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Iron in PDB 6icp: Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine

Enzymatic activity of Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine

All present enzymatic activity of Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine:
1.14.13.178;

Protein crystallography data

The structure of Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine, PDB code: 6icp 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) 33.67 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.243, 136.243, 154.087, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 22.1

Iron Binding Sites:

The binding sites of Iron atom in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine (pdb code 6icp). 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 Ql Mutant with Caffeine, PDB code: 6icp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 6icp

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Iron binding site 1 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe400

b:21.6
occ:1.00
 FE1 A:FES400 0.0 21.6 1.0
S2 A:FES400 2.2 21.9 1.0
S1 A:FES400 2.2 22.6 1.0
SG A:CYS81 2.4 25.4 1.0
SG A:CYS62 2.4 22.6 1.0
FE2 A:FES400 2.7 22.5 1.0
CB A:CYS62 3.1 19.3 1.0
CB A:CYS81 3.3 19.8 1.0
CB A:HIS64 4.2 24.3 1.0
CB A:TYR83 4.3 24.5 1.0
N A:HIS84 4.5 24.8 1.0
ND1 A:HIS64 4.6 24.7 1.0
CB A:ALA67 4.6 19.0 1.0
CA A:CYS62 4.6 23.4 1.0
ND1 A:HIS84 4.6 27.4 1.0
N A:ARG65 4.7 25.5 1.0
CA A:CYS81 4.7 21.4 1.0
N A:TYR83 4.9 25.9 1.0
CG A:HIS64 4.9 25.9 1.0
CB A:TRP86 4.9 23.2 1.0
CG A:TRP86 5.0 24.2 1.0
N A:HIS64 5.0 24.4 1.0

Iron binding site 2 out of 9 in 6icp

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Iron binding site 2 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe400

b:22.5
occ:1.00
 FE2 A:FES400 0.0 22.5 1.0
S1 A:FES400 2.2 22.6 1.0
S2 A:FES400 2.2 21.9 1.0
ND1 A:HIS84 2.2 27.4 1.0
ND1 A:HIS64 2.3 24.7 1.0
FE1 A:FES400 2.7 21.6 1.0
CE1 A:HIS84 3.2 25.6 1.0
CG A:HIS84 3.2 23.9 1.0
CG A:HIS64 3.2 25.9 1.0
CE1 A:HIS64 3.3 22.1 1.0
CB A:HIS64 3.4 24.3 1.0
CB A:HIS84 3.5 23.2 1.0
N A:HIS84 3.8 24.8 1.0
CB A:TYR83 4.0 24.5 1.0
N A:ARG65 4.2 25.5 1.0
CA A:HIS84 4.2 24.0 1.0
CB A:ARG65 4.3 24.9 1.0
NE2 A:HIS84 4.3 26.6 1.0
CD2 A:HIS84 4.3 25.6 1.0
CG A:TYR83 4.4 27.0 1.0
CD2 A:HIS64 4.4 25.1 1.0
NE2 A:HIS64 4.4 25.0 1.0
SG A:CYS62 4.4 22.6 1.0
CG A:ARG65 4.5 25.2 1.0
CD2 A:TYR83 4.5 22.8 1.0
SG A:CYS81 4.6 25.4 1.0
C A:TYR83 4.7 28.9 1.0
CA A:HIS64 4.7 21.6 1.0
C A:HIS64 4.8 24.5 1.0
CA A:ARG65 4.8 24.1 1.0
NE1 A:TRP86 4.9 22.0 1.0
CA A:TYR83 4.9 25.2 1.0
CD1 A:TRP86 5.0 22.3 1.0
C A:HIS84 5.0 25.2 1.0

Iron binding site 3 out of 9 in 6icp

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Iron binding site 3 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:28.6
occ:1.00
 NE2 A:HIS178 2.0 25.4 1.0
OD1 A:ASP289 2.1 29.2 1.0
NE2 A:HIS173 2.1 30.6 1.0
O A:HOH641 2.1 33.4 1.0
OD2 A:ASP289 2.4 25.9 1.0
CG A:ASP289 2.6 29.1 1.0
CE1 A:HIS178 2.9 25.6 1.0
CD2 A:HIS178 3.0 26.3 1.0
CD2 A:HIS173 3.1 28.8 1.0
CE1 A:HIS173 3.1 32.3 1.0
O A:HOH502 3.2 39.9 1.0
ND2 A:ASN167 3.7 23.4 1.0
OD1 A:ASN167 4.0 28.3 1.0
ND1 A:HIS178 4.0 25.5 1.0
CB A:ASP289 4.1 26.4 1.0
CG A:HIS178 4.1 31.3 1.0
ND1 A:HIS173 4.2 32.0 1.0
CG A:HIS173 4.2 27.8 1.0
CG A:ASN167 4.3 26.2 1.0
CE1 A:PHE174 4.6 31.7 1.0
CG2 A:ILE177 4.6 27.8 1.0
O A:ASN167 4.7 23.1 1.0
CG1 A:VAL285 4.7 32.1 1.0
O11 A:CFF402 4.9 43.7 1.0
CA A:ASP289 4.9 24.9 1.0
CD1 A:PHE174 5.0 32.0 1.0

