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Iron in PDB 8jc1: Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum

Protein crystallography data

The structure of Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum, PDB code: 8jc1 was solved by N.Jantarit, G.Kurisu, H.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.49 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.279, 138.553, 68.947, 90, 94.18, 90
R / Rfree (%) 19.5 / 23.9

Other elements in 8jc1:

The structure of Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum also contains other interesting chemical elements:

Sodium (Na) 8 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum (pdb code 8jc1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum, PDB code: 8jc1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8jc1

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Iron binding site 1 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:97.0
occ:1.00
 FE1 A:FES301 0.0 97.0 1.0
S1 A:FES301 2.2 78.1 1.0
S2 A:FES301 2.2 90.2 1.0
SG A:CYS38 2.3 89.2 1.0
SG A:CYS43 2.4 90.6 1.0
FE2 A:FES301 2.7 97.8 1.0
N A:CYS43 3.3 86.4 1.0
CB A:CYS43 3.4 88.0 1.0
N A:CYS38 3.5 88.9 1.0
CB A:CYS38 3.6 89.3 1.0
CA A:CYS43 3.6 85.4 1.0
C A:CYS43 3.8 88.9 1.0
CA A:CYS38 3.9 89.4 1.0
C A:CYS38 4.0 92.5 1.0
O A:CYS43 4.0 89.8 1.0
N A:SER42 4.1 90.3 1.0
N A:ARG39 4.2 90.6 1.0
SG A:CYS46 4.3 86.4 1.0
OG A:SER42 4.3 91.7 1.0
N A:SER44 4.4 86.5 1.0
C A:SER42 4.4 92.4 1.0
SG A:CYS75 4.4 83.0 1.0
O A:CYS38 4.5 90.2 1.0
N A:SER37 4.6 89.5 1.0
N A:SER45 4.6 83.0 1.0
C A:SER37 4.6 94.3 1.0
CA A:SER42 4.7 92.3 1.0
N A:CYS46 4.7 88.0 1.0
C A:GLY41 4.8 89.5 1.0
CB A:CYS46 4.8 82.0 1.0
CA A:ARG39 4.8 84.8 1.0
CB A:SER37 4.9 91.1 1.0
N A:GLY41 4.9 87.3 1.0
CA A:SER37 4.9 91.3 1.0

Iron binding site 2 out of 8 in 8jc1

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Iron binding site 2 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:97.8
occ:1.00
 FE2 A:FES301 0.0 97.8 1.0
S1 A:FES301 2.2 78.1 1.0
S2 A:FES301 2.2 90.2 1.0
SG A:CYS46 2.3 86.4 1.0
SG A:CYS75 2.3 83.0 1.0
FE1 A:FES301 2.7 97.0 1.0
CB A:CYS46 2.8 82.0 1.0
CB A:CYS75 3.4 79.0 1.0
CA A:CYS46 4.0 86.8 1.0
N A:CYS46 4.1 88.0 1.0
N A:CYS75 4.2 77.1 1.0
SG A:CYS38 4.3 89.2 1.0
CA A:CYS75 4.4 75.1 1.0
SG A:CYS43 4.5 90.6 1.0
CA A:ARG39 4.7 84.8 1.0
O A:CYS38 4.9 90.2 1.0
C A:CYS38 4.9 92.5 1.0
N A:ARG39 4.9 90.6 1.0
CB A:LEU73 4.9 74.1 1.0
N A:GLY41 4.9 87.3 1.0
C A:CYS46 5.0 84.2 1.0

Iron binding site 3 out of 8 in 8jc1

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Iron binding site 3 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:42.3
occ:1.00
 FE1 B:FES301 0.0 42.3 1.0
S1 B:FES301 2.2 44.0 1.0
S2 B:FES301 2.2 41.2 1.0
SG B:CYS38 2.3 45.6 1.0
SG B:CYS43 2.3 45.7 1.0
FE2 B:FES301 2.7 44.6 1.0
CB B:CYS38 3.5 42.7 1.0
CB B:CYS43 3.5 41.2 1.0
N B:CYS38 3.5 41.8 1.0
N B:CYS43 3.6 43.0 1.0
N B:ARG39 3.6 45.9 1.0
CA B:CYS38 3.9 43.9 1.0
CA B:CYS43 3.9 43.5 1.0
O B:CYS43 4.0 41.9 1.0
C B:CYS43 4.1 44.9 1.0
C B:CYS38 4.1 48.2 1.0
N B:SER42 4.2 49.8 1.0
N B:ALA40 4.2 43.7 1.0
N B:GLY41 4.3 49.0 1.0
SG B:CYS75 4.4 45.7 1.0
O B:HOH439 4.4 45.2 1.0
C B:SER42 4.5 44.8 1.0
CA B:ARG39 4.5 48.4 1.0
SG B:CYS46 4.5 44.4 1.0
C B:SER37 4.6 44.3 1.0
N B:SER37 4.6 42.1 1.0
N B:SER45 4.8 50.3 1.0
N B:CYS46 4.8 42.6 1.0
N B:SER44 4.8 43.4 1.0
CA B:GLY41 4.9 49.9 1.0
C B:ARG39 4.9 47.5 1.0
C B:GLY41 4.9 52.0 1.0
CB B:CYS46 5.0 46.7 1.0
CA B:SER42 5.0 48.6 1.0

