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Iron in PDB 6rp2: Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1

Enzymatic activity of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1

All present enzymatic activity of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1:
1.12.99.6;

Protein crystallography data

The structure of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1, PDB code: 6rp2 was solved by S.B.Carr, F.A.Armstrong, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.07 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.720, 97.520, 183.060, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 15.9

Other elements in 6rp2:

The structure of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iron atom in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 (pdb code 6rp2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 26 binding sites of Iron where determined in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1, PDB code: 6rp2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 26 in 6rp2

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Iron binding site 1 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:10.8
occ:1.00
 FE1 S:SF4401 0.0 10.8 1.0
SG S:CYS215 2.3 11.3 1.0
S2 S:SF4401 2.3 11.2 1.0
S3 S:SF4401 2.3 10.9 1.0
S4 S:SF4401 2.3 11.1 1.0
FE3 S:SF4401 2.7 11.3 1.0
FE4 S:SF4401 2.7 10.9 1.0
FE2 S:SF4401 2.7 10.7 1.0
CB S:CYS215 3.4 11.4 1.0
N S:LEU216 3.8 10.4 1.0
S1 S:SF4401 3.9 10.9 1.0
CA S:CYS215 3.9 11.3 1.0
N S:TYR217 4.2 11.4 1.0
CB S:PHE196 4.3 12.5 1.0
C S:CYS215 4.3 10.8 1.0
CD1 S:PHE196 4.4 12.6 1.0
ND1 S:HIS187 4.4 10.9 1.0
CB S:TYR217 4.6 13.3 1.0
O S:ARG192 4.7 11.3 1.0
CB S:ARG192 4.7 10.9 1.0
CG S:PHE196 4.8 12.9 1.0
CA S:LEU216 4.8 10.3 1.0
CA S:TYR217 4.8 12.3 1.0
C S:LEU216 4.8 10.8 1.0
SG S:CYS190 4.9 11.0 1.0
SG S:CYS221 4.9 10.5 1.0
CE1 S:HIS187 4.9 11.4 1.0
C S:ARG192 5.0 10.3 1.0

Iron binding site 2 out of 26 in 6rp2

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Iron binding site 2 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:10.7
occ:1.00
 FE2 S:SF4401 0.0 10.7 1.0
S4 S:SF4401 2.3 11.1 1.0
S1 S:SF4401 2.3 10.9 1.0
SG S:CYS221 2.3 10.5 1.0
S3 S:SF4401 2.3 10.9 1.0
FE3 S:SF4401 2.7 11.3 1.0
FE1 S:SF4401 2.7 10.8 1.0
FE4 S:SF4401 2.7 10.9 1.0
CB S:CYS221 3.2 11.1 1.0
S2 S:SF4401 3.9 11.2 1.0
CD1 S:ILE243 3.9 10.9 1.0
CG1 S:ILE243 4.4 10.0 1.0
CA S:GLY223 4.5 11.5 1.0
CD S:PRO224 4.5 11.9 1.0
N S:GLY223 4.6 10.8 1.0
CA S:CYS221 4.6 10.0 1.0
ND1 S:HIS187 4.6 10.9 1.0
SG S:CYS215 4.7 11.3 1.0
N S:TYR217 4.7 11.4 1.0
SG S:CYS190 4.8 11.0 1.0
N S:LEU216 4.8 10.4 1.0
C S:CYS221 4.9 10.8 1.0
C S:LEU216 4.9 10.8 1.0
CB S:LEU216 5.0 11.3 1.0
O S:CYS221 5.0 10.4 1.0

Iron binding site 3 out of 26 in 6rp2

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Iron binding site 3 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:11.3
occ:1.00
 FE3 S:SF4401 0.0 11.3 1.0
ND1 S:HIS187 2.0 10.9 1.0
S1 S:SF4401 2.3 10.9 1.0
S4 S:SF4401 2.3 11.1 1.0
S2 S:SF4401 2.3 11.2 1.0
FE4 S:SF4401 2.7 10.9 1.0
FE1 S:SF4401 2.7 10.8 1.0
FE2 S:SF4401 2.7 10.7 1.0
CE1 S:HIS187 3.0 11.4 1.0
CG S:HIS187 3.1 11.8 1.0
CB S:HIS187 3.6 11.3 1.0
S3 S:SF4401 3.9 10.9 1.0
CA S:HIS187 4.0 11.3 1.0
NE2 S:HIS187 4.1 11.6 1.0
CD2 S:HIS187 4.2 11.5 1.0
CG S:PRO224 4.3 13.3 1.0
CD S:PRO224 4.4 11.9 1.0
CB S:CYS190 4.6 10.1 1.0
SG S:CYS215 4.6 11.3 1.0
SG S:CYS190 4.7 11.0 1.0
O S:HIS187 4.7 13.6 1.0
CD1 S:PHE196 4.8 12.6 1.0
SG S:CYS221 4.8 10.5 1.0
CD S:ARG193 4.9 16.1 1.0
N S:PRO224 4.9 11.0 1.0
C S:HIS187 5.0 12.0 1.0
CG S:PHE196 5.0 12.9 1.0

