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Iron in PDB 7vju: Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1

Protein crystallography data

The structure of Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1, PDB code: 7vju was solved by J.K.Mahto, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.15 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.561, 134.213, 145.01, 90, 90, 90
R / Rfree (%) 15.7 / 22.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1 (pdb code 7vju). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1, PDB code: 7vju:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7vju

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Iron binding site 1 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:33.1
occ:1.00
 FE1 A:FES501 0.0 33.1 1.0
ND1 A:HIS105 2.1 35.1 1.0
ND1 A:HIS84 2.2 31.0 1.0
S1 A:FES501 2.2 32.5 1.0
S2 A:FES501 2.2 32.1 1.0
FE2 A:FES501 2.7 31.5 1.0
CE1 A:HIS105 3.1 35.4 1.0
CE1 A:HIS84 3.1 31.5 1.0
CG A:HIS105 3.1 34.3 1.0
CG A:HIS84 3.2 32.9 1.0
CB A:HIS105 3.4 33.0 1.0
CB A:HIS84 3.6 33.1 1.0
N A:HIS105 3.8 33.4 1.0
CB A:TYR104 4.0 33.4 1.0
NE2 A:HIS105 4.2 34.2 1.0
CD2 A:HIS105 4.2 34.0 1.0
CA A:HIS105 4.2 33.8 1.0
CG A:TYR104 4.3 33.4 1.0
NE2 A:HIS84 4.3 32.3 1.0
N A:ARG85 4.3 33.5 1.0
CD2 A:HIS84 4.4 32.6 1.0
SG A:CYS82 4.4 34.2 1.0
CD1 A:TYR104 4.4 31.7 1.0
C A:TYR104 4.5 33.2 1.0
SG A:CYS102 4.5 34.1 1.0
CB A:ARG85 4.7 32.8 1.0
CA A:TYR104 4.7 32.8 1.0
CG A:ARG85 4.8 36.6 1.0
CA A:HIS84 4.8 34.1 1.0
CD1 A:TRP107 4.8 35.0 1.0
NE1 A:TRP107 4.9 34.3 1.0
C A:HIS105 4.9 34.3 1.0

Iron binding site 2 out of 9 in 7vju

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Iron binding site 2 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:31.5
occ:1.00
 FE2 A:FES501 0.0 31.5 1.0
S2 A:FES501 2.2 32.1 1.0
SG A:CYS82 2.2 34.2 1.0
S1 A:FES501 2.3 32.5 1.0
SG A:CYS102 2.3 34.1 1.0
FE1 A:FES501 2.7 33.1 1.0
CB A:CYS102 3.1 35.7 1.0
CB A:CYS82 3.1 32.5 1.0
CB A:TYR104 4.2 33.4 1.0
CB A:HIS84 4.2 33.1 1.0
CB A:ALA87 4.4 27.5 1.0
ND1 A:HIS84 4.4 31.0 1.0
CA A:CYS102 4.5 35.7 1.0
CA A:CYS82 4.5 32.5 1.0
ND1 A:HIS105 4.5 35.1 1.0
N A:HIS105 4.6 33.4 1.0
N A:TYR104 4.7 32.2 1.0
N A:ARG85 4.8 33.5 1.0
CG A:HIS84 4.8 32.9 1.0
CB A:TRP107 4.9 36.0 1.0
CA A:TYR104 4.9 32.8 1.0
N A:HIS84 5.0 34.2 1.0
N A:ALA87 5.0 29.7 1.0

Iron binding site 3 out of 9 in 7vju

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Iron binding site 3 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:42.1
occ:1.00
 NE2 A:HIS215 2.0 46.5 1.0
NE2 A:HIS210 2.0 43.6 1.0
OD1 A:ASP356 2.0 40.8 1.0
O A:HOH736 2.1 54.4 1.0
O A:HOH757 2.5 52.9 1.0
CG A:ASP356 2.7 42.3 1.0
OD2 A:ASP356 2.8 42.6 1.0
CE1 A:HIS210 2.9 42.7 1.0
CE1 A:HIS215 2.9 46.5 1.0
CD2 A:HIS215 3.1 46.9 1.0
CD2 A:HIS210 3.2 43.8 1.0
ND2 A:ASN204 4.0 38.0 1.0
ND1 A:HIS210 4.1 42.3 1.0
ND1 A:HIS215 4.1 44.5 1.0
CG A:HIS215 4.2 48.3 1.0
CB A:ASP356 4.2 41.2 1.0
CG A:HIS210 4.2 40.7 1.0
O A:HOH806 4.3 58.9 1.0
O A:HOH739 4.4 51.2 1.0
CG2 A:ILE352 4.5 44.4 1.0
O A:HOH708 4.5 55.0 1.0
CA A:ASP356 4.8 41.8 1.0
O A:HOH623 4.9 55.0 1.0
CG A:ASN204 4.9 41.4 1.0
OD1 A:ASN204 5.0 43.9 1.0