Iron binding site 4 out of 9 in 6icp

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Iron binding site 4 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:21.9
occ:1.00
 FE1 B:FES400 0.0 21.9 1.0
S1 B:FES400 2.2 24.1 1.0
S2 B:FES400 2.2 22.2 1.0
SG B:CYS81 2.4 22.1 1.0
SG B:CYS62 2.4 21.3 1.0
FE2 B:FES400 2.8 22.1 1.0
CB B:CYS62 3.1 20.1 1.0
CB B:CYS81 3.2 20.2 1.0
CB B:HIS64 4.1 22.9 1.0
CB B:TYR83 4.3 24.2 1.0
N B:HIS84 4.4 22.5 1.0
ND1 B:HIS64 4.5 24.6 1.0
CB B:ALA67 4.6 23.9 1.0
CA B:CYS62 4.6 21.8 1.0
N B:ARG65 4.7 23.5 1.0
CA B:CYS81 4.7 20.1 1.0
ND1 B:HIS84 4.8 25.2 1.0
N B:TYR83 4.8 22.9 1.0
CG B:HIS64 4.8 27.3 1.0
CB B:TRP86 4.9 22.0 1.0
CG B:TRP86 4.9 24.4 1.0
N B:HIS64 5.0 24.2 1.0
CA B:TYR83 5.0 21.2 1.0

Iron binding site 5 out of 9 in 6icp

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Iron binding site 5 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:22.1
occ:1.00
 FE2 B:FES400 0.0 22.1 1.0
S2 B:FES400 2.2 22.2 1.0
S1 B:FES400 2.2 24.1 1.0
ND1 B:HIS64 2.3 24.6 1.0
ND1 B:HIS84 2.3 25.2 1.0
FE1 B:FES400 2.8 21.9 1.0
CG B:HIS84 3.2 25.3 1.0
CG B:HIS64 3.2 27.3 1.0
CE1 B:HIS64 3.2 22.9 1.0
CE1 B:HIS84 3.3 25.1 1.0
CB B:HIS84 3.4 24.9 1.0
CB B:HIS64 3.5 22.9 1.0
N B:HIS84 3.6 22.5 1.0
CB B:TYR83 4.0 24.2 1.0
CA B:HIS84 4.1 23.8 1.0
N B:ARG65 4.2 23.5 1.0
CD2 B:HIS84 4.3 27.3 1.0
NE2 B:HIS64 4.3 24.8 1.0
NE2 B:HIS84 4.3 28.7 1.0
CD2 B:HIS64 4.4 23.3 1.0
CG B:TYR83 4.4 20.5 1.0
CB B:ARG65 4.4 23.4 1.0
SG B:CYS62 4.5 21.3 1.0
CD2 B:TYR83 4.6 19.5 1.0
C B:TYR83 4.6 24.7 1.0
CG B:ARG65 4.7 23.2 1.0
SG B:CYS81 4.7 22.1 1.0
CA B:HIS64 4.7 21.9 1.0
NE1 B:TRP86 4.7 21.1 1.0
C B:HIS64 4.8 26.2 1.0
CD1 B:TRP86 4.8 22.4 1.0
C B:HIS84 4.8 24.4 1.0
CA B:ARG65 4.9 21.4 1.0
CA B:TYR83 4.9 21.2 1.0

Iron binding site 6 out of 9 in 6icp

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Iron binding site 6 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:28.9
occ:1.00
 NE2 B:HIS178 2.0 29.9 1.0
OD1 B:ASP289 2.1 28.4 1.0
NE2 B:HIS173 2.2 29.8 1.0
O B:HOH621 2.2 31.6 1.0
OD2 B:ASP289 2.4 30.9 1.0
CG B:ASP289 2.5 30.1 1.0
CD2 B:HIS178 3.0 28.5 1.0
CE1 B:HIS178 3.0 27.9 1.0
CD2 B:HIS173 3.1 30.2 1.0
CE1 B:HIS173 3.2 29.2 1.0
ND2 B:ASN167 3.8 24.1 1.0
OD1 B:ASN167 4.0 27.7 1.0
O B:HOH513 4.0 30.8 1.0
CB B:ASP289 4.0 25.4 1.0
ND1 B:HIS178 4.1 28.4 1.0
CG B:HIS178 4.2 30.7 1.0
CG B:ASN167 4.3 30.0 1.0
ND1 B:HIS173 4.3 33.7 1.0
CG B:HIS173 4.3 31.3 1.0
O B:HOH589 4.3 39.7 1.0
CG2 B:ILE177 4.5 26.6 1.0
O B:ASN167 4.7 25.8 1.0
CE1 B:PHE174 4.7 33.1 1.0
CG1 B:VAL285 4.7 27.1 1.0
CA B:ASP289 4.8 26.2 1.0
O11 B:CFF402 4.9 48.8 1.0

