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Iron in PDB 6c3x: Wild Type Structure of Sirhp

Enzymatic activity of Wild Type Structure of Sirhp

All present enzymatic activity of Wild Type Structure of Sirhp:
1.8.1.2;

Protein crystallography data

The structure of Wild Type Structure of Sirhp, PDB code: 6c3x was solved by M.E.Stroupe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.37 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.794, 77.317, 87.586, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.1

Other elements in 6c3x:

The structure of Wild Type Structure of Sirhp also contains other interesting chemical elements:

Potassium (K) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Wild Type Structure of Sirhp (pdb code 6c3x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Wild Type Structure of Sirhp, PDB code: 6c3x:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 6c3x

Go back to Iron Binding Sites List in 6c3x
Iron binding site 1 out of 5 in the Wild Type Structure of Sirhp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Wild Type Structure of Sirhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:7.6
occ:1.00
FE1 A:SF4603 0.0 7.6 1.0
S4 A:SF4603 2.2 7.8 1.0
S3 A:SF4603 2.2 7.7 1.0
S2 A:SF4603 2.3 7.2 1.0
SG A:CYS434 2.3 7.9 1.0
FE4 A:SF4603 2.6 8.1 1.0
FE2 A:SF4603 2.7 8.4 1.0
FE3 A:SF4603 2.7 8.5 1.0
CB A:CYS434 3.3 6.9 1.0
N A:GLY478 3.7 7.2 1.0
S1 A:SF4603 3.8 8.4 1.0
N A:SER436 4.0 9.1 1.0
CA A:GLY478 4.0 6.0 1.0
CA A:SER436 4.2 8.7 1.0
CB A:SER436 4.3 8.7 1.0
N A:CYS479 4.4 6.8 1.0
CB A:CYS483 4.4 7.3 1.0
SG A:CYS483 4.5 7.3 1.0
OG1 A:THR477 4.5 10.8 1.0
C A:GLY478 4.5 7.4 1.0
CA A:CYS434 4.6 8.6 1.0
N A:VAL435 4.7 9.1 1.0
C A:CYS434 4.7 9.2 1.0
C A:THR477 4.8 7.7 1.0
SG A:CYS440 4.9 9.0 1.0
SG A:CYS479 5.0 8.5 1.0

Iron binding site 2 out of 5 in 6c3x

Go back to Iron Binding Sites List in 6c3x
Iron binding site 2 out of 5 in the Wild Type Structure of Sirhp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Wild Type Structure of Sirhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:8.4
occ:1.00
FE2 A:SF4603 0.0 8.4 1.0
S3 A:SF4603 2.2 7.7 1.0
S1 A:SF4603 2.3 8.4 1.0
S4 A:SF4603 2.3 7.8 1.0
SG A:CYS440 2.3 9.0 1.0
FE4 A:SF4603 2.7 8.1 1.0
FE1 A:SF4603 2.7 7.6 1.0
FE3 A:SF4603 2.7 8.5 1.0
CB A:CYS440 3.3 12.0 1.0
S2 A:SF4603 3.8 7.2 1.0
C3A A:SRM604 4.3 9.4 1.0
CA A:SER436 4.4 8.7 1.0
CBA A:SRM604 4.4 12.2 1.0
N A:SER436 4.5 9.1 1.0
N A:ALA443 4.5 11.8 1.0
CDA A:SRM604 4.6 10.2 1.0
CB A:LEU442 4.6 10.6 1.0
CA A:CYS440 4.7 9.8 1.0
SG A:CYS479 4.7 8.5 1.0
C4A A:SRM604 4.7 8.2 1.0
C A:LEU442 4.8 10.6 1.0
CA A:ALA443 4.8 9.5 1.0
SG A:CYS434 4.8 7.9 1.0
SG A:CYS483 4.9 7.3 1.0
C2A A:SRM604 5.0 9.3 1.0
CAA A:SRM604 5.0 11.4 1.0

Iron binding site 3 out of 5 in 6c3x

Go back to Iron Binding Sites List in 6c3x
Iron binding site 3 out of 5 in the Wild Type Structure of Sirhp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Wild Type Structure of Sirhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:8.5
occ:1.00
FE3 A:SF4603 0.0 8.5 1.0
S2 A:SF4603 2.2 7.2 1.0
S1 A:SF4603 2.3 8.4 1.0
S4 A:SF4603 2.3 7.8 1.0
SG A:CYS479 2.3 8.5 1.0
FE4 A:SF4603 2.7 8.1 1.0
FE2 A:SF4603 2.7 8.4 1.0
FE1 A:SF4603 2.7 7.6 1.0
CB A:CYS479 3.3 7.5 1.0
N A:CYS479 3.5 6.8 1.0
CA A:CYS479 3.8 7.4 1.0
S3 A:SF4603 3.9 7.7 1.0
O A:CYS479 4.1 7.6 1.0
C A:CYS479 4.1 7.7 1.0
C A:GLY478 4.2 7.4 1.0
CB A:ASN481 4.2 8.0 1.0
ND2 A:ASN481 4.3 12.6 1.0
SG A:CYS440 4.6 9.0 1.0
CB A:LEU442 4.7 10.6 1.0
CA A:GLY478 4.7 6.0 1.0
SG A:CYS483 4.7 7.3 1.0
N A:GLY478 4.7 7.2 1.0
O A:LEU442 4.7 11.8 1.0
CG A:ASN481 4.8 7.8 1.0
N A:ASN481 4.8 7.1 1.0
C A:LEU442 4.8 10.6 1.0
O A:GLY478 4.9 8.9 1.0
SG A:CYS434 4.9 7.9 1.0
CA A:ALA443 5.0 9.5 1.0
N A:GLY482 5.0 7.5 1.0
N A:ALA443 5.0 11.8 1.0