Iron binding site 4 out of 9 in 7vju

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Iron binding site 4 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:34.2
occ:1.00
 FE1 C:FES502 0.0 34.2 1.0
ND1 C:HIS105 2.1 39.1 1.0
ND1 C:HIS84 2.2 30.4 1.0
S1 C:FES502 2.2 34.3 1.0
S2 C:FES502 2.3 34.0 1.0
FE2 C:FES502 2.6 33.4 1.0
CE1 C:HIS105 3.1 39.1 1.0
CG C:HIS105 3.1 38.7 1.0
CE1 C:HIS84 3.1 30.6 1.0
CG C:HIS84 3.2 30.9 1.0
CB C:HIS105 3.4 37.5 1.0
CB C:HIS84 3.4 30.9 1.0
N C:HIS105 3.7 38.6 1.0
CB C:TYR104 4.0 35.9 1.0
CA C:HIS105 4.2 38.0 1.0
NE2 C:HIS105 4.2 37.7 1.0
CD2 C:HIS105 4.2 37.9 1.0
NE2 C:HIS84 4.3 30.6 1.0
CD2 C:HIS84 4.3 31.0 1.0
SG C:CYS82 4.4 33.7 1.0
N C:ARG85 4.4 31.8 1.0
CG C:TYR104 4.4 33.6 1.0
SG C:CYS102 4.4 36.6 1.0
CD1 C:TYR104 4.5 33.0 1.0
C C:TYR104 4.5 39.9 1.0
CA C:HIS84 4.7 30.8 1.0
CA C:TYR104 4.8 37.5 1.0
CB C:ARG85 4.8 33.2 1.0
NE1 C:TRP107 4.9 34.0 1.0
CD1 C:TRP107 4.9 34.6 1.0
C C:HIS105 4.9 39.7 1.0
CG C:ARG85 5.0 35.3 1.0

Iron binding site 5 out of 9 in 7vju

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Iron binding site 5 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:33.4
occ:1.00
 FE2 C:FES502 0.0 33.4 1.0
S2 C:FES502 2.2 34.0 1.0
S1 C:FES502 2.2 34.3 1.0
SG C:CYS102 2.3 36.6 1.0
SG C:CYS82 2.3 33.7 1.0
FE1 C:FES502 2.6 34.2 1.0
CB C:CYS82 3.1 33.7 1.0
CB C:CYS102 3.1 39.3 1.0
CB C:HIS84 4.1 30.9 1.0
CB C:TYR104 4.3 35.9 1.0
CB C:ALA87 4.3 29.6 1.0
ND1 C:HIS84 4.4 30.4 1.0
ND1 C:HIS105 4.4 39.1 1.0
N C:HIS105 4.5 38.6 1.0
CA C:CYS102 4.6 39.6 1.0
CA C:CYS82 4.6 33.0 1.0
N C:ARG85 4.7 31.8 1.0
CG C:HIS84 4.7 30.9 1.0
N C:TYR104 4.8 39.1 1.0
N C:ALA87 4.8 29.1 1.0
N C:HIS84 4.9 31.7 1.0
CB C:TRP107 5.0 37.3 1.0
CA C:TYR104 5.0 37.5 1.0
C C:CYS102 5.0 40.2 1.0

Iron binding site 6 out of 9 in 7vju

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Iron binding site 6 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:38.3
occ:1.00
 OD1 C:ASP356 1.8 36.2 1.0
NE2 C:HIS215 2.1 41.2 1.0
NE2 C:HIS210 2.1 37.7 1.0
O C:HOH745 2.2 51.5 1.0
O C:HOH771 2.3 53.9 1.0
CG C:ASP356 2.7 38.7 1.0
CE1 C:HIS210 2.9 37.3 1.0
OD2 C:ASP356 3.0 44.2 1.0
CE1 C:HIS215 3.0 40.1 1.0
CD2 C:HIS215 3.1 39.1 1.0
CD2 C:HIS210 3.2 38.2 1.0
ND1 C:HIS210 4.1 36.6 1.0
ND2 C:ASN204 4.1 31.5 1.0
O C:HOH770 4.1 47.3 1.0
ND1 C:HIS215 4.2 39.1 1.0
CB C:ASP356 4.2 35.5 1.0
CG C:HIS215 4.2 41.4 1.0
CG C:HIS210 4.3 36.7 1.0
CG2 C:ILE352 4.5 46.7 1.0
O C:HOH834 4.6 61.2 1.0
O C:HOH758 4.6 53.0 1.0
CD2 C:LEU214 4.7 38.3 1.0
CA C:ASP356 4.8 37.8 1.0
CG C:ASN204 4.9 32.6 1.0
OD1 C:ASN204 4.9 36.0 1.0

