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Iron in PDB 6g7m: Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2

Enzymatic activity of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2

All present enzymatic activity of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2:
1.12.99.6;

Protein crystallography data

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m was solved by S.B.Carr, F.A.Armstrong, L.Zhang, S.E.Beaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.75 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.237, 100.986, 169.425, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19

Other elements in 6g7m:

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 (pdb code 6g7m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 6g7m

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Iron binding site 1 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:15.0
occ:1.00
 FE1 S:SF4401 0.0 15.0 1.0
S2 S:SF4401 2.3 15.9 1.0
SG S:CYS220 2.3 15.7 1.0
S4 S:SF4401 2.3 15.1 1.0
S3 S:SF4401 2.3 15.4 1.0
FE3 S:SF4401 2.7 16.3 1.0
FE4 S:SF4401 2.7 14.6 1.0
FE2 S:SF4401 2.8 15.0 1.0
CB S:CYS220 3.4 14.9 1.0
N S:LEU221 3.9 13.6 1.0
S1 S:SF4401 3.9 15.4 1.0
CA S:CYS220 4.0 14.6 1.0
N S:CYS222 4.1 16.4 1.0
C S:CYS220 4.4 15.0 1.0
ND1 S:HIS192 4.5 16.9 1.0
CB S:PHE201 4.5 17.1 1.0
CB S:ARG197 4.5 15.8 1.0
CD2 S:PHE201 4.5 18.2 1.0
CB S:CYS222 4.6 20.6 1.0
O S:ARG197 4.6 15.7 1.0
CA S:CYS222 4.7 17.3 1.0
CE1 S:HIS192 4.8 16.3 1.0
C S:LEU221 4.8 15.5 1.0
SG S:CYS195 4.8 14.1 1.0
CA S:LEU221 4.8 14.5 1.0
C S:ARG197 4.9 15.5 1.0
SG S:CYS226 4.9 13.7 1.0
CG S:PHE201 5.0 17.8 1.0

Iron binding site 2 out of 24 in 6g7m

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Iron binding site 2 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:15.0
occ:1.00
 FE2 S:SF4401 0.0 15.0 1.0
S1 S:SF4401 2.3 15.4 1.0
S3 S:SF4401 2.3 15.4 1.0
SG S:CYS226 2.3 13.7 1.0
S4 S:SF4401 2.3 15.1 1.0
FE4 S:SF4401 2.7 14.6 1.0
FE3 S:SF4401 2.8 16.3 1.0
FE1 S:SF4401 2.8 15.0 1.0
CB S:CYS226 3.3 14.1 1.0
S2 S:SF4401 3.9 15.9 1.0
CA S:GLY228 4.6 15.2 1.0
CD S:PRO229 4.6 16.0 1.0
N S:GLY228 4.6 14.1 1.0
CA S:CYS226 4.6 14.2 1.0
SG S:CYS195 4.7 14.1 1.0
ND1 S:HIS192 4.7 16.9 1.0
N S:CYS222 4.7 16.4 1.0
SG S:CYS220 4.8 15.7 1.0
CG2 S:VAL249 4.8 14.1 1.0
N S:LEU221 4.9 13.6 1.0
C S:CYS226 4.9 15.4 1.0

Iron binding site 3 out of 24 in 6g7m

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Iron binding site 3 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:16.3
occ:1.00
 FE3 S:SF4401 0.0 16.3 1.0
ND1 S:HIS192 2.1 16.9 1.0
S4 S:SF4401 2.3 15.1 1.0
S2 S:SF4401 2.3 15.9 1.0
S1 S:SF4401 2.3 15.4 1.0
FE1 S:SF4401 2.7 15.0 1.0
FE4 S:SF4401 2.7 14.6 1.0
FE2 S:SF4401 2.8 15.0 1.0
CE1 S:HIS192 2.9 16.3 1.0
CG S:HIS192 3.2 16.7 1.0
CB S:HIS192 3.6 15.2 1.0
S3 S:SF4401 3.9 15.4 1.0
CA S:HIS192 4.0 14.1 1.0
NE2 S:HIS192 4.1 16.3 1.0
CD2 S:HIS192 4.3 17.0 1.0
CD S:PRO229 4.3 16.0 1.0
CG S:PRO229 4.4 16.9 1.0
CB S:CYS195 4.6 14.2 1.0
SG S:CYS195 4.6 14.1 1.0
SG S:CYS220 4.7 15.7 1.0
O S:HIS192 4.8 13.6 1.0
CD2 S:PHE201 4.8 18.2 1.0
SG S:CYS226 4.8 13.7 1.0
N S:PRO229 4.9 15.1 1.0
C S:HIS192 5.0 14.1 1.0

