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Iron in PDB 6ick: Pseudomonas Putida CBB5 Ndma

Enzymatic activity of Pseudomonas Putida CBB5 Ndma

All present enzymatic activity of Pseudomonas Putida CBB5 Ndma:
1.14.13.178;

Protein crystallography data

The structure of Pseudomonas Putida CBB5 Ndma, PDB code: 6ick was solved by J.H.Kim, B.H.Kim, S.Y.Kang, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.80 / 1.95
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.630, 135.630, 155.070, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 20

Iron Binding Sites:

The binding sites of Iron atom in the Pseudomonas Putida CBB5 Ndma (pdb code 6ick). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Pseudomonas Putida CBB5 Ndma, PDB code: 6ick:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 6ick

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Iron binding site 1 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe400

b:20.9
occ:1.00
 FE1 A:FES400 0.0 20.9 1.0
S2 A:FES400 2.2 21.2 1.0
S1 A:FES400 2.2 20.3 1.0
SG A:CYS81 2.3 20.6 1.0
SG A:CYS62 2.4 20.1 1.0
FE2 A:FES400 2.7 21.0 1.0
CB A:CYS62 3.1 18.7 1.0
CB A:CYS81 3.2 17.6 1.0
CB A:HIS64 4.1 22.5 1.0
CB A:TYR83 4.2 20.6 1.0
N A:HIS84 4.4 22.3 1.0
ND1 A:HIS64 4.5 21.6 1.0
ND1 A:HIS84 4.6 22.2 1.0
CA A:CYS62 4.6 21.4 1.0
CA A:CYS81 4.6 20.4 1.0
N A:ARG65 4.7 21.1 1.0
CB A:ALA67 4.7 20.1 1.0
N A:TYR83 4.7 19.7 1.0
CG A:HIS64 4.8 22.8 1.0
CB A:TRP86 4.8 23.6 1.0
CG A:TRP86 4.9 20.5 1.0
CA A:TYR83 4.9 19.0 1.0
N A:HIS64 5.0 20.3 1.0

Iron binding site 2 out of 9 in 6ick

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Iron binding site 2 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe400

b:21.0
occ:1.00
 FE2 A:FES400 0.0 21.0 1.0
S2 A:FES400 2.2 21.2 1.0
S1 A:FES400 2.2 20.3 1.0
ND1 A:HIS84 2.2 22.2 1.0
ND1 A:HIS64 2.2 21.6 1.0
FE1 A:FES400 2.7 20.9 1.0
CE1 A:HIS84 3.1 24.0 1.0
CG A:HIS64 3.2 22.8 1.0
CG A:HIS84 3.2 21.1 1.0
CE1 A:HIS64 3.3 23.7 1.0
CB A:HIS64 3.4 22.5 1.0
CB A:HIS84 3.6 19.8 1.0
N A:HIS84 3.7 22.3 1.0
CB A:TYR83 4.0 20.6 1.0
N A:ARG65 4.1 21.1 1.0
CA A:HIS84 4.2 20.9 1.0
NE2 A:HIS84 4.3 21.1 1.0
CD2 A:HIS64 4.3 21.8 1.0
CD2 A:HIS84 4.3 24.0 1.0
NE2 A:HIS64 4.3 21.9 1.0
CB A:ARG65 4.4 19.7 1.0
SG A:CYS62 4.4 20.1 1.0
CG A:TYR83 4.4 19.8 1.0
CD2 A:TYR83 4.5 21.0 1.0
CG A:ARG65 4.5 22.9 1.0
C A:TYR83 4.6 23.8 1.0
SG A:CYS81 4.6 20.6 1.0
CA A:HIS64 4.6 21.4 1.0
C A:HIS64 4.7 23.4 1.0
NE1 A:TRP86 4.8 22.8 1.0
CD1 A:TRP86 4.8 21.8 1.0
CA A:ARG65 4.8 21.8 1.0
CA A:TYR83 4.9 19.0 1.0
C A:HIS84 4.9 21.5 1.0

