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Iron in PDB 4jea: Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds

Protein crystallography data

The structure of Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds, PDB code: 4jea was solved by F.A.Tezcan, A.M.Medina-Morales, A.Perez, J.D.Brodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.94 / 1.22
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.850, 64.788, 74.177, 90.00, 98.18, 90.00
R / Rfree (%) 13.1 / 17.9

Other elements in 4jea:

The structure of Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds (pdb code 4jea). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds, PDB code: 4jea:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4jea

Go back to Iron Binding Sites List in 4jea
Iron binding site 1 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:12.8
occ:1.00
FE A:HEM201 0.0 12.8 1.0
NA A:HEM201 2.0 13.4 1.0
NE2 A:HIS102 2.0 13.4 1.0
NC A:HEM201 2.0 12.6 1.0
ND A:HEM201 2.1 12.8 1.0
NB A:HEM201 2.1 12.2 1.0
SD A:MET7 2.4 13.5 1.0
CE1 A:HIS102 3.0 13.4 1.0
CD2 A:HIS102 3.1 13.7 1.0
C4A A:HEM201 3.1 13.4 1.0
C4B A:HEM201 3.1 12.4 1.0
C1A A:HEM201 3.1 14.3 1.0
C1D A:HEM201 3.1 14.0 1.0
C4D A:HEM201 3.1 14.2 1.0
C1C A:HEM201 3.1 12.1 1.0
C1B A:HEM201 3.1 13.8 1.0
C4C A:HEM201 3.1 12.4 1.0
CE A:MET7 3.4 16.0 1.0
CG A:MET7 3.5 15.1 1.0
CHC A:HEM201 3.5 13.8 1.0
CHA A:HEM201 3.5 15.0 1.0
CHB A:HEM201 3.5 13.2 1.0
CHD A:HEM201 3.5 13.4 1.0
ND1 A:HIS102 4.2 13.3 1.0
CB A:MET7 4.2 13.9 1.0
CG A:HIS102 4.2 13.5 1.0
C3A A:HEM201 4.3 14.8 1.0
C2A A:HEM201 4.4 15.0 1.0
C3B A:HEM201 4.4 13.6 1.0
C3C A:HEM201 4.4 13.0 1.0
C2C A:HEM201 4.4 12.1 1.0
C3D A:HEM201 4.4 14.9 1.0
C2B A:HEM201 4.4 13.6 1.0
C2D A:HEM201 4.4 15.8 1.0

Iron binding site 2 out of 4 in 4jea

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Iron binding site 2 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:17.9
occ:1.00
FE B:HEM201 0.0 17.9 1.0
NA B:HEM201 2.0 19.1 1.0
NC B:HEM201 2.0 17.3 1.0
NE2 B:HIS102 2.0 19.5 1.0
NB B:HEM201 2.1 15.8 1.0
ND B:HEM201 2.1 18.3 1.0
SD B:MET7 2.4 18.6 1.0
CD2 B:HIS102 3.0 18.9 1.0
CE1 B:HIS102 3.1 18.9 1.0
C4B B:HEM201 3.1 15.8 1.0
C1D B:HEM201 3.1 19.4 1.0
C1C B:HEM201 3.1 15.5 1.0
C1A B:HEM201 3.1 20.2 1.0
C4D B:HEM201 3.1 22.6 1.0
C1B B:HEM201 3.1 17.0 1.0
C4A B:HEM201 3.1 20.3 1.0
C4C B:HEM201 3.2 16.9 1.0
CE B:MET7 3.4 20.2 1.0
CHC B:HEM201 3.5 15.6 1.0
CHD B:HEM201 3.5 18.0 1.0
CG B:MET7 3.5 20.1 1.0
CHA B:HEM201 3.5 21.7 1.0
CHB B:HEM201 3.5 17.9 1.0
ND1 B:HIS102 4.2 19.9 1.0
CG B:HIS102 4.2 20.2 1.0
CB B:MET7 4.3 20.1 1.0
C3B B:HEM201 4.4 16.2 1.0
C2D B:HEM201 4.4 21.3 1.0
C2C B:HEM201 4.4 15.5 1.0
C3A B:HEM201 4.4 21.7 1.0
C3D B:HEM201 4.4 22.6 1.0
C2A B:HEM201 4.4 23.3 1.0
C3C B:HEM201 4.4 17.4 1.0
C2B B:HEM201 4.4 17.0 1.0