Iron binding site 4 out of 24 in 6g7m

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Iron binding site 4 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:14.6
occ:1.00
 FE4 S:SF4401 0.0 14.6 1.0
SG S:CYS195 2.2 14.1 1.0
S3 S:SF4401 2.3 15.4 1.0
S2 S:SF4401 2.3 15.9 1.0
S1 S:SF4401 2.3 15.4 1.0
FE2 S:SF4401 2.7 15.0 1.0
FE3 S:SF4401 2.7 16.3 1.0
FE1 S:SF4401 2.7 15.0 1.0
CB S:CYS195 3.1 14.2 1.0
S4 S:SF4401 3.9 15.1 1.0
CB S:ARG197 4.0 15.8 1.0
ND1 S:HIS192 4.5 16.9 1.0
CA S:CYS195 4.6 14.1 1.0
CA S:ARG197 4.6 15.6 1.0
C S:ARG197 4.6 15.5 1.0
N S:ARG197 4.6 14.8 1.0
N S:ARG198 4.7 14.6 1.0
SG S:CYS226 4.8 13.7 1.0
CG1 S:VAL249 4.9 13.7 1.0
CG S:ARG197 4.9 15.6 1.0
C S:CYS195 4.9 14.2 1.0
SG S:CYS220 5.0 15.7 1.0

Iron binding site 5 out of 24 in 6g7m

Go back to Iron Binding Sites List in 6g7m
Iron binding site 5 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:12.3
occ:1.00
 FE1 S:F3S402 0.0 12.3 1.0
S1 S:F3S402 2.2 12.8 1.0
S2 S:F3S402 2.3 12.4 1.0
S3 S:F3S402 2.3 13.5 1.0
SG S:CYS258 2.3 12.4 1.0
FE3 S:F3S402 2.7 12.6 1.0
FE4 S:F3S402 2.7 12.5 1.0
CB S:CYS258 3.5 12.5 1.0
O L:HOH818 3.7 13.3 1.0
N S:CYS258 3.7 12.6 1.0
S4 S:F3S402 3.8 12.4 1.0
CA S:CYS258 4.0 12.2 1.0
N S:ASN259 4.2 11.7 1.0
OD1 S:ASN259 4.2 12.4 1.0
O S:HOH571 4.3 13.4 1.0
C S:CYS258 4.4 12.4 1.0
SG S:CYS235 4.7 13.9 1.0
C S:GLY257 4.8 12.3 1.0
CG S:ASN259 4.9 12.4 1.0
O S:HOH505 4.9 16.1 1.0
SG S:CYS255 4.9 13.7 1.0
OE1 L:GLN216 5.0 13.8 1.0
CE L:LYS211 5.0 13.9 1.0
N S:GLY257 5.0 11.8 1.0

Iron binding site 6 out of 24 in 6g7m

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Iron binding site 6 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:12.6
occ:1.00
 FE3 S:F3S402 0.0 12.6 1.0
S4 S:F3S402 2.2 12.4 1.0
S1 S:F3S402 2.2 12.8 1.0
SG S:CYS235 2.3 13.9 1.0
S3 S:F3S402 2.3 13.5 1.0
FE4 S:F3S402 2.7 12.5 1.0
FE1 S:F3S402 2.7 12.3 1.0
CB S:CYS235 3.3 13.3 1.0
S2 S:F3S402 4.0 12.4 1.0
O S:HOH571 4.1 13.4 1.0
CD1 S:ILE191 4.2 13.8 1.0
CE1 S:PHE240 4.5 11.1 1.0
CZ S:PHE240 4.5 11.6 1.0
CA S:CYS235 4.7 13.0 1.0
SG S:CYS255 4.7 13.7 1.0
OD1 S:ASN259 4.7 12.4 1.0
SG S:CYS258 4.8 12.4 1.0
O S:HOH589 5.0 13.7 1.0
ND2 S:ASN259 5.0 11.7 1.0

Iron binding site 7 out of 24 in 6g7m

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Iron binding site 7 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:12.5
occ:1.00
 FE4 S:F3S402 0.0 12.5 1.0
S4 S:F3S402 2.2 12.4 1.0
S3 S:F3S402 2.3 13.5 1.0
S2 S:F3S402 2.3 12.4 1.0
SG S:CYS255 2.4 13.7 1.0
FE3 S:F3S402 2.7 12.6 1.0
FE1 S:F3S402 2.7 12.3 1.0
CB S:CYS255 3.3 13.7 1.0
CA S:CYS255 3.7 13.0 1.0
S1 S:F3S402 3.9 12.8 1.0
N S:TYR256 3.9 11.1 1.0
N S:GLY257 4.0 11.8 1.0
C S:CYS255 4.2 13.1 1.0
CD1 S:ILE191 4.3 13.8 1.0
N S:CYS258 4.4 12.6 1.0
CA S:GLY257 4.5 12.6 1.0
NE2 L:GLN216 4.7 12.6 1.0
SG S:CYS235 4.7 13.9 1.0
CG2 S:THR231 4.8 15.0 1.0
SG S:CYS258 4.9 12.4 1.0
C S:TYR256 4.9 12.1 1.0
C S:GLY257 4.9 12.3 1.0
CA S:TYR256 4.9 12.1 1.0

