 4.7 18.8 1.0
ND1 C:HIS97 4.7 16.3 1.0
C C:CYS94 4.8 21.0 1.0
N C:TYR96 4.8 15.9 1.0
N C:ARG77 4.9 24.0 1.0
CG C:HIS76 4.9 23.5 1.0
CG C:TRP99 5.0 18.6 1.0
CA C:TYR96 5.0 15.9 1.0
O C:CYS94 5.0 23.3 1.0

Iron binding site 5 out of 12 in 9jp5

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Iron binding site 5 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:13.3
occ:1.00
 FE2 C:FES501 0.0 13.3 1.0
ND1 C:HIS76 2.2 22.2 1.0
S1 C:FES501 2.2 14.8 1.0
S2 C:FES501 2.2 13.4 1.0
ND1 C:HIS97 2.3 16.3 1.0
FE1 C:FES501 2.8 13.5 1.0
CG C:HIS76 3.1 23.5 1.0
CE1 C:HIS76 3.2 23.3 1.0
CG C:HIS97 3.2 15.5 1.0
CE1 C:HIS97 3.3 15.3 1.0
CB C:HIS76 3.4 21.8 1.0
CB C:HIS97 3.4 16.3 1.0
N C:HIS97 3.7 17.0 1.0
CB C:TYR96 4.1 15.6 1.0
CA C:HIS97 4.1 16.9 1.0
N C:ARG77 4.2 24.0 1.0
CD2 C:HIS76 4.3 24.2 1.0
NE2 C:HIS76 4.3 25.3 1.0
CD2 C:HIS97 4.3 15.3 1.0
NE2 C:HIS97 4.3 15.3 1.0
CG C:TYR96 4.4 15.7 1.0
SG C:CYS74 4.4 10.1 1.0
CD2 C:TYR96 4.4 15.6 1.0
C C:TYR96 4.5 16.4 1.0
SG C:CYS94 4.5 22.0 1.0
CA C:HIS76 4.6 21.3 1.0
CB C:ARG77 4.6 31.4 1.0
C C:HIS76 4.8 22.6 1.0
CA C:TYR96 4.8 15.9 1.0
C C:HIS97 4.9 18.1 1.0
CD1 C:TRP99 4.9 18.4 1.0
CG C:ARG77 4.9 39.0 1.0
CA C:ARG77 5.0 26.4 1.0

Iron binding site 6 out of 12 in 9jp5

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Iron binding site 6 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:4.3
occ:1.00
 OD1 C:ASP363 1.8 12.7 1.0
NE2 C:HIS203 2.2 29.0 1.0
NE2 C:HIS208 2.2 20.6 1.0
O C:HOH696 2.3 0.5 1.0
CG C:ASP363 2.6 13.4 1.0
OD2 C:ASP363 2.7 14.1 1.0
CE1 C:HIS208 3.1 20.4 1.0
CE1 C:HIS203 3.1 27.4 1.0
CD2 C:HIS203 3.2 27.7 1.0
CD2 C:HIS208 3.3 23.7 1.0
ND2 C:ASN196 4.0 15.3 1.0
CB C:ASP363 4.0 13.0 1.0
O C:HOH651 4.1 16.1 1.0
ND1 C:HIS203 4.3 26.1 1.0
ND1 C:HIS208 4.3 21.0 1.0
CG C:HIS203 4.3 26.2 1.0
CG C:HIS208 4.4 22.8 1.0
CD2 C:PHE359 4.8 16.4 1.0
CA C:ASP363 4.9 12.8 1.0
CE2 C:PHE353 5.0 16.6 1.0

Iron binding site 7 out of 12 in 9jp5

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Iron binding site 7 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:19.3
occ:1.00
 FE1 E:FES501 0.0 19.3 1.0
ND1 E:HIS97 2.0 22.1 1.0
S2 E:FES501 2.2 18.8 1.0
S1 E:FES501 2.2 16.6 1.0
ND1 E:HIS76 2.5 18.4 1.0
FE2 E:FES501 2.8 19.0 1.0
CE1 E:HIS97 2.9 21.9 1.0
CG E:HIS97 3.0 23.2 1.0
CE1 E:HIS76 3.3 18.3 1.0
CG E:HIS76 3.4 18.6 1.0
CB E:HIS97 3.4 24.8 1.0
CB E:HIS76 3.6 19.0 1.0
CB E:TYR96 3.9 19.8 1.0
N E:HIS97 3.9 23.4 1.0
NE2 E:HIS97 4.0 21.2 1.0
CD2 E:HIS97 4.1 23.7 1.0
N E:ARG77 4.1 24.2 1.0
CG E:TYR96 4.2 18.8 1.0
CA E:HIS97 4.3 24.9 1.0
CD2 E:TYR96 4.3 17.7 1.0
NE2 E:HIS76 4.4 20.0 1.0
CD2 E:HIS76 4.4 18.8 1.0
CB E:ARG77 4.4 34.1 1.0
SG E:CYS74 4.5 21.3 1.0
SG E:CYS94 4.5 23.2 1.0
C E:TYR96 4.6 20.5 1.0
CG E:ARG77 4.7 43.5 1.0
CA E:HIS76 4.7 19.6 1.0
C E:HIS76 4.8 21.4 1.0
CA E:TYR96 4.8 19.7 1.0
CA E:ARG77 4.9 27.3 1.0
CD1 E:TYR96 4.9 19.1 1.0
CD1 E:TRP99 5.0 23.6 1.0