Iron binding site 4 out of 5 in 6c3x

Go back to Iron Binding Sites List in 6c3x
Iron binding site 4 out of 5 in the Wild Type Structure of Sirhp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Wild Type Structure of Sirhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:8.1
occ:1.00
FE4 A:SF4603 0.0 8.1 1.0
S1 A:SF4603 2.2 8.4 1.0
S3 A:SF4603 2.3 7.7 1.0
SG A:CYS483 2.3 7.3 1.0
S2 A:SF4603 2.3 7.2 1.0
FE1 A:SF4603 2.6 7.6 1.0
FE2 A:SF4603 2.7 8.4 1.0
FE3 A:SF4603 2.7 8.5 1.0
CB A:CYS483 3.2 7.3 1.0
S4 A:SF4603 3.8 7.8 1.0
NA A:SRM604 3.9 6.3 1.0
C4A A:SRM604 4.0 8.2 1.0
N A:CYS483 4.2 5.9 1.0
C1A A:SRM604 4.3 7.8 1.0
CA A:CYS483 4.3 5.5 1.0
CHB A:SRM604 4.4 9.6 1.0
FE A:SRM604 4.4 8.8 1.0
C3A A:SRM604 4.4 9.4 1.0
CB A:ASN481 4.5 8.0 1.0
SG A:CYS434 4.6 7.9 1.0
ND A:SRM604 4.6 8.1 1.0
CB A:CYS434 4.6 6.9 1.0
SG A:CYS479 4.7 8.5 1.0
SG A:CYS440 4.7 9.0 1.0
CHA A:SRM604 4.7 8.1 1.0
C4D A:SRM604 4.8 8.5 1.0
C1B A:SRM604 4.8 9.4 1.0
NB A:SRM604 4.8 7.8 1.0
C2A A:SRM604 4.9 9.3 1.0
N A:GLY482 5.0 7.5 1.0

Iron binding site 5 out of 5 in 6c3x

Go back to Iron Binding Sites List in 6c3x
Iron binding site 5 out of 5 in the Wild Type Structure of Sirhp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Wild Type Structure of Sirhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:8.8
occ:1.00
FE A:SRM604 0.0 8.8 1.0
ND A:SRM604 2.0 8.1 1.0
NA A:SRM604 2.0 6.3 1.0
NB A:SRM604 2.0 7.8 1.0
NC A:SRM604 2.0 7.4 1.0
O1 A:PO4601 2.2 9.7 1.0
SG A:CYS483 2.7 7.3 1.0
C4B A:SRM604 3.0 10.2 1.0
C1D A:SRM604 3.0 8.0 1.0
C4A A:SRM604 3.0 8.2 1.0
C4C A:SRM604 3.0 7.7 1.0
C4D A:SRM604 3.0 8.5 1.0
C1C A:SRM604 3.0 6.8 1.0
C1B A:SRM604 3.0 9.4 1.0
C1A A:SRM604 3.0 7.8 1.0
P A:PO4601 3.3 9.5 1.0
CHD A:SRM604 3.4 8.2 1.0
CHB A:SRM604 3.4 9.6 1.0
CHC A:SRM604 3.4 7.7 1.0
CHA A:SRM604 3.4 8.1 1.0
O3 A:PO4601 3.5 8.3 1.0
CB A:CYS483 3.6 7.3 1.0
NH2 A:ARG83 4.2 13.0 0.7
C3B A:SRM604 4.2 8.9 1.0
O2 A:PO4601 4.3 11.3 1.0
C3D A:SRM604 4.3 7.5 1.0
C2C A:SRM604 4.3 6.5 1.0
C3A A:SRM604 4.3 9.4 1.0
C3C A:SRM604 4.3 7.8 1.0
C2D A:SRM604 4.3 9.0 1.0
C2B A:SRM604 4.3 8.1 1.0
C2A A:SRM604 4.4 9.3 1.0
FE4 A:SF4603 4.4 8.1 1.0
O4 A:PO4601 4.4 10.4 1.0
CA A:CYS483 4.5 5.5 1.0
NZ A:LYS215 4.5 10.9 1.0
NH2 A:ARG83 4.6 13.3 0.3
CAB A:SRM604 4.8 9.6 1.0
NZ A:LYS217 4.9 8.2 1.0

Reference:

M.R.Cepeda, L.Mcgarry, J.M.Pennington, J.Krzystek, M.E.Stroupe. The Role of Extended FE4S4CLUSTER Ligands in Mediating Sulfite Reductase Hemoprotein Activity. Biochim. Biophys. Acta V.1866 933 2018.
ISSN: ISSN 0006-3002
PubMed: 29852252
DOI: 10.1016/J.BBAPAP.2018.05.013
Page generated: Sun Dec 13 16:22:00 2020

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