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Iron in PDB 4zgd: Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1

Enzymatic activity of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1

All present enzymatic activity of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1:
4.2.1.84;

Protein crystallography data

The structure of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1, PDB code: 4zgd was solved by R.Wu, S.Martinez, R.Holz, D.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.49 / 2.25
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 111.590, 111.590, 474.604, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.3

Iron Binding Sites:

The binding sites of Iron atom in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 (pdb code 4zgd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1, PDB code: 4zgd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4zgd

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Iron binding site 1 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:29.0
occ:0.75
 N A:SER103 2.0 32.1 1.0
N A:CSD104 2.2 30.8 0.8
SG A:CSD102 2.2 28.6 0.9
SG A:CSD104 2.3 33.2 0.8
SG A:CYS99 2.4 35.5 1.0
OD1 A:CSD104 2.8 30.9 0.8
CA A:SER103 2.8 35.1 1.0
C A:SER103 2.8 33.9 1.0
OD2 A:CSD102 2.9 32.1 0.9
OD1 A:CSD102 3.1 25.6 0.9
C A:CSD102 3.1 30.3 0.9
CB A:CSD102 3.2 27.6 0.9
CB A:CSD104 3.2 32.5 0.8
CA A:CSD104 3.2 30.9 0.8
OD2 A:CSD104 3.4 26.5 0.8
CB A:CYS99 3.5 24.6 1.0
CA A:CSD102 3.5 24.0 0.9
OG A:SER103 3.7 39.6 1.0
CB A:SER103 3.9 33.6 1.0
N A:CSD102 3.9 24.1 0.9
O A:SER103 4.0 37.1 1.0
O A:CSD102 4.2 30.2 0.9
C A:CSD104 4.5 33.6 0.8
O A:CSD104 4.9 31.1 0.8
CA A:CYS99 4.9 23.8 1.0
NH2 B:ARG137 4.9 22.6 1.0
C A:LEU101 5.0 27.2 1.0

Iron binding site 2 out of 8 in 4zgd

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Iron binding site 2 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:33.5
occ:0.72
 N C:SER103 2.1 30.7 0.7
N C:CSD104 2.1 30.9 0.8
SG C:CSD102 2.2 32.5 0.8
SG C:CSD104 2.2 33.5 0.8
SG C:CYS99 2.3 34.3 1.0
C C:SER103 2.8 30.5 0.7
CA C:SER103 2.9 31.6 0.7
OD2 C:CSD102 3.0 33.3 0.8
OD1 C:CSD104 3.0 29.7 0.8
OD1 C:CSD102 3.1 22.9 0.8
CA C:CSD104 3.1 30.9 0.8
CB C:CSD102 3.2 28.1 0.8
CB C:CSD104 3.2 28.8 0.8
C C:CSD102 3.2 29.9 0.8
OD2 C:CSD104 3.2 26.6 0.8
CB C:CYS99 3.5 20.0 1.0
CA C:CSD102 3.5 23.1 0.8
N C:CSD102 3.8 21.2 0.8
OG C:SER103 3.9 35.8 0.7
CB C:SER103 4.0 35.3 0.7
O C:SER103 4.0 32.4 0.7
O C:CSD102 4.3 32.1 0.8
C C:CSD104 4.4 33.4 0.8
O C:CSD104 4.7 26.5 0.8
CA C:CYS99 4.8 21.2 1.0
O C:CYS99 4.9 20.4 1.0
NH2 D:ARG137 4.9 24.3 1.0
C C:LEU101 4.9 25.1 1.0
O C:HOH454 4.9 29.1 1.0

Iron binding site 3 out of 8 in 4zgd

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Iron binding site 3 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:31.4
occ:0.71
 N E:CSD104 2.1 28.2 0.8
N E:SER103 2.1 30.7 0.7
SG E:CSD102 2.2 27.4 0.8
SG E:CSD104 2.3 28.9 0.8
SG E:CYS99 2.4 31.5 1.0
C E:SER103 2.8 28.9 0.7
CA E:SER103 2.9 30.0 0.7
OD2 E:CSD102 2.9 29.2 0.8
OD1 E:CSD104 3.0 28.5 0.8
OD1 E:CSD102 3.1 22.9 0.8
CA E:CSD104 3.1 29.8 0.8
CB E:CSD104 3.1 26.3 0.8
CB E:CSD102 3.2 24.2 0.8
C E:CSD102 3.2 30.5 0.8
OD2 E:CSD104 3.3 30.2 0.8
CB E:CYS99 3.5 19.9 1.0
CA E:CSD102 3.5 24.5 0.8
OG E:SER103 3.8 34.1 0.7
O E:SER103 3.9 30.2 0.7
N E:CSD102 3.9 21.2 0.8
CB E:SER103 4.0 33.6 0.7
O E:CSD102 4.3 29.5 0.8
C E:CSD104 4.4 31.4 0.8
O E:CSD104 4.7 25.8 0.8
NH2 F:ARG137 4.9 22.0 1.0
O E:HOH462 4.9 31.5 1.0
CA E:CYS99 4.9 21.6 1.0
O E:HOH402 4.9 32.2 1.0
C E:LEU101 5.0 26.4 1.0