Iron binding site 3 out of 9 in 6ick

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Iron binding site 3 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:25.9
occ:1.00
 NE2 A:HIS178 2.0 27.3 1.0
O A:HOH735 2.1 36.5 1.0
NE2 A:HIS173 2.2 27.6 1.0
OD2 A:ASP289 2.2 25.1 1.0
OD1 A:ASP289 2.3 26.1 1.0
CG A:ASP289 2.6 25.9 1.0
CD2 A:HIS178 3.0 29.1 1.0
CE1 A:HIS178 3.1 26.0 1.0
CD2 A:HIS173 3.1 28.6 1.0
CE1 A:HIS173 3.2 29.8 1.0
ND2 A:ASN167 3.9 22.4 1.0
OD1 A:ASN167 4.1 27.2 1.0
CB A:ASP289 4.1 21.4 1.0
CG A:HIS178 4.1 32.5 1.0
ND1 A:HIS178 4.2 28.0 1.0
CG A:HIS173 4.3 27.4 1.0
ND1 A:HIS173 4.3 28.5 1.0
CG1 A:VAL285 4.3 27.1 1.0
CG A:ASN167 4.4 27.1 1.0
CE1 A:PHE174 4.7 33.8 1.0
O A:ASN167 4.7 25.5 1.0
CG2 A:ILE177 4.8 25.7 1.0
O A:VAL285 5.0 23.7 1.0
CA A:ASP289 5.0 21.2 1.0
CD1 A:PHE174 5.0 38.5 1.0
CD1 A:LEU182 5.0 35.6 1.0

Iron binding site 4 out of 9 in 6ick

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Iron binding site 4 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:22.8
occ:1.00
 FE1 B:FES400 0.0 22.8 1.0
S1 B:FES400 2.2 24.4 1.0
S2 B:FES400 2.2 22.3 1.0
SG B:CYS81 2.3 22.7 1.0
SG B:CYS62 2.4 22.1 1.0
FE2 B:FES400 2.7 24.2 1.0
CB B:CYS62 3.1 21.8 1.0
CB B:CYS81 3.2 20.7 1.0
CB B:HIS64 4.1 21.5 1.0
CB B:TYR83 4.2 22.4 1.0
N B:HIS84 4.4 22.5 1.0
ND1 B:HIS64 4.5 24.0 1.0
CA B:CYS62 4.6 22.2 1.0
ND1 B:HIS84 4.6 23.1 1.0
CB B:ALA67 4.6 21.6 1.0
CA B:CYS81 4.7 22.8 1.0
N B:ARG65 4.7 23.3 1.0
N B:TYR83 4.8 20.9 1.0
CB B:TRP86 4.8 22.0 1.0
CG B:HIS64 4.8 26.5 1.0
CG B:TRP86 4.9 22.1 1.0
N B:HIS64 5.0 22.2 1.0
CA B:TYR83 5.0 23.4 1.0

Iron binding site 5 out of 9 in 6ick

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Iron binding site 5 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:24.2
occ:1.00
 FE2 B:FES400 0.0 24.2 1.0
S1 B:FES400 2.2 24.4 1.0
ND1 B:HIS84 2.2 23.1 1.0
S2 B:FES400 2.2 22.3 1.0
ND1 B:HIS64 2.3 24.0 1.0
FE1 B:FES400 2.7 22.8 1.0
CE1 B:HIS84 3.1 24.7 1.0
CG B:HIS64 3.2 26.5 1.0
CG B:HIS84 3.2 27.2 1.0
CE1 B:HIS64 3.3 25.3 1.0
CB B:HIS64 3.4 21.5 1.0
CB B:HIS84 3.6 23.1 1.0
N B:HIS84 3.7 22.5 1.0
CB B:TYR83 4.0 22.4 1.0
N B:ARG65 4.1 23.3 1.0
CA B:HIS84 4.2 24.0 1.0
NE2 B:HIS84 4.2 25.9 1.0
CB B:ARG65 4.3 25.5 1.0
CD2 B:HIS84 4.3 26.3 1.0
CD2 B:HIS64 4.3 24.7 1.0
CG B:TYR83 4.4 22.9 1.0
NE2 B:HIS64 4.4 25.9 1.0
SG B:CYS62 4.4 22.1 1.0
CD2 B:TYR83 4.5 22.4 1.0
CG B:ARG65 4.5 26.7 1.0
SG B:CYS81 4.6 22.7 1.0
C B:TYR83 4.6 26.4 1.0
CA B:HIS64 4.7 23.4 1.0
NE1 B:TRP86 4.8 25.7 1.0
C B:HIS64 4.8 24.6 1.0
CD1 B:TRP86 4.8 22.7 1.0
CA B:ARG65 4.8 23.1 1.0
CA B:TYR83 4.9 23.4 1.0
C B:HIS84 4.9 26.0 1.0

