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Iron in PDB 4n59: The Crystal Structure of Pectocin M2 at 2.3 Angstroms

Protein crystallography data

The structure of The Crystal Structure of Pectocin M2 at 2.3 Angstroms, PDB code: 4n59 was solved by K.Zeth, R.Grinter, A.W.Roszak, R.J.Cogdell, D.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.52 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.649, 116.745, 60.790, 90.00, 94.96, 90.00
R / Rfree (%) 20.6 / 27.4

Other elements in 4n59:

The structure of The Crystal Structure of Pectocin M2 at 2.3 Angstroms also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Pectocin M2 at 2.3 Angstroms (pdb code 4n59). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structure of Pectocin M2 at 2.3 Angstroms, PDB code: 4n59:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4n59

Go back to Iron Binding Sites List in 4n59
Iron binding site 1 out of 4 in the The Crystal Structure of Pectocin M2 at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Pectocin M2 at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:61.6
occ:1.00
FE1 A:FES301 0.0 61.6 1.0
S1 A:FES301 2.2 58.8 1.0
S2 A:FES301 2.2 63.4 1.0
SG A:CYS38 2.3 67.8 1.0
SG A:CYS43 2.4 65.2 1.0
FE2 A:FES301 2.9 61.6 1.0
CB A:CYS38 3.4 70.2 1.0
CB A:CYS43 3.6 64.9 1.0
N A:CYS43 3.6 64.7 1.0
N A:CYS38 3.6 69.3 1.0
N A:ARG39 3.7 69.8 1.0
CA A:CYS38 3.9 70.5 1.0
CA A:CYS43 3.9 65.2 1.0
C A:CYS43 4.1 63.1 1.0
C A:CYS38 4.1 69.9 1.0
N A:ALA42 4.2 65.8 1.0
O A:CYS43 4.4 63.5 1.0
N A:ALA40 4.4 70.2 1.0
N A:GLY41 4.5 68.0 1.0
N A:SER45 4.5 53.5 1.0
C A:ALA42 4.5 66.2 1.0
SG A:CYS75 4.5 63.6 1.0
CA A:ARG39 4.6 69.9 1.0
N A:SER44 4.6 60.1 1.0
N A:SER37 4.6 66.3 1.0
C A:SER37 4.7 71.1 1.0
OG A:SER37 4.7 66.9 1.0
SG A:CYS46 4.7 53.8 1.0
CB A:SER45 4.8 56.9 1.0
C A:GLY41 4.9 66.8 1.0
CA A:GLY41 4.9 66.9 1.0
CA A:ALA42 5.0 66.6 1.0

Iron binding site 2 out of 4 in 4n59

Go back to Iron Binding Sites List in 4n59
Iron binding site 2 out of 4 in the The Crystal Structure of Pectocin M2 at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Pectocin M2 at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:61.6
occ:1.00
FE2 A:FES301 0.0 61.6 1.0
S2 A:FES301 2.2 63.4 1.0
SG A:CYS75 2.2 63.6 1.0
S1 A:FES301 2.2 58.8 1.0
SG A:CYS46 2.3 53.8 1.0
FE1 A:FES301 2.9 61.6 1.0
CB A:CYS75 3.3 62.5 1.0
CB A:CYS46 3.4 52.5 1.0
N A:CYS75 4.2 58.8 1.0
N A:CYS46 4.3 51.5 1.0
CA A:CYS75 4.3 61.7 1.0
N A:ARG39 4.3 69.8 1.0
N A:GLY41 4.4 68.0 1.0
CA A:ARG39 4.4 69.9 1.0
CA A:CYS46 4.5 51.6 1.0
SG A:CYS38 4.5 67.8 1.0
N A:ALA40 4.7 70.2 1.0
CA A:GLY41 4.7 66.9 1.0
CB A:LEU73 4.8 52.6 1.0
C A:ARG39 4.8 68.9 1.0
SG A:CYS43 4.9 65.2 1.0
CD2 A:LEU73 5.0 52.4 1.0