Iron binding site 7 out of 9 in 6icp

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Iron binding site 7 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe400

b:23.1
occ:1.00
 FE1 C:FES400 0.0 23.1 1.0
ND1 C:HIS84 2.2 23.4 1.0
S2 C:FES400 2.2 22.9 1.0
S1 C:FES400 2.2 23.5 1.0
ND1 C:HIS64 2.3 24.2 1.0
FE2 C:FES400 2.8 21.4 1.0
CG C:HIS84 3.1 23.8 1.0
CE1 C:HIS84 3.2 23.1 1.0
CG C:HIS64 3.2 24.2 1.0
CE1 C:HIS64 3.3 22.2 1.0
CB C:HIS84 3.4 23.4 1.0
CB C:HIS64 3.4 23.4 1.0
N C:HIS84 3.7 20.9 1.0
CB C:TYR83 4.0 22.7 1.0
CA C:HIS84 4.1 22.2 1.0
N C:ARG65 4.2 23.7 1.0
CD2 C:HIS84 4.3 24.0 1.0
NE2 C:HIS84 4.3 23.6 1.0
CB C:ARG65 4.3 19.1 1.0
CG C:TYR83 4.4 21.3 1.0
CD2 C:HIS64 4.4 26.0 1.0
NE2 C:HIS64 4.4 26.9 1.0
SG C:CYS62 4.5 18.4 1.0
CG C:ARG65 4.5 23.9 1.0
CD2 C:TYR83 4.6 21.0 1.0
C C:TYR83 4.6 23.9 1.0
CA C:HIS64 4.6 23.7 1.0
SG C:CYS81 4.6 22.4 1.0
C C:HIS64 4.7 27.2 1.0
CA C:ARG65 4.9 22.0 1.0
C C:HIS84 4.9 23.4 1.0
CA C:TYR83 4.9 21.5 1.0
NE1 C:TRP86 4.9 24.1 1.0
CD1 C:TRP86 5.0 21.4 1.0

Iron binding site 8 out of 9 in 6icp

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Iron binding site 8 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe400

b:21.4
occ:1.00
 FE2 C:FES400 0.0 21.4 1.0
S2 C:FES400 2.2 22.9 1.0
S1 C:FES400 2.2 23.5 1.0
SG C:CYS62 2.3 18.4 1.0
SG C:CYS81 2.4 22.4 1.0
FE1 C:FES400 2.8 23.1 1.0
CB C:CYS62 3.1 18.3 1.0
CB C:CYS81 3.2 22.0 1.0
CB C:HIS64 4.1 23.4 1.0
CB C:TYR83 4.3 22.7 1.0
N C:HIS84 4.5 20.9 1.0
CA C:CYS62 4.6 22.7 1.0
CB C:ALA67 4.6 21.4 1.0
ND1 C:HIS64 4.6 24.2 1.0
CA C:CYS81 4.7 23.3 1.0
N C:ARG65 4.7 23.7 1.0
ND1 C:HIS84 4.7 23.4 1.0
N C:HIS64 4.8 24.4 1.0
N C:TYR83 4.8 21.3 1.0
CG C:HIS64 4.8 24.2 1.0
CB C:TRP86 4.9 23.3 1.0
CG C:TRP86 5.0 24.9 1.0
CA C:HIS64 5.0 23.7 1.0

Iron binding site 9 out of 9 in 6icp

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Iron binding site 9 out of 9 in the Pseudomonas Putida CBB5 Ndma Ql Mutant with Caffeine


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 Ql Mutant with Caffeine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:26.4
occ:1.00
 NE2 C:HIS178 2.0 25.9 1.0
OD1 C:ASP289 2.1 22.2 1.0
NE2 C:HIS173 2.1 26.4 1.0
O C:HOH670 2.1 35.2 1.0
OD2 C:ASP289 2.4 24.5 1.0
CG C:ASP289 2.5 25.4 1.0
CD2 C:HIS178 3.0 24.9 1.0
CE1 C:HIS178 3.0 26.5 1.0
CE1 C:HIS173 3.1 26.1 1.0
CD2 C:HIS173 3.1 25.0 1.0
ND2 C:ASN167 3.8 25.1 1.0
O C:HOH514 3.9 30.9 1.0
OD1 C:ASN167 4.0 25.8 1.0
CB C:ASP289 4.0 21.0 1.0
ND1 C:HIS178 4.2 24.1 1.0
CG C:HIS178 4.2 26.7 1.0
ND1 C:HIS173 4.2 32.7 1.0
CG C:HIS173 4.2 27.8 1.0
CG C:ASN167 4.3 27.2 1.0
O C:HOH613 4.3 37.3 1.0
CG2 C:ILE177 4.5 21.9 1.0
O C:ASN167 4.5 26.8 1.0
CE1 C:PHE174 4.7 34.5 1.0
CG1 C:VAL285 4.7 28.4 1.0
CA C:ASP289 4.8 23.6 1.0
O11 C:CFF402 4.9 44.6 1.0
O C:VAL285 5.0 22.5 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 22:54:53 2024

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