Iron binding site 3 out of 4 in 4jea

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Iron binding site 3 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:14.0
occ:1.00
FE C:HEM201 0.0 14.0 1.0
NE2 C:HIS102 2.0 15.4 1.0
NC C:HEM201 2.0 13.7 1.0
NA C:HEM201 2.0 14.8 1.0
ND C:HEM201 2.1 14.2 1.0
NB C:HEM201 2.1 13.5 1.0
SD C:MET7 2.4 15.0 1.0
CE1 C:HIS102 3.0 15.2 1.0
CD2 C:HIS102 3.1 14.0 1.0
C1D C:HEM201 3.1 15.4 1.0
C1A C:HEM201 3.1 16.4 1.0
C4C C:HEM201 3.1 13.4 1.0
C1C C:HEM201 3.1 12.8 1.0
C1B C:HEM201 3.1 14.6 1.0
C4D C:HEM201 3.1 15.2 1.0
C4B C:HEM201 3.1 12.9 1.0
C4A C:HEM201 3.2 16.8 1.0
CE C:MET7 3.4 17.3 1.0
CHA C:HEM201 3.4 16.3 1.0
CHC C:HEM201 3.5 13.9 1.0
CHB C:HEM201 3.5 16.5 1.0
CHD C:HEM201 3.5 15.2 1.0
CG C:MET7 3.5 15.5 1.0
ND1 C:HIS102 4.2 16.5 1.0
CG C:HIS102 4.2 14.7 1.0
CB C:MET7 4.2 15.8 1.0
C2A C:HEM201 4.3 18.1 1.0
C3B C:HEM201 4.4 14.0 1.0
C2C C:HEM201 4.4 12.8 1.0
C3D C:HEM201 4.4 16.2 1.0
C2B C:HEM201 4.4 15.2 1.0
C3C C:HEM201 4.4 14.0 1.0
C3A C:HEM201 4.4 17.0 1.0
C2D C:HEM201 4.4 14.8 1.0
NH2 C:ARG106 4.9 28.1 1.0

Iron binding site 4 out of 4 in 4jea

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Iron binding site 4 out of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds


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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:19.6
occ:1.00
FE D:HEM201 0.0 19.6 1.0
NC D:HEM201 2.0 17.5 1.0
NA D:HEM201 2.0 22.3 1.0
NB D:HEM201 2.1 20.3 1.0
NE2 D:HIS102 2.1 20.7 1.0
ND D:HEM201 2.1 19.8 1.0
SD D:MET7 2.3 20.2 1.0
CE1 D:HIS102 3.0 19.8 1.0
CD2 D:HIS102 3.1 19.0 1.0
C1C D:HEM201 3.1 16.6 1.0
C1D D:HEM201 3.1 18.4 1.0
C4D D:HEM201 3.1 21.3 1.0
C4B D:HEM201 3.1 16.3 1.0
C1A D:HEM201 3.1 22.8 1.0
C4A D:HEM201 3.1 23.7 1.0
C4C D:HEM201 3.1 17.0 1.0
C1B D:HEM201 3.1 18.8 1.0
CE D:MET7 3.4 21.8 1.0
CHC D:HEM201 3.5 17.7 1.0
CHA D:HEM201 3.5 23.2 1.0
CHD D:HEM201 3.5 17.2 1.0
CG D:MET7 3.5 22.8 1.0
CHB D:HEM201 3.5 22.4 1.0
ND1 D:HIS102 4.2 20.9 1.0
CG D:HIS102 4.3 19.2 1.0
CB D:MET7 4.3 26.7 1.0
C2C D:HEM201 4.4 15.9 1.0
C3C D:HEM201 4.4 15.8 1.0
C3A D:HEM201 4.4 25.6 1.0
C2A D:HEM201 4.4 28.0 1.0
C3B D:HEM201 4.4 17.3 1.0
C3D D:HEM201 4.4 24.4 1.0
C2D D:HEM201 4.4 21.6 1.0
C2B D:HEM201 4.4 19.9 1.0
NH2 D:ARG106 4.8 36.8 1.0

Reference:

A.Medina-Morales, A.Perez, J.D.Brodin, F.A.Tezcan. In Vitro and Cellular Self-Assembly of A Zn-Binding Protein Cryptand Via Templated Disulfide Bonds. J.Am.Chem.Soc. V. 135 12013 2013.
ISSN: ISSN 0002-7863
PubMed: 23905754
DOI: 10.1021/JA405318D
Page generated: Mon Aug 5 04:37:14 2024

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