Iron binding site 4 out of 8 in 4zgd

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Iron binding site 4 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:35.7
occ:0.79
 N G:SER103 2.1 31.6 0.7
N G:CSD104 2.2 32.4 0.7
SG G:CSD102 2.3 30.5 0.8
SG G:CSD104 2.3 29.7 0.7
SG G:CYS99 2.5 33.0 1.0
C G:SER103 2.8 29.4 0.7
CA G:SER103 2.9 28.7 0.7
OD2 G:CSD102 3.0 34.8 0.8
OD1 G:CSD104 3.0 33.0 0.7
CA G:CSD104 3.1 32.0 0.7
OD1 G:CSD102 3.1 23.8 0.8
C G:CSD102 3.2 29.4 0.8
CB G:CSD104 3.2 28.6 0.7
CB G:CSD102 3.2 27.0 0.8
OD2 G:CSD104 3.3 29.0 0.7
CA G:CSD102 3.5 24.9 0.8
CB G:CYS99 3.6 21.7 1.0
OG G:SER103 3.8 34.5 0.7
N G:CSD102 3.9 21.5 0.8
CB G:SER103 3.9 30.7 0.7
O G:SER103 4.0 29.4 0.7
O G:CSD102 4.3 31.8 0.8
C G:CSD104 4.4 33.4 0.7
O G:CSD104 4.7 28.0 0.7
O G:HOH485 4.9 34.8 1.0
NH2 H:ARG137 4.9 26.1 1.0
CA G:CYS99 4.9 22.2 1.0
C G:LEU101 5.0 27.6 1.0

Iron binding site 5 out of 8 in 4zgd

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Iron binding site 5 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe301

b:32.7
occ:0.80
 N I:CSD104 2.1 28.4 0.8
N I:SER103 2.1 31.9 1.0
SG I:CSD102 2.2 26.1 0.8
SG I:CSD104 2.3 32.0 0.8
SG I:CYS99 2.4 34.8 1.0
C I:SER103 2.8 33.2 1.0
OD2 I:CSD102 2.8 29.3 0.8
OD1 I:CSD104 2.9 32.1 0.8
CA I:SER103 2.9 34.0 1.0
CA I:CSD104 3.1 28.1 0.8
CB I:CSD102 3.1 26.8 0.8
CB I:CSD104 3.1 31.0 0.8
C I:CSD102 3.2 31.0 0.8
OD1 I:CSD102 3.2 25.7 0.8
OD2 I:CSD104 3.4 27.6 0.8
CA I:CSD102 3.5 24.6 0.8
CB I:CYS99 3.6 23.8 1.0
OG I:SER103 3.7 37.7 1.0
CB I:SER103 3.9 31.8 1.0
N I:CSD102 4.0 22.2 0.8
O I:SER103 4.0 34.7 1.0
O I:CSD102 4.3 28.8 0.8
C I:CSD104 4.4 31.5 0.8
O I:CSD104 4.8 26.6 0.8
O I:HOH464 4.9 29.7 1.0
CA I:CYS99 5.0 23.0 1.0

Iron binding site 6 out of 8 in 4zgd

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Iron binding site 6 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe301

b:30.1
occ:0.68
 N K:SER103 2.1 34.1 0.7
N K:CSD104 2.2 32.8 0.8
SG K:CSD104 2.2 33.0 0.8
SG K:CSD102 2.2 39.8 1.0
SG K:CYS99 2.4 32.4 1.0
O K:HOH404 2.8 42.5 1.0
C K:SER103 2.8 32.8 0.7
CA K:SER103 2.9 31.4 0.7
OD2 K:CSD104 3.0 28.7 0.8
OD2 K:CSD102 3.0 39.7 1.0
OD1 K:CSD104 3.1 32.3 0.8
OD1 K:CSD102 3.1 30.0 1.0
CB K:CSD104 3.1 28.4 0.8
CA K:CSD104 3.1 32.6 0.8
C K:CSD102 3.2 34.4 1.0
CB K:CSD102 3.2 33.9 1.0
CB K:CYS99 3.5 22.2 1.0
CA K:CSD102 3.6 28.3 1.0
N K:CSD102 3.9 25.4 1.0
OG K:SER103 3.9 36.7 0.7
O K:SER103 3.9 33.1 0.7
CB K:SER103 4.0 34.9 0.7
O K:CSD102 4.3 36.5 1.0
C K:CSD104 4.5 34.3 0.8
O K:CSD104 4.8 28.4 0.8
CA K:CYS99 4.9 22.3 1.0
NH2 L:ARG137 4.9 22.8 1.0
O K:HOH485 5.0 32.2 1.0
O K:CYS99 5.0 23.8 1.0
C K:LEU101 5.0 28.4 1.0