Iron binding site 6 out of 9 in 6ick

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Iron binding site 6 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:24.6
occ:1.00
 O B:HOH724 2.0 36.6 1.0
NE2 B:HIS178 2.1 26.3 1.0
OD2 B:ASP289 2.1 25.7 1.0
NE2 B:HIS173 2.1 25.9 1.0
OD1 B:ASP289 2.3 25.1 1.0
CG B:ASP289 2.5 23.6 1.0
CD2 B:HIS178 3.0 26.1 1.0
CD2 B:HIS173 3.1 27.7 1.0
CE1 B:HIS178 3.1 25.4 1.0
CE1 B:HIS173 3.2 29.4 1.0
ND2 B:ASN167 3.8 22.6 1.0
O B:HOH546 3.9 28.7 1.0
CB B:ASP289 4.1 21.1 1.0
OD1 B:ASN167 4.1 27.2 1.0
CG B:HIS178 4.2 28.0 1.0
ND1 B:HIS178 4.2 25.1 1.0
ND1 B:HIS173 4.2 26.6 1.0
CG B:HIS173 4.3 27.6 1.0
CG B:ASN167 4.3 25.3 1.0
CG1 B:VAL285 4.3 26.4 1.0
CE1 B:PHE174 4.6 35.2 1.0
O B:ASN167 4.7 23.5 1.0
CG2 B:ILE177 4.7 23.3 1.0
CA B:ASP289 4.9 21.5 1.0
CD1 B:PHE174 4.9 35.8 1.0
CD1 B:LEU182 5.0 35.3 1.0
O B:VAL285 5.0 23.1 1.0

Iron binding site 7 out of 9 in 6ick

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Iron binding site 7 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe400

b:22.9
occ:1.00
 FE1 C:FES400 0.0 22.9 1.0
S1 C:FES400 2.2 22.0 1.0
S2 C:FES400 2.2 23.3 1.0
ND1 C:HIS84 2.2 21.6 1.0
ND1 C:HIS64 2.3 23.7 1.0
FE2 C:FES400 2.7 21.7 1.0
CG C:HIS64 3.2 24.5 1.0
CE1 C:HIS84 3.2 23.2 1.0
CG C:HIS84 3.2 23.2 1.0
CE1 C:HIS64 3.3 26.9 1.0
CB C:HIS64 3.3 22.8 1.0
CB C:HIS84 3.5 22.2 1.0
N C:HIS84 3.7 23.3 1.0
CB C:TYR83 4.0 22.9 1.0
N C:ARG65 4.1 22.3 1.0
CA C:HIS84 4.1 23.1 1.0
NE2 C:HIS84 4.3 25.3 1.0
CB C:ARG65 4.3 21.9 1.0
CD2 C:HIS84 4.3 24.6 1.0
CD2 C:HIS64 4.3 23.7 1.0
CG C:TYR83 4.4 21.6 1.0
NE2 C:HIS64 4.4 25.8 1.0
SG C:CYS62 4.4 20.3 1.0
CD2 C:TYR83 4.5 24.9 1.0
CG C:ARG65 4.5 21.9 1.0
SG C:CYS81 4.5 21.3 1.0
CA C:HIS64 4.6 22.8 1.0
C C:TYR83 4.6 26.4 1.0
C C:HIS64 4.7 23.7 1.0
NE1 C:TRP86 4.8 24.6 1.0
CD1 C:TRP86 4.8 23.9 1.0
CA C:ARG65 4.8 21.6 1.0
C C:HIS84 4.9 27.0 1.0
CA C:TYR83 4.9 22.4 1.0

