Atomistry » Iron » PDB 6i95-6j55 » 6ick
Atomistry »
  Iron »
    PDB 6i95-6j55 »
      6ick »

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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Go back to Iron Binding Sites List in 6ick
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy