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Iron in PDB 4djd: Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)

Protein crystallography data

The structure of Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), PDB code: 4djd was solved by Y.Kung, T.I.Doukov, L.C.Blasiak, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.83 / 2.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.614, 242.843, 79.665, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.9

Other elements in 4djd:

The structure of Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) (pdb code 4djd). 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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), PDB code: 4djd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4djd

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Iron binding site 1 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:0.3
occ:1.00
 FE1 C:SF4501 0.0 0.3 1.0
SG C:CYS20 2.3 0.3 1.0
S2 C:SF4501 2.3 0.8 1.0
S3 C:SF4501 2.3 0.4 1.0
S4 C:SF4501 2.3 0.5 1.0
FE3 C:SF4501 2.7 0.2 1.0
FE4 C:SF4501 2.7 1.0 1.0
FE2 C:SF4501 2.7 0.6 1.0
CB C:CYS20 3.3 0.1 1.0
N C:CYS20 3.8 0.3 1.0
S1 C:SF4501 3.9 0.1 1.0
CA C:CYS20 4.2 0.3 1.0
CD2 C:PHE28 4.4 0.7 1.0
N C:GLY18 4.5 0.7 1.0
N C:GLU19 4.5 0.9 1.0
O C:THR22 4.5 0.0 1.0
CG C:PHE28 4.7 1.0 1.0
SG C:CYS42 4.7 0.3 1.0
O C:THR24 4.7 0.9 1.0
CB C:PHE28 4.7 0.2 1.0
CA C:GLY18 4.8 0.7 1.0
SG C:CYS25 4.8 0.0 1.0
CB C:CYS42 4.9 0.4 1.0
C C:GLY18 4.9 1.0 1.0
SG C:CYS17 4.9 0.7 1.0
CA C:CYS25 4.9 0.8 1.0
C C:GLU19 4.9 0.6 1.0
CE2 C:PHE28 5.0 99.8 1.0

Iron binding site 2 out of 8 in 4djd

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Iron binding site 2 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:0.6
occ:1.00
 FE2 C:SF4501 0.0 0.6 1.0
S3 C:SF4501 2.3 0.4 1.0
S4 C:SF4501 2.3 0.5 1.0
S1 C:SF4501 2.3 0.1 1.0
SG C:CYS17 2.3 0.7 1.0
FE4 C:SF4501 2.7 1.0 1.0
FE1 C:SF4501 2.7 0.3 1.0
FE3 C:SF4501 2.7 0.2 1.0
N C:CYS17 3.5 0.0 1.0
CB C:CYS17 3.7 0.5 1.0
S2 C:SF4501 3.9 0.8 1.0
N C:GLY18 4.0 0.7 1.0
CA C:CYS17 4.0 0.3 1.0
CB C:LYS15 4.3 0.5 1.0
N C:GLU19 4.4 0.9 1.0
C C:CYS17 4.4 0.0 1.0
N C:ASN16 4.4 0.3 1.0
C C:ASN16 4.6 0.1 1.0
CB C:GLU19 4.7 0.8 1.0
SG C:CYS25 4.7 0.0 1.0
CA C:ASN16 4.8 0.4 1.0
SG C:CYS42 4.8 0.3 1.0
SG C:CYS20 4.8 0.3 1.0
CA C:GLY18 4.9 0.7 1.0

Iron binding site 3 out of 8 in 4djd

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Iron binding site 3 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:0.2
occ:1.00
 FE3 C:SF4501 0.0 0.2 1.0
SG C:CYS42 2.3 0.3 1.0
S2 C:SF4501 2.3 0.8 1.0
S1 C:SF4501 2.3 0.1 1.0
S4 C:SF4501 2.3 0.5 1.0
FE1 C:SF4501 2.7 0.3 1.0
FE4 C:SF4501 2.7 1.0 1.0
FE2 C:SF4501 2.7 0.6 1.0
CB C:CYS42 3.3 0.4 1.0
S3 C:SF4501 3.9 0.4 1.0
CA C:CYS42 4.0 0.3 1.0
CD C:PRO13 4.4 0.3 1.0
CG C:PRO13 4.4 0.1 1.0
CD C:PRO43 4.6 0.6 1.0
SG C:CYS20 4.7 0.3 1.0
SG C:CYS17 4.7 0.7 1.0
C C:CYS42 4.8 0.1 1.0
SG C:CYS25 4.8 0.0 1.0
CB C:CYS20 4.9 0.1 1.0
N C:PRO43 5.0 0.7 1.0

Iron binding site 4 out of 8 in 4djd

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Iron binding site 4 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:1.0
occ:1.00
 FE4 C:SF4501 0.0 1.0 1.0
SG C:CYS25 2.3 0.0 1.0
S2 C:SF4501 2.3 0.8 1.0
S1 C:SF4501 2.3 0.1 1.0
S3 C:SF4501 2.3 0.4 1.0
FE2 C:SF4501 2.7 0.6 1.0
FE1 C:SF4501 2.7 0.3 1.0
FE3 C:SF4501 2.7 0.2 1.0
CB C:CYS25 3.4 0.4 1.0
CA C:CYS25 3.7 0.8 1.0
S4 C:SF4501 3.9 0.5 1.0
N C:CYS25 4.0 98.1 1.0
N C:ASN16 4.0 0.3 1.0
N C:LYS15 4.4 0.4 1.0
CA C:ASN16 4.5 0.4 1.0
C C:THR24 4.6 0.6 1.0
SG C:CYS17 4.7 0.7 1.0
N C:CYS17 4.7 0.0 1.0
SG C:CYS42 4.8 0.3 1.0
CD C:PRO13 4.8 0.3 1.0
N C:LYS14 4.8 0.9 1.0
SG C:CYS20 4.8 0.3 1.0
CB C:LYS15 4.9 0.5 1.0
O C:THR24 4.9 0.9 1.0
CA C:LYS15 5.0 0.1 1.0
C C:LYS15 5.0 0.7 1.0

Iron binding site 5 out of 8 in 4djd

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Iron binding site 5 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.6
occ:1.00
 FE1 E:SF4501 0.0 0.6 1.0
SG E:CYS20 2.3 100.0 1.0
S4 E:SF4501 2.3 0.9 1.0
S2 E:SF4501 2.3 0.3 1.0
S3 E:SF4501 2.3 0.4 1.0
FE3 E:SF4501 2.7 0.8 1.0
FE4 E:SF4501 2.7 0.3 1.0
FE2 E:SF4501 2.7 0.9 1.0
CB E:CYS20 3.2 0.4 1.0
N E:CYS20 3.7 0.2 1.0
S1 E:SF4501 3.9 0.3 1.0
CA E:CYS20 4.1 0.8 1.0
N E:GLY18 4.3 0.2 1.0
N E:GLU19 4.4 0.1 1.0
O E:THR22 4.5 0.4 1.0
CA E:GLY18 4.6 0.8 1.0
C E:GLY18 4.6 0.1 1.0
SG E:CYS42 4.7 0.8 1.0
CB E:PHE28 4.8 0.6 1.0
CG E:PHE28 4.8 1.0 1.0
SG E:CYS17 4.8 0.8 1.0
SG E:CYS25 4.8 0.7 1.0
CB E:CYS42 4.8 0.0 1.0
C E:GLU19 4.9 0.8 1.0
N E:CYS17 4.9 0.1 1.0