Iron binding site 8 out of 9 in 6ick

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Iron binding site 8 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe400

b:21.7
occ:1.00
 FE2 C:FES400 0.0 21.7 1.0
S2 C:FES400 2.2 23.3 1.0
S1 C:FES400 2.2 22.0 1.0
SG C:CYS81 2.3 21.3 1.0
SG C:CYS62 2.4 20.3 1.0
FE1 C:FES400 2.7 22.9 1.0
CB C:CYS62 3.1 21.1 1.0
CB C:CYS81 3.2 22.0 1.0
CB C:HIS64 4.1 22.8 1.0
CB C:TYR83 4.3 22.9 1.0
N C:HIS84 4.4 23.3 1.0
ND1 C:HIS64 4.5 23.7 1.0
ND1 C:HIS84 4.6 21.6 1.0
CB C:ALA67 4.6 19.1 1.0
CA C:CYS62 4.6 24.4 1.0
CA C:CYS81 4.6 22.9 1.0
N C:ARG65 4.7 22.3 1.0
CG C:HIS64 4.8 24.5 1.0
CB C:TRP86 4.8 22.3 1.0
N C:TYR83 4.8 21.2 1.0
CG C:TRP86 4.9 22.8 1.0
N C:HIS64 4.9 19.9 1.0

Iron binding site 9 out of 9 in 6ick

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Iron binding site 9 out of 9 in the Pseudomonas Putida CBB5 Ndma


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Pseudomonas Putida CBB5 Ndma within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:26.5
occ:1.00
 NE2 C:HIS178 2.1 27.6 1.0
NE2 C:HIS173 2.1 29.4 1.0
OD2 C:ASP289 2.1 27.8 1.0
O C:HOH705 2.2 36.3 1.0
OD1 C:ASP289 2.4 25.3 1.0
CG C:ASP289 2.6 25.6 1.0
CD2 C:HIS178 3.0 29.1 1.0
CE1 C:HIS178 3.1 25.7 1.0
CD2 C:HIS173 3.1 29.4 1.0
CE1 C:HIS173 3.1 30.1 1.0
O C:HOH541 3.8 34.4 1.0
ND2 C:ASN167 3.9 23.9 1.0
CB C:ASP289 4.1 21.3 1.0
OD1 C:ASN167 4.1 28.2 1.0
CG C:HIS178 4.2 28.7 1.0
ND1 C:HIS178 4.2 29.2 1.0
ND1 C:HIS173 4.2 30.5 1.0
CG C:HIS173 4.2 28.2 1.0
CG C:ASN167 4.4 29.0 1.0
CG1 C:VAL285 4.4 26.2 1.0
O C:ASN167 4.6 27.4 1.0
CE1 C:PHE174 4.7 35.2 1.0
CG2 C:ILE177 4.7 25.0 1.0
O C:VAL285 4.9 24.1 1.0
CA C:ASP289 4.9 22.4 1.0

Reference:

J.H.Kim, B.H.Kim, S.Brooks, S.Y.Kang, R.M.Summers, H.K.Song. Structural and Mechanistic Insights Into Caffeine Degradation By the Bacterial N-Demethylase Complex. J.Mol.Biol. V. 431 3647 2019.
ISSN: ESSN 1089-8638
PubMed: 31412262
DOI: 10.1016/J.JMB.2019.08.004
Page generated: Tue Aug 6 22:53:15 2024

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