Iron binding site 7 out of 8 in 4zgd

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Iron binding site 7 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe301

b:33.3
occ:0.80
 N M:SER103 2.1 33.6 1.0
N M:CSD104 2.1 32.5 0.8
SG M:CSD102 2.2 32.4 0.9
SG M:CSD104 2.3 32.5 0.8
SG M:CYS99 2.4 33.3 1.0
OD2 M:CSD102 2.8 29.7 0.9
C M:SER103 2.8 33.2 1.0
CA M:SER103 2.9 34.4 1.0
OD1 M:CSD104 2.9 30.6 0.8
CB M:CSD104 3.1 31.8 0.8
CA M:CSD104 3.1 29.9 0.8
CB M:CSD102 3.2 27.0 0.9
C M:CSD102 3.2 31.5 0.9
OD1 M:CSD102 3.2 24.2 0.9
OD2 M:CSD104 3.4 31.0 0.8
CA M:CSD102 3.5 24.2 0.9
CB M:CYS99 3.6 23.3 1.0
OG M:SER103 3.7 38.5 1.0
CB M:SER103 3.9 33.8 1.0
N M:CSD102 4.0 24.6 0.9
O M:SER103 4.0 32.3 1.0
O M:CSD102 4.3 30.1 0.9
C M:CSD104 4.5 32.1 0.8
O M:HOH419 4.8 28.6 1.0
O M:CSD104 4.8 30.3 0.8
NH2 N:ARG137 4.9 24.2 1.0
CA M:CYS99 4.9 24.5 1.0
O M:CYS99 5.0 21.4 1.0

Iron binding site 8 out of 8 in 4zgd

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Iron binding site 8 out of 8 in the Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Mutant R157A of Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe301

b:35.3
occ:0.81
 N O:SER103 2.1 32.7 1.0
SG O:CSD102 2.2 29.0 0.8
N O:CSD104 2.2 30.7 0.8
SG O:CSD104 2.3 31.6 0.8
SG O:CYS99 2.4 32.0 1.0
OD2 O:CSD102 2.8 33.3 0.8
C O:SER103 2.9 35.0 1.0
CA O:SER103 2.9 34.2 1.0
OD1 O:CSD104 3.0 31.0 0.8
CB O:CSD102 3.1 27.0 0.8
C O:CSD102 3.1 31.1 0.8
OD1 O:CSD102 3.2 26.6 0.8
CB O:CSD104 3.2 29.0 0.8
CA O:CSD104 3.2 28.8 0.8
OD2 O:CSD104 3.3 28.2 0.8
CA O:CSD102 3.5 25.5 0.8
CB O:CYS99 3.6 22.8 1.0
OG O:SER103 3.7 39.4 1.0
N O:CSD102 3.9 24.4 0.8
CB O:SER103 3.9 34.5 1.0
O O:SER103 4.0 35.9 1.0
O O:CSD102 4.3 29.4 0.8
C O:CSD104 4.5 32.5 0.8
O O:HOH443 4.8 30.7 1.0
O O:CSD104 4.9 30.3 0.8
NH2 P:ARG137 4.9 25.3 1.0
NE P:ARG52 5.0 32.8 1.0
CA O:CYS99 5.0 24.3 1.0
C O:LEU101 5.0 25.8 1.0

Reference:

S.Martinez, R.Wu, K.Krzywda, V.Opalka, H.Chan, D.Liu, R.C.Holz. Analyzing the Catalytic Role of Active Site Residues in the Fe-Type Nitrile Hydratase From Comamonas Testosteroni NI1. J.Biol.Inorg.Chem. V. 20 885 2015.
ISSN: ESSN 1432-1327
PubMed: 26077812
DOI: 10.1007/S00775-015-1273-3
Page generated: Mon Aug 5 18:11:45 2024

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