Iron binding site 7 out of 9 in 7vju

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Iron binding site 7 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:39.0
occ:1.00
 FE1 E:FES501 0.0 39.0 1.0
ND1 E:HIS84 2.1 34.5 1.0
S1 E:FES501 2.1 39.2 1.0
ND1 E:HIS105 2.1 37.5 1.0
S2 E:FES501 2.3 37.2 1.0
FE2 E:FES501 2.7 36.4 1.0
CG E:HIS105 3.0 39.0 1.0
CE1 E:HIS84 3.1 35.6 1.0
CG E:HIS84 3.1 35.6 1.0
CE1 E:HIS105 3.2 39.5 1.0
CB E:HIS105 3.2 39.4 1.0
CB E:HIS84 3.4 37.3 1.0
N E:HIS105 3.8 42.2 1.0
CB E:TYR104 3.9 35.9 1.0
CA E:HIS105 4.1 41.1 1.0
CD2 E:HIS105 4.2 40.1 1.0
NE2 E:HIS84 4.2 34.1 1.0
CD2 E:HIS84 4.2 35.7 1.0
NE2 E:HIS105 4.2 40.6 1.0
N E:ARG85 4.3 39.9 1.0
CG E:TYR104 4.3 36.0 1.0
SG E:CYS82 4.4 37.0 1.0
CD1 E:TYR104 4.4 35.9 1.0
SG E:CYS102 4.5 41.8 1.0
C E:TYR104 4.5 39.4 1.0
CA E:HIS84 4.7 38.2 1.0
CA E:TYR104 4.8 38.4 1.0
C E:HIS105 4.9 45.3 1.0
CB E:ARG85 4.9 39.4 1.0
C E:HIS84 4.9 39.4 1.0
CG E:ARG85 5.0 43.0 1.0
NE1 E:TRP107 5.0 40.8 1.0

Iron binding site 8 out of 9 in 7vju

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Iron binding site 8 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


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 Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:36.4
occ:1.00
 FE2 E:FES501 0.0 36.4 1.0
S2 E:FES501 2.2 37.2 1.0
SG E:CYS102 2.2 41.8 1.0
S1 E:FES501 2.3 39.2 1.0
SG E:CYS82 2.3 37.0 1.0
FE1 E:FES501 2.7 39.0 1.0
CB E:CYS82 3.1 37.2 1.0
CB E:CYS102 3.2 43.6 1.0
CB E:HIS84 4.0 37.3 1.0
CB E:TYR104 4.1 35.9 1.0
ND1 E:HIS84 4.3 34.5 1.0
CB E:ALA87 4.4 35.0 1.0
ND1 E:HIS105 4.5 37.5 1.0
N E:HIS105 4.5 42.2 1.0
CA E:CYS82 4.6 36.3 1.0
CA E:CYS102 4.6 43.4 1.0
CG E:HIS84 4.7 35.6 1.0
N E:ARG85 4.8 39.9 1.0
N E:TYR104 4.8 37.2 1.0
N E:ALA87 4.9 36.8 1.0
CA E:TYR104 4.9 38.4 1.0
N E:HIS84 5.0 38.6 1.0
CA E:HIS84 5.0 38.2 1.0

Iron binding site 9 out of 9 in 7vju

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Iron binding site 9 out of 9 in the Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Terephthalate Dioxygenase From Comamonas Testosteroni KF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe502

b:43.0
occ:1.00
 OD1 E:ASP356 1.9 41.6 1.0
NE2 E:HIS215 2.1 48.1 1.0
NE2 E:HIS210 2.2 36.0 1.0
O E:HOH776 2.5 48.8 1.0
O E:HOH751 2.5 54.4 1.0
CG E:ASP356 2.7 42.3 1.0
OD2 E:ASP356 2.9 46.2 1.0
CD2 E:HIS215 3.1 47.9 1.0
CE1 E:HIS210 3.1 34.9 1.0
CE1 E:HIS215 3.1 48.1 1.0
CD2 E:HIS210 3.2 35.9 1.0
ND2 E:ASN204 4.1 33.6 1.0
CB E:ASP356 4.2 41.4 1.0
ND1 E:HIS215 4.2 47.5 1.0
CG E:HIS215 4.2 49.5 1.0
ND1 E:HIS210 4.2 35.8 1.0
O E:HOH791 4.3 53.2 1.0
CG E:HIS210 4.3 36.4 1.0
O E:HOH734 4.4 57.9 1.0
CG2 E:ILE352 4.5 43.7 1.0
CD2 E:LEU214 4.6 40.5 1.0
CA E:ASP356 4.9 43.9 1.0
CG E:ASN204 4.9 35.8 1.0
OD1 E:ASN204 5.0 36.5 1.0
O E:HOH603 5.0 41.1 1.0

Reference:

J.K.Mahto, N.Neetu, M.Sharma, M.Dubey, B.P.Vellanki, P.Kumar. Structural Insights Into Dihydroxylation of Terephthalate, A Product of Polyethylene Terephthalate Degradation. J.Bacteriol. V. 204 54321 2022.
ISSN: ESSN 1098-5530
PubMed: 35007143
DOI: 10.1128/JB.00543-21
Page generated: Fri Aug 9 05:30:26 2024

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