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Iron in PDB 6qgt: The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri

Enzymatic activity of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri

All present enzymatic activity of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri:
1.12.98.1;

Protein crystallography data

The structure of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri, PDB code: 6qgt was solved by Y.Ilina, C.Lorent, S.Katz, J.H.Jeoung, S.Shima, M.Horch, I.Zebger, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.06 / 1.99
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 235.429, 235.429, 235.429, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.9

Other elements in 6qgt:

The structure of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iron atom in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri (pdb code 6qgt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 19 binding sites of Iron where determined in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri, PDB code: 6qgt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 19 in 6qgt

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Iron binding site 1 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:35.6
occ:1.00
 FE1 G:SF4301 0.0 35.6 1.0
SG G:CYS31 2.2 37.5 1.0
S2 G:SF4301 2.3 35.2 1.0
S4 G:SF4301 2.3 35.8 1.0
S3 G:SF4301 2.4 36.3 1.0
FE4 G:SF4301 2.7 36.3 1.0
FE3 G:SF4301 2.7 35.2 1.0
FE2 G:SF4301 2.8 36.1 1.0
CB G:CYS31 3.2 33.5 1.0
N G:CYS31 3.7 33.1 1.0
S1 G:SF4301 3.8 38.0 1.0
NE2 A:HIS162 3.9 33.6 1.0
CA G:CYS31 4.0 34.7 1.0
N G:GLY33 4.1 34.2 1.0
CA G:GLY33 4.4 32.4 1.0
N G:CYS34 4.4 31.9 1.0
C G:CYS31 4.5 36.8 1.0
N G:THR32 4.6 37.8 1.0
CE1 A:HIS162 4.6 32.9 1.0
SG G:CYS106 4.7 36.4 1.0
SG G:CYS34 4.8 36.4 1.0
C G:GLY33 4.8 37.6 1.0
SG G:CYS145 4.8 35.6 1.0
C G:GLY30 4.9 38.4 1.0
CD2 A:HIS162 5.0 31.0 1.0

Iron binding site 2 out of 19 in 6qgt

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Iron binding site 2 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:36.1
occ:1.00
 FE2 G:SF4301 0.0 36.1 1.0
SG G:CYS106 2.2 36.4 1.0
S1 G:SF4301 2.3 38.0 1.0
S3 G:SF4301 2.4 36.3 1.0
S4 G:SF4301 2.5 35.8 1.0
FE1 G:SF4301 2.8 35.6 1.0
FE3 G:SF4301 2.8 35.2 1.0
FE4 G:SF4301 2.9 36.3 1.0
CB G:CYS106 3.1 37.7 1.0
O G:HOH432 3.7 33.0 1.0
N G:CYS106 3.8 31.9 1.0
ND2 G:ASN111 3.9 34.4 1.0
S2 G:SF4301 4.0 35.2 1.0
CA G:CYS106 4.1 32.1 1.0
O A:HOH775 4.5 36.4 1.0
N G:CYS31 4.7 33.1 1.0
SG G:CYS145 4.7 35.6 1.0
SG G:CYS31 4.8 37.5 1.0
SG G:CYS34 4.8 36.4 1.0
CG G:ASN111 4.8 35.4 1.0
CA G:GLY30 4.9 34.6 1.0

Iron binding site 3 out of 19 in 6qgt

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Iron binding site 3 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:35.2
occ:1.00
 FE3 G:SF4301 0.0 35.2 1.0
S2 G:SF4301 2.3 35.2 1.0
SG G:CYS145 2.3 35.6 1.0
S4 G:SF4301 2.4 35.8 1.0
S1 G:SF4301 2.4 38.0 1.0
FE1 G:SF4301 2.7 35.6 1.0
FE2 G:SF4301 2.8 36.1 1.0
FE4 G:SF4301 2.9 36.3 1.0
CB G:CYS145 3.2 31.9 1.0
CA G:CYS145 3.7 32.9 1.0
NE2 A:HIS162 3.8 33.6 1.0
ND2 G:ASN111 3.9 34.4 1.0
S3 G:SF4301 4.1 36.3 1.0
CD2 A:HIS162 4.2 31.0 1.0
C G:CYS145 4.4 37.1 1.0
CG A:ARG61 4.4 33.3 1.0
SG G:CYS106 4.5 36.4 1.0
CA G:PRO146 4.6 36.2 1.0
SG G:CYS31 4.6 37.5 1.0
O G:GLY144 4.6 38.2 1.0
N G:PRO146 4.7 36.0 1.0
CG G:ASN111 4.8 35.4 1.0
NE A:ARG61 4.9 36.8 1.0
N G:CYS145 4.9 36.8 1.0
CE1 A:HIS162 4.9 32.9 1.0
SG G:CYS34 5.0 36.4 1.0

Iron binding site 4 out of 19 in 6qgt

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Iron binding site 4 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:36.3
occ:1.00
 FE4 G:SF4301 0.0 36.3 1.0
S1 G:SF4301 2.3 38.0 1.0
SG G:CYS34 2.3 36.4 1.0
S2 G:SF4301 2.4 35.2 1.0
S3 G:SF4301 2.4 36.3 1.0
FE1 G:SF4301 2.7 35.6 1.0
FE2 G:SF4301 2.9 36.1 1.0
FE3 G:SF4301 2.9 35.2 1.0
CB G:CYS34 3.5 39.0 1.0
O G:HOH432 3.6 33.0 1.0
N G:CYS34 3.7 31.9 1.0
CA G:CYS34 4.0 38.4 1.0
CD G:PRO147 4.1 38.9 1.0
S4 G:SF4301 4.1 35.8 1.0
C G:GLY33 4.5 37.6 1.0
CA G:GLY104 4.5 37.4 1.0
SG G:CYS31 4.6 37.5 1.0
O G:GLY144 4.8 38.2 1.0
CG G:PRO147 4.8 41.4 1.0
N G:SER105 4.8 41.3 1.0
CA G:GLY33 4.9 32.4 1.0
SG G:CYS106 4.