Iron binding site 3 out of 4 in 4n59

Go back to Iron Binding Sites List in 4n59
Iron binding site 3 out of 4 in the The Crystal Structure of Pectocin M2 at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Pectocin M2 at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:89.7
occ:1.00
FE1 B:FES301 0.0 89.7 1.0
SG B:CYS43 1.9 89.1 1.0
S2 B:FES301 2.2 91.6 1.0
S1 B:FES301 2.2 86.3 1.0
SG B:CYS38 2.4 0.3 1.0
FE2 B:FES301 2.9 82.8 1.0
CB B:CYS38 3.2 0.9 1.0
CB B:CYS43 3.3 93.6 1.0
N B:CYS38 3.4 95.2 1.0
N B:CYS43 3.5 99.2 1.0
N B:ARG39 3.7 96.6 1.0
CA B:CYS38 3.7 99.1 1.0
CA B:CYS43 3.8 95.8 1.0
C B:CYS43 3.9 91.3 1.0
O B:CYS43 4.0 90.3 1.0
C B:CYS38 4.0 99.5 1.0
N B:ALA42 4.3 0.1 1.0
C B:SER37 4.4 92.3 1.0
SG B:CYS75 4.5 94.9 1.0
N B:SER44 4.5 88.7 1.0
C B:ALA42 4.5 0.8 1.0
N B:SER37 4.5 84.3 1.0
N B:GLY41 4.6 0.3 1.0
N B:SER45 4.6 82.7 1.0
N B:ALA40 4.6 0.4 1.0
CA B:ARG39 4.7 95.5 1.0
SG B:CYS46 4.7 79.8 1.0
CB B:SER37 4.8 88.5 1.0
CA B:SER37 4.8 89.1 1.0
CB B:SER45 4.9 80.1 1.0
CA B:GLY41 5.0 0.4 1.0

Iron binding site 4 out of 4 in 4n59

Go back to Iron Binding Sites List in 4n59
Iron binding site 4 out of 4 in the The Crystal Structure of Pectocin M2 at 2.3 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Pectocin M2 at 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:82.8
occ:1.00
FE2 B:FES301 0.0 82.8 1.0
SG B:CYS75 2.1 94.9 1.0
S1 B:FES301 2.2 86.3 1.0
S2 B:FES301 2.2 91.6 1.0
SG B:CYS46 2.5 79.8 1.0
CB B:CYS75 2.8 95.3 1.0
FE1 B:FES301 2.9 89.7 1.0
CB B:CYS46 3.5 75.0 1.0
CA B:CYS75 4.0 94.0 1.0
N B:CYS75 4.1 91.1 1.0
N B:GLY41 4.2 0.3 1.0
N B:ARG39 4.2 96.6 1.0
SG B:CYS38 4.3 0.3 1.0
CA B:ARG39 4.4 95.5 1.0
SG B:CYS43 4.4 89.1 1.0
CB B:LEU73 4.5 86.4 1.0
CA B:GLY41 4.6 0.4 1.0
N B:ALA40 4.6 0.4 1.0
N B:CYS46 4.6 74.7 1.0
CA B:CYS46 4.7 74.1 1.0
C B:ARG39 4.7 98.6 1.0
C B:CYS75 4.8 1.0 1.0
O B:CYS43 4.9 90.3 1.0

Reference:

R.Grinter, I.Josts, K.Zeth, A.W.Roszak, L.C.Mccaughey, R.J.Cogdell, J.J.Milner, S.M.Kelly, O.Byron, D.Walker. Structure of the Atypical Bacteriocin Pectocin M2 Implies A Novel Mechanism of Protein Uptake. Mol.Microbiol. V. 93 234 2014.
ISSN: ISSN 0950-382X
PubMed: 24865810
DOI: 10.1111/MMI.12655
Page generated: Sun Dec 13 15:42:21 2020

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