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Iron in PDB 4y8w: Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex

Protein crystallography data

The structure of Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex, PDB code: 4y8w was solved by P.S.Pallan, L.Lei, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.383, 86.860, 108.923, 90.00, 102.11, 90.00
R / Rfree (%) 23.1 / 28.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex (pdb code 4y8w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex, PDB code: 4y8w:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 4y8w

Go back to Iron Binding Sites List in 4y8w
Iron binding site 1 out of 3 in the Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex


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 Human Cytochrome P450 21A2 Progesterone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:25.7
occ:1.00
FE A:HEM603 0.0 25.7 1.0
ND A:HEM603 1.9 25.8 1.0
NA A:HEM603 2.0 25.9 1.0
NC A:HEM603 2.1 25.8 1.0
NB A:HEM603 2.1 26.6 1.0
SG A:CYS429 2.2 26.4 1.0
C4D A:HEM603 2.9 25.4 1.0
C1D A:HEM603 2.9 25.5 1.0
C1A A:HEM603 3.0 25.8 1.0
C4A A:HEM603 3.0 26.0 1.0
C4C A:HEM603 3.1 25.8 1.0
C1B A:HEM603 3.1 26.6 1.0
C4B A:HEM603 3.1 26.7 1.0
C1C A:HEM603 3.1 25.8 1.0
CHA A:HEM603 3.4 25.6 1.0
CHD A:HEM603 3.4 25.7 1.0
CB A:CYS429 3.4 27.5 1.0
CHB A:HEM603 3.5 26.3 1.0
CHC A:HEM603 3.5 26.4 1.0
C21 A:STR604 4.0 31.7 1.0
CA A:CYS429 4.1 27.9 1.0
C3D A:HEM603 4.2 25.2 1.0
C2D A:HEM603 4.2 25.4 1.0
C2A A:HEM603 4.2 26.1 1.0
C3A A:HEM603 4.2 25.9 1.0
C3C A:HEM603 4.3 25.5 1.0
C2C A:HEM603 4.3 25.5 1.0
C2B A:HEM603 4.3 26.9 1.0
C3B A:HEM603 4.4 26.9 1.0
O A:GLY292 4.4 32.7 1.0
N A:LEU430 4.8 29.1 1.0
C A:CYS429 4.8 28.4 1.0
C16 A:STR604 4.8 31.5 1.0
N A:GLY431 4.9 29.7 1.0

Iron binding site 2 out of 3 in 4y8w

Go back to Iron Binding Sites List in 4y8w
Iron binding site 2 out of 3 in the Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex


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 Human Cytochrome P450 21A2 Progesterone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:27.3
occ:1.00
FE B:HEM602 0.0 27.3 1.0
ND B:HEM602 1.9 27.4 1.0
NA B:HEM602 2.0 27.5 1.0
NC B:HEM602 2.1 27.5 1.0
NB B:HEM602 2.1 28.1 1.0
SG B:CYS429 2.3 28.6 1.0
C4D B:HEM602 2.9 27.5 1.0
C1D B:HEM602 2.9 27.5 1.0
C1A B:HEM602 3.0 27.4 1.0
C4C B:HEM602 3.1 27.6 1.0
C4A B:HEM602 3.1 27.1 1.0
C1B B:HEM602 3.1 27.7 1.0
C4B B:HEM602 3.1 28.3 1.0
C1C B:HEM602 3.1 27.8 1.0
CHA B:HEM602 3.4 27.6 1.0
CB B:CYS429 3.4 29.7 1.0
CHD B:HEM602 3.4 27.6 1.0
CHB B:HEM602 3.5 27.2 1.0
CHC B:HEM602 3.5 28.0 1.0
CA B:CYS429 4.0 30.2 1.0
C21 B:STR603 4.1 33.8 1.0
C3D B:HEM602 4.2 27.5 1.0
C2D B:HEM602 4.2 27.5 1.0
C2A B:HEM602 4.2 27.6 1.0
C3A B:HEM602 4.2 27.2 1.0
C3C B:HEM602 4.3 27.6 1.0
C2C B:HEM602 4.3 27.9 1.0
C2B B:HEM602 4.3 28.2 1.0
C3B B:HEM602 4.4 28.4 1.0
O B:GLY292 4.5 31.4 1.0
C B:CYS429 4.8 30.9 1.0
CG2 B:THR296 4.9 35.2 1.0
C16 B:STR603 4.9 31.6 1.0
N B:LEU430 4.9 31.6 1.0

Iron binding site 3 out of 3 in 4y8w

Go back to Iron Binding Sites List in 4y8w
Iron binding site 3 out of 3 in the Crystal Structure of Human Cytochrome P450 21A2 Progesterone Complex


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 Human Cytochrome P450 21A2 Progesterone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe602

b:25.6
occ:1.00
FE C:HEM602 0.0 25.6 1.0
ND C:HEM602 1.9 25.8 1.0
NA C:HEM602 2.0 26.0 1.0
NC C:HEM602 2.1 25.9 1.0
NB C:HEM602 2.1 25.9 1.0
SG C:CYS429 2.3 26.6 1.0
C4D C:HEM602 2.9 25.8 1.0
C1D C:HEM602 2.9 25.8 1.0
C1A C:HEM602 3.0 25.7 1.0
C4A C:HEM602 3.1 26.0 1.0
C4C C:HEM602 3.1 25.7 1.0
C4B C:HEM602 3.1 25.8 1.0
C1B C:HEM602 3.1 26.1 1.0
C1C C:HEM602 3.1 25.5 1.0
CB C:CYS429 3.3 27.4 1.0
CHA C:HEM602 3.4 25.7 1.0
CHD C:HEM602 3.4 25.7 1.0
CHB C:HEM602 3.5 25.8 1.0
CHC C:HEM602 3.5 25.5 1.0
CA C:CYS429 4.0 28.1 1.0
C21 C:STR603 4.1 36.7 1.0
C3D C:HEM602 4.2 25.8 1.0
C2D C:HEM602 4.2 25.9 1.0
C2A C:HEM602 4.2 26.3 1.0
C3A C:HEM602 4.2 26.1 1.0
C3C C:HEM602 4.3 25.6 1.0
C2C C:HEM602 4.3 25.3 1.0
C2B C:HEM602 4.3 26.0 1.0
C3B C:HEM602 4.4 25.7 1.0
O C:GLY292 4.7 32.4 1.0
N C:LEU430 4.7 29.4 1.0
C C:CYS429 4.7 28.9 1.0
CG2 C:THR296 4.9 37.0 1.0
C16 C:STR603 4.9 35.8 1.0

Reference:

P.S.Pallan, C.Wang, L.Lei, F.K.Yoshimoto, R.J.Auchus, M.R.Waterman, F.P.Guengerich, M.Egli. Human Cytochrome P450 21A2, the Major Steroid 21-Hydroxylase: Structure of the Enzyme-Progesterone Substrate Complex and Rate-Limiting C-H Bond Cleavage. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 25855791
DOI: 10.1074/JBC.M115.646307
Page generated: Mon Aug 5 16:08:11 2024

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