Iron binding site 4 out of 26 in 6rp2

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Iron binding site 4 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:10.9
occ:1.00
 FE4 S:SF4401 0.0 10.9 1.0
S2 S:SF4401 2.3 11.2 1.0
SG S:CYS190 2.3 11.0 1.0
S3 S:SF4401 2.3 10.9 1.0
S1 S:SF4401 2.3 10.9 1.0
FE3 S:SF4401 2.7 11.3 1.0
FE1 S:SF4401 2.7 10.8 1.0
FE2 S:SF4401 2.7 10.7 1.0
CB S:CYS190 3.1 10.1 1.0
S4 S:SF4401 3.9 11.1 1.0
CB S:ARG192 4.2 10.9 1.0
CD1 S:ILE243 4.2 10.9 1.0
CG2 S:ILE243 4.4 11.1 1.0
ND1 S:HIS187 4.5 10.9 1.0
CA S:CYS190 4.6 10.2 1.0
C S:ARG192 4.6 10.3 1.0
N S:ARG192 4.7 10.4 1.0
N S:ARG193 4.7 10.3 1.0
CA S:ARG192 4.7 10.5 1.0
SG S:CYS221 4.8 10.5 1.0
CG1 S:ILE243 4.8 10.0 1.0
SG S:CYS215 4.9 11.3 1.0
CA S:HIS187 5.0 11.3 1.0

Iron binding site 5 out of 26 in 6rp2

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Iron binding site 5 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:10.7
occ:1.00
 FE1 S:F3S402 0.0 10.7 1.0
S1 S:F3S402 2.2 10.5 1.0
S2 S:F3S402 2.3 11.2 1.0
SG S:CYS252 2.3 11.0 1.0
S3 S:F3S402 2.3 10.7 1.0
FE3 S:F3S402 2.7 10.6 1.0
FE4 S:F3S402 2.7 10.7 1.0
CB S:CYS252 3.4 9.8 1.0
O L:HOH719 3.7 10.3 1.0
N S:CYS252 3.8 10.5 1.0
S4 S:F3S402 3.9 11.4 1.0
O S:HOH607 4.0 10.9 1.0
CA S:CYS252 4.0 10.2 1.0
N S:ALA253 4.5 10.2 1.0
C S:CYS252 4.5 10.6 1.0
O L:HOH1024 4.5 11.2 1.0
ND2 S:ASN228 4.6 9.8 1.0
SG S:CYS230 4.7 10.4 1.0
SG S:CYS249 4.7 11.0 1.0
C S:GLY251 4.9 11.0 1.0

Iron binding site 6 out of 26 in 6rp2

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Iron binding site 6 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:10.6
occ:1.00
 FE3 S:F3S402 0.0 10.6 1.0
S4 S:F3S402 2.2 11.4 1.0
S1 S:F3S402 2.2 10.5 1.0
S3 S:F3S402 2.3 10.7 1.0
SG S:CYS230 2.3 10.4 1.0
FE1 S:F3S402 2.7 10.7 1.0
FE4 S:F3S402 2.7 10.7 1.0
CB S:CYS230 3.3 10.0 1.0
S2 S:F3S402 3.9 11.2 1.0
ND2 S:ASN228 4.0 9.8 1.0
CD1 S:ILE186 4.3 12.5 1.0
O S:HOH607 4.3 10.9 1.0
NE1 S:TRP235 4.3 9.5 1.0
CD S:PRO242 4.5 10.1 1.0
CG S:PRO242 4.5 9.6 1.0
CG S:ASN228 4.6 9.9 1.0
CA S:CYS230 4.7 10.2 1.0
CB S:ASN228 4.7 11.2 1.0
SG S:CYS252 4.7 11.0 1.0
CG1 S:ILE186 4.8 12.3 1.0
SG S:CYS249 4.8 11.0 1.0

Iron binding site 7 out of 26 in 6rp2

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Iron binding site 7 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:10.7
occ:1.00
 FE4 S:F3S402 0.0 10.7 1.0
S4 S:F3S402 2.2 11.4 1.0
SG S:CYS249 2.3 11.0 1.0
S2 S:F3S402 2.3 11.2 1.0
S3 S:F3S402 2.3 10.7 1.0
FE1 S:F3S402 2.7 10.7 1.0
FE3 S:F3S402 2.7 10.6 1.0
CB S:CYS249 3.2 10.2 1.0
CA S:CYS249 3.6 9.8 1.0
S1 S:F3S402 3.8 10.5 1.0
N S:LEU250 4.1 10.2 1.0
N S:GLY251 4.2 10.6 1.0
C S:CYS249 4.3 10.0 1.0
N S:CYS252 4.4 10.5 1.0
CG1 S:ILE186 4.6 12.3 1.0
CG2 S:THR226 4.6 10.1 1.0
CA S:GLY251 4.8 10.8 1.0
SG S:CYS252 4.8 11.0 1.0
CG S:PRO242 4.8 9.6 1.0
SG S:CYS230 4.8 10.4 1.0
N S:CYS249 4.9 9.6 1.0

Iron binding site 8 out of 26 in 6rp2

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Iron binding site 8 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:10.8
occ:1.00
 FE1 S:SF3403 0.0 10.8 1.0
S1 S:SF3403 2.3 11.2 1.0
SG S:CYS115 2.3 11.2 1.0
S3 S:SF3403 2.3 10.6 1.0
S2 S:SF3403 2.3 11.0 1.0
FE4 S:SF3403 2.6 11.1 1.0
FE3 S:SF3403 2.8 10.5 1.0
FE7 S:SF3403 2.8 9.0 0.7
CB S:CYS115 3.3 10.1 1.0
FE7 S:SF3403 3.7 16.8 0.3
O S:HOH540 3.9 11.4 1.0
SG S:CYS19 4.0 11.3 1.0
N S:CYS115 4.1 10.2 1.0
O S:HOH587 4.2 11.1 1.0
CA S:CYS115 4.2 10.3 1.0
SG S:CYS120 4.4 10.6 1.0
CB S:CYS120 4.4 9.7 1.0
N S:CYS17 4.5 10.5 1.0
SG S:CYS20 4.6 10.7 1.0
SG S:CYS17 4.7 11.2 1.0
SG S:CYS149 4.7 10.2 1.0
CA S:GLU16 4.9 11.2 1.0

Iron binding site 9 out of 26 in 6rp2

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Iron binding site 9 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:10.5
occ:1.00
 FE3 S:SF3403 0.0 10.5 1.0
SG S:CYS149 2.3 10.2 1.0
S3 S:SF3403 2.3 10.6 1.0
S1 S:SF3403 2.3 11.2 1.0
SG S:CYS120 2.3 10.6 1.0
FE1 S:SF3403 2.8 10.8 1.0
CB S:CYS149 3.3 9.5 1.0
CB S:CYS120 3.5 9.7 1.0
FE4 S:SF3403 3.6 11.1 1.0
CA S:CYS149 3.9 9.7 1.0
FE7 S:SF3403 4.0 9.0 0.7
SG S:CYS115 4.0 11.2 1.0
SG S:CYS19 4.2 11.3 1.0
CG L:ARG74 4.4 9.4 1.0
N S:CYS115 4.5 10.2 1.0
CB S:THR114 4.6 10.5 1.0
S2 S:SF3403 4.7 11.0 1.0
C S:CYS149 4.8 9.6 1.0
CA S:CYS120 4.9 9.7 1.0
O S:GLY148 4.9 10.0 1.0
N S:VAL121 4.9 9.3 1.0
N S:THR114 5.0 10.4 1.0

Iron binding site 10 out of 26 in 6rp2

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Iron binding site 10 out of 26 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:11.1
occ:1.00
 FE4 S:SF3403 0.0 11.1 1.0
SG S:CYS17 2.3 11.2 1.0
S3 S:SF3403 2.3 10.6 1.0
S2 S:SF3403 2.3 11.0 1.0
SG S:CYS19 2.3 11.3 1.0
FE1 S:SF3403 2.6 10.8 1.0
FE7 S:SF3403 2.7 9.0 0.7
FE7 S:SF3403 3.1 16.8 0.3
CB S:CYS17 3.4 10.7 1.0
CB S:CYS19 3.4 10.1 1.0
FE3 S:SF3403 3.6 10.5 1.0
N S:CYS19 3.7 9.2 1.0
S1 S:SF3403 3.7 11.2 1.0
N S:CYS17 3.7 10.5 1.0
CA S:CYS17 3.9 10.8 1.0
CA S:CYS19 4.1 9.2 1.0
N S:THR18 4.2 10.2 1.0
NE2 L:HIS229 4.2 9.9 1.0
C S:CYS17 4.2 11.4 1.0
SG S:CYS149 4.4 10.2 1.0
O S:HOH587 4.5 11.1 1.0
SG S:CYS115 4.6 11.2 1.0
N S:CYS20 4.7 9.8 1.0
CD2 L:HIS229 4.8 8.9 1.0
C S:THR18 4.8 10.2 1.0
C S:CYS19 4.8 10.2 1.0
C S:GLU16 4.9 10.7 1.0
CG L:ARG74 5.0 9.4 1.0
O S:CYS17 5.0 11.0 1.0

Reference:

L.Zhang, S.E.Beaton, S.B.Carr, F.A.Armstrong. Direct Visible Light Activation of A Surface Cysteine-Engineered [Nife]-Hydrogenase By Silver Nanoclusters Energy Environ Sci 2018.
ISSN: ESSN 1754-5706
DOI: 10.1039/C8EE02361A
Page generated: Wed Aug 7 08:51:32 2024

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