Iron binding site 6 out of 8 in 4djd

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Iron binding site 6 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.9
occ:1.00
 FE2 E:SF4501 0.0 0.9 1.0
S4 E:SF4501 2.3 0.9 1.0
S1 E:SF4501 2.3 0.3 1.0
S3 E:SF4501 2.3 0.4 1.0
SG E:CYS17 2.3 0.8 1.0
FE4 E:SF4501 2.7 0.3 1.0
FE1 E:SF4501 2.7 0.6 1.0
FE3 E:SF4501 2.7 0.8 1.0
N E:CYS17 3.3 0.1 1.0
CB E:CYS17 3.5 0.2 1.0
CA E:CYS17 3.7 0.1 1.0
N E:GLY18 3.8 0.2 1.0
S2 E:SF4501 3.9 0.3 1.0
C E:CYS17 3.9 0.2 1.0
N E:GLU19 4.1 0.1 1.0
CB E:LYS15 4.4 0.3 1.0
N E:ASN16 4.5 0.6 1.0
C E:ASN16 4.5 0.7 1.0
CB E:GLU19 4.6 0.1 1.0
O E:CYS17 4.7 0.7 1.0
SG E:CYS25 4.7 0.7 1.0
CA E:GLY18 4.8 0.8 1.0
SG E:CYS42 4.8 0.8 1.0
CA E:ASN16 4.8 0.2 1.0
SG E:CYS20 4.8 100.0 1.0
N E:CYS20 4.8 0.2 1.0
CA E:GLU19 4.9 0.4 1.0
C E:GLY18 4.9 0.1 1.0

Iron binding site 7 out of 8 in 4djd

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Iron binding site 7 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.8
occ:1.00
 FE3 E:SF4501 0.0 0.8 1.0
S4 E:SF4501 2.3 0.9 1.0
SG E:CYS42 2.3 0.8 1.0
S2 E:SF4501 2.3 0.3 1.0
S1 E:SF4501 2.3 0.3 1.0
FE1 E:SF4501 2.7 0.6 1.0
FE2 E:SF4501 2.7 0.9 1.0
FE4 E:SF4501 2.7 0.3 1.0
CB E:CYS42 3.3 0.0 1.0
S3 E:SF4501 3.9 0.4 1.0
CA E:CYS42 4.2 0.1 1.0
O E:TYR44 4.5 0.8 1.0
CG E:PRO13 4.5 0.6 1.0
SG E:CYS20 4.6 100.0 1.0
CB E:CYS20 4.7 0.4 1.0
SG E:CYS17 4.7 0.8 1.0
SG E:CYS25 4.8 0.7 1.0
CD E:PRO43 4.9 0.6 1.0
C E:CYS42 4.9 0.8 1.0
CD E:PRO13 4.9 0.1 1.0

Iron binding site 8 out of 8 in 4djd

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Iron binding site 8 out of 8 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


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 Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.3
occ:1.00
 FE4 E:SF4501 0.0 0.3 1.0
S2 E:SF4501 2.3 0.3 1.0
S3 E:SF4501 2.3 0.4 1.0
S1 E:SF4501 2.3 0.3 1.0
SG E:CYS25 2.3 0.7 1.0
FE1 E:SF4501 2.7 0.6 1.0
FE2 E:SF4501 2.7 0.9 1.0
FE3 E:SF4501 2.7 0.8 1.0
CB E:CYS25 3.5 0.3 1.0
CA E:CYS25 3.8 0.6 1.0
N E:ASN16 3.8 0.6 1.0
S4 E:SF4501 3.9 0.9 1.0
N E:CYS25 4.1 0.4 1.0
CA E:ASN16 4.3 0.2 1.0
N E:CYS17 4.3 0.1 1.0
N E:LYS15 4.7 0.7 1.0
CG E:PRO13 4.7 0.6 1.0
CB E:LYS15 4.8 0.3 1.0
C E:THR24 4.8 0.7 1.0
SG E:CYS17 4.8 0.8 1.0
C E:ASN16 4.8 0.7 1.0
C E:LYS15 4.8 0.8 1.0
SG E:CYS20 4.9 100.0 1.0
SG E:CYS42 4.9 0.8 1.0
OD1 E:ASN16 4.9 0.3 1.0

Reference:

Y.Kung, N.Ando, T.I.Doukov, L.C.Blasiak, G.Bender, J.Seravalli, S.W.Ragsdale, C.L.Drennan. Visualizing Molecular Juggling Within A B12-Dependent Methyltransferase Complex. Nature V. 484 265 2012.
ISSN: ISSN 0028-0836
PubMed: 22419154
DOI: 10.1038/NATURE10916
Page generated: Mon Aug 5 01:18:47 2024

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