Iron binding site 8 out of 24 in 6g7m

Go back to Iron Binding Sites List in 6g7m
Iron binding site 8 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:14.6
occ:1.00
 FE1 S:SF4403 0.0 14.6 1.0
SG S:CYS22 2.3 13.1 1.0
S4 S:SF4403 2.3 15.6 1.0
S2 S:SF4403 2.3 13.9 1.0
S3 S:SF4403 2.5 24.1 1.0
FE3 S:SF4403 2.7 12.9 1.0
FE4 S:SF4403 2.8 26.2 1.0
FE2 S:SF4403 3.0 16.7 1.0
CB S:CYS22 3.4 12.2 1.0
N S:CYS22 3.7 12.6 1.0
S1 S:SF4403 3.9 15.6 1.0
CA S:CYS22 4.0 12.2 1.0
N S:GLY24 4.0 13.3 1.0
O S:HOH501 4.3 30.0 1.0
NE2 L:HIS214 4.3 11.7 1.0
CA S:GLY24 4.4 12.3 1.0
N S:THR23 4.4 12.2 1.0
C S:CYS22 4.4 12.7 1.0
SG S:CYS154 4.7 13.0 1.0
SG S:CYS25 4.7 18.4 1.0
O S:HOH593 4.8 14.5 1.0
N S:CYS25 4.8 12.8 1.0
CD2 L:HIS214 4.9 12.7 1.0
C S:GLU21 4.9 15.7 1.0

Iron binding site 9 out of 24 in 6g7m

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Iron binding site 9 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:16.7
occ:1.00
 FE2 S:SF4403 0.0 16.7 1.0
S1 S:SF4403 2.3 15.6 1.0
S4 S:SF4403 2.3 15.6 1.0
SG S:CYS120 2.4 15.2 1.0
S3 S:SF4403 2.5 24.1 1.0
FE3 S:SF4403 2.6 12.9 1.0
FE4 S:SF4403 2.9 26.2 1.0
FE1 S:SF4403 3.0 14.6 1.0
CB S:CYS120 3.3 13.6 1.0
O S:HOH527 3.9 12.4 1.0
O S:HOH607 3.9 17.1 1.0
N S:CYS120 4.0 12.7 1.0
O S:HOH593 4.0 14.5 1.0
S2 S:SF4403 4.1 13.9 1.0
CA S:CYS120 4.2 13.6 1.0
SG S:CYS154 4.5 13.0 1.0
SG S:CYS25 4.8 18.4 1.0

Iron binding site 10 out of 24 in 6g7m

Go back to Iron Binding Sites List in 6g7m
Iron binding site 10 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:12.9
occ:1.00
 FE3 S:SF4403 0.0 12.9 1.0
S1 S:SF4403 2.2 15.6 1.0
SG S:CYS154 2.3 13.0 1.0
S4 S:SF4403 2.3 15.6 1.0
S2 S:SF4403 2.3 13.9 1.0
FE2 S:SF4403 2.6 16.7 1.0
FE1 S:SF4403 2.7 14.6 1.0
FE4 S:SF4403 2.8 26.2 1.0
CB S:CYS154 3.4 11.7 1.0
CA S:CYS154 3.5 11.8 1.0
O S:HOH607 3.8 17.1 1.0
C S:CYS154 3.9 12.5 1.0
S3 S:SF4403 3.9 24.1 1.0
O S:CYS154 4.4 11.6 1.0
CG L:ARG59 4.4 12.4 1.0
N S:PRO155 4.4 12.5 1.0
SG S:CYS120 4.5 15.2 1.0
CD2 L:HIS214 4.6 12.7 1.0
SG S:CYS22 4.6 13.1 1.0
O S:GLY153 4.6 11.1 1.0
NE2 L:HIS214 4.7 11.7 1.0
N S:CYS154 4.8 10.9 1.0
CA S:PRO155 4.8 12.1 1.0
SG S:CYS25 4.9 18.4 1.0
NE L:ARG59 4.9 12.1 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 2019.
ISSN: ISSN 1754-5706
DOI: 10.1039/C8EE02361A
Page generated: Tue Aug 6 19:12:01 2024

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