Iron binding site 8 out of 12 in 9jp5

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Iron binding site 8 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:19.0
occ:1.00
 FE2 E:FES501 0.0 19.0 1.0
SG E:CYS94 2.2 23.2 1.0
S1 E:FES501 2.2 16.6 1.0
S2 E:FES501 2.2 18.8 1.0
SG E:CYS74 2.4 21.3 1.0
FE1 E:FES501 2.8 19.3 1.0
CB E:CYS94 3.1 24.1 1.0
CB E:CYS74 3.3 17.1 1.0
CB E:TYR96 4.2 19.8 1.0
CB E:HIS76 4.4 19.0 1.0
ND1 E:HIS97 4.4 22.1 1.0
N E:HIS97 4.5 23.4 1.0
CA E:CYS94 4.5 24.7 1.0
CB E:MET79 4.6 21.6 1.0
ND1 E:HIS76 4.6 18.4 1.0
CB E:TRP99 4.7 23.6 1.0
CA E:CYS74 4.7 16.4 1.0
C E:CYS94 4.9 22.4 1.0
N E:ARG77 4.9 24.2 1.0
N E:TYR96 4.9 19.6 1.0
CG E:TRP99 4.9 23.5 1.0
O E:CYS94 5.0 21.6 1.0
CA E:TYR96 5.0 19.7 1.0

Iron binding site 9 out of 12 in 9jp5

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Iron binding site 9 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe502

b:6.6
occ:1.00
 OD1 E:ASP363 2.0 10.7 1.0
NE2 E:HIS203 2.1 20.7 1.0
NE2 E:HIS208 2.1 24.1 1.0
O E:HOH679 2.5 3.3 1.0
OD2 E:ASP363 2.5 10.8 1.0
CG E:ASP363 2.6 10.5 1.0
CE1 E:HIS208 3.0 25.0 1.0
CE1 E:HIS203 3.0 19.9 1.0
CD2 E:HIS203 3.1 21.1 1.0
CD2 E:HIS208 3.3 24.8 1.0
ND2 E:ASN196 4.0 18.4 1.0
CB E:ASP363 4.1 10.7 1.0
ND1 E:HIS208 4.2 25.6 1.0
ND1 E:HIS203 4.2 19.7 1.0
CG E:HIS203 4.2 20.6 1.0
CG E:HIS208 4.3 24.8 1.0
CD2 E:PHE359 4.8 16.4 1.0
CA E:ASP363 4.9 11.0 1.0
CG E:ASN196 5.0 18.5 1.0

Iron binding site 10 out of 12 in 9jp5

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Iron binding site 10 out of 12 in the Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Phthalate 3,4-Dioxygenase From Rhodococcus Jostii RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:9.2
occ:1.00
 FE1 G:FES501 0.0 9.2 1.0
ND1 G:HIS76 2.2 9.8 1.0
S1 G:FES501 2.2 9.1 1.0
S2 G:FES501 2.2 9.3 1.0
ND1 G:HIS97 2.3 9.1 1.0
FE2 G:FES501 2.7 9.2 1.0
CG G:HIS76 3.0 10.1 1.0
CE1 G:HIS76 3.2 9.8 1.0
CG G:HIS97 3.2 9.3 1.0
CE1 G:HIS97 3.2 9.0 1.0
CB G:HIS76 3.3 10.8 1.0
CB G:HIS97 3.5 9.6 1.0
N G:ARG77 3.8 15.9 1.0
N G:HIS97 3.9 10.4 1.0
CB G:TYR96 4.1 12.0 1.0
SG G:CYS74 4.2 6.9 1.0
CD2 G:HIS76 4.2 9.8 1.0
NE2 G:HIS76 4.2 9.8 1.0
CA G:HIS97 4.3 10.3 1.0
NE2 G:HIS97 4.3 9.1 1.0
CD2 G:HIS97 4.3 9.3 1.0
CB G:ARG77 4.3 21.6 1.0
CA G:HIS76 4.4 11.7 1.0
CG G:TYR96 4.5 11.4 1.0
SG G:CYS94 4.5 14.5 1.0
CG G:ARG77 4.5 26.6 1.0
CD2 G:TYR96 4.5 11.3 1.0
C G:HIS76 4.5 13.6 1.0
CA G:ARG77 4.6 17.4 1.0
C G:TYR96 4.7 10.7 1.0
CD1 G:TRP99 4.9 11.7 1.0
CA G:TYR96 5.0 11.2 1.0
NE1 G:TRP99 5.0 11.6 1.0

Reference:

K.A.Kumar, K.A.Kumar, P.Kumar. N/A N/A.
Page generated: Wed Nov 13 11:08:20 2024

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