Iron binding site 4 out of 8 in 8jc1

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Iron binding site 4 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:44.6
occ:1.00
 FE2 B:FES301 0.0 44.6 1.0
S2 B:FES301 2.2 41.2 1.0
S1 B:FES301 2.2 44.0 1.0
SG B:CYS75 2.3 45.7 1.0
SG B:CYS46 2.3 44.4 1.0
FE1 B:FES301 2.7 42.3 1.0
CB B:CYS75 3.2 50.2 1.0
CB B:CYS46 3.2 46.7 1.0
O B:HOH439 4.0 45.2 1.0
N B:CYS75 4.2 55.1 1.0
CA B:CYS75 4.3 55.3 1.0
N B:GLY41 4.3 49.0 1.0
N B:CYS46 4.4 42.6 1.0
CA B:CYS46 4.4 40.9 1.0
SG B:CYS38 4.4 45.6 1.0
N B:ARG39 4.5 45.9 1.0
CA B:ARG39 4.5 48.4 1.0
N B:ALA40 4.6 43.7 1.0
CA B:GLY41 4.7 49.9 1.0
SG B:CYS43 4.7 45.7 1.0
CB B:LEU73 4.8 52.0 1.0
C B:ARG39 4.9 47.5 1.0
CD2 B:LEU73 5.0 54.4 1.0

Iron binding site 5 out of 8 in 8jc1

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Iron binding site 5 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:59.0
occ:1.00
 FE1 C:FES302 0.0 59.0 1.0
S1 C:FES302 2.2 60.3 1.0
S2 C:FES302 2.2 50.2 1.0
SG C:CYS43 2.3 54.9 1.0
SG C:CYS38 2.4 59.5 1.0
FE2 C:FES302 2.7 52.7 1.0
N C:CYS43 3.4 58.3 1.0
CB C:CYS43 3.5 59.9 1.0
CB C:CYS38 3.7 57.6 1.0
CA C:CYS43 3.8 61.9 1.0
C C:CYS43 3.9 63.1 1.0
C C:CYS38 4.0 63.9 1.0
N C:CYS38 4.0 65.2 1.0
O C:CYS38 4.0 72.7 1.0
O C:CYS43 4.0 61.7 1.0
CA C:CYS38 4.1 63.7 1.0
N C:SER42 4.3 60.6 1.0
N C:SER45 4.5 60.6 1.0
SG C:CYS75 4.5 53.2 1.0
C C:SER42 4.5 62.3 1.0
N C:ARG39 4.5 62.9 1.0
N C:SER44 4.6 63.1 1.0
SG C:CYS46 4.6 51.4 1.0
N C:GLY41 4.7 60.2 1.0
N C:SER37 4.7 63.9 1.0
CB C:SER45 4.7 65.0 1.0
N C:CYS46 4.7 60.7 1.0
N C:ALA40 4.8 55.0 1.0
CA C:ARG39 4.9 61.2 1.0
C C:SER37 4.9 70.3 1.0
CA C:GLY41 5.0 59.7 1.0

Iron binding site 6 out of 8 in 8jc1

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Iron binding site 6 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:52.7
occ:1.00
 FE2 C:FES302 0.0 52.7 1.0
S2 C:FES302 2.2 50.2 1.0
S1 C:FES302 2.2 60.3 1.0
SG C:CYS75 2.3 53.2 1.0
SG C:CYS46 2.4 51.4 1.0
FE1 C:FES302 2.7 59.0 1.0
CB C:CYS75 3.3 57.6 1.0
CB C:CYS46 3.4 58.5 1.0
N C:CYS75 4.2 51.8 1.0
CA C:CYS75 4.3 58.5 1.0
N C:GLY41 4.3 60.2 1.0
N C:CYS46 4.4 60.7 1.0
SG C:CYS38 4.4 59.5 1.0
CB C:LEU73 4.5 54.1 1.0
CA C:CYS46 4.5 61.4 1.0
CA C:GLY41 4.6 59.7 1.0
O C:CYS38 4.7 72.7 1.0
CA C:ARG39 4.8 61.2 1.0
SG C:CYS43 4.8 54.9 1.0
CG C:LEU73 4.8 55.8 1.0
N C:ALA40 4.8 55.0 1.0
CD1 C:LEU73 4.9 55.6 1.0
O C:CYS43 5.0 61.7 1.0
C C:ARG39 5.0 58.4 1.0
C C:CYS75 5.0 57.5 1.0

Iron binding site 7 out of 8 in 8jc1

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Iron binding site 7 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:59.8
occ:1.00
 FE1 D:FES301 0.0 59.8 1.0
S1 D:FES301 2.2 60.5 1.0
S2 D:FES301 2.2 52.8 1.0
SG D:CYS43 2.3 67.7 1.0
SG D:CYS38 2.4 69.2 1.0
FE2 D:FES301 2.7 56.1 1.0
N D:CYS43 3.4 63.9 1.0
CB D:CYS38 3.4 64.3 1.0
CB D:CYS43 3.6 63.3 1.0
N D:ARG39 3.7 65.4 1.0
N D:CYS38 3.8 63.0 1.0
CA D:CYS43 3.9 64.3 1.0
N D:SER42 3.9 61.5 1.0
CA D:CYS38 4.0 66.2 1.0
C D:CYS43 4.1 66.4 1.0
C D:SER42 4.1 65.7 1.0
C D:CYS38 4.3 67.8 1.0
O D:CYS43 4.3 65.8 1.0
OG D:SER37 4.3 67.2 1.0
SG D:CYS75 4.4 50.0 1.0
N D:ALA40 4.4 60.6 1.0
CA D:SER42 4.5 65.2 1.0
CA D:ARG39 4.5 62.8 1.0
N D:SER45 4.5 59.0 1.0
N D:GLY41 4.5 60.2 1.0
SG D:CYS46 4.5 50.9 1.0
CB D:SER45 4.6 63.6 1.0
N D:SER44 4.7 65.9 1.0
N D:SER37 4.7 66.8 1.0
C D:GLY41 4.7 59.4 1.0
C D:SER37 4.8 69.8 1.0
O D:SER42 4.8 72.1 1.0
N D:CYS46 4.9 54.5 1.0
CA D:GLY41 4.9 53.4 1.0

Iron binding site 8 out of 8 in 8jc1

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Iron binding site 8 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:56.1
occ:1.00
 FE2 D:FES301 0.0 56.1 1.0
S2 D:FES301 2.2 52.8 1.0
S1 D:FES301 2.2 60.5 1.0
SG D:CYS46 2.3 50.9 1.0
SG D:CYS75 2.3 50.0 1.0
FE1 D:FES301 2.7 59.8 1.0
CB D:CYS46 3.2 55.1 1.0
CB D:CYS75 3.5 48.3 1.0
SG D:CYS38 4.2 69.2 1.0
N D:ARG39 4.3 65.4 1.0
N D:CYS46 4.3 54.5 1.0
CA D:ARG39 4.3 62.8 1.0
N D:GLY41 4.3 60.2 1.0
N D:CYS75 4.3 43.9 1.0
CA D:CYS46 4.4 56.8 1.0
CA D:CYS75 4.5 47.6 1.0
CB D:LEU73 4.6 47.1 1.0
N D:ALA40 4.6 60.6 1.0
CA D:GLY41 4.6 53.4 1.0
SG D:CYS43 4.7 67.7 1.0
C D:ARG39 4.8 61.5 1.0
N D:SER42 5.0 61.5 1.0

Reference:

N.Jantarit, H.Tanaka, Y.Lin, Y.H.Lee, G.Kurisu. Crystal Structure of Pectocin M1 Reveals Diverse Conformations and Interactions During Its Initial Step Via the Ferredoxin Uptake System. Febs Open Bio 2024.
ISSN: ESSN 2211-5463
PubMed: 39123319
DOI: 10.1002/2211-5463.13874
Page generated: Sat Sep 28 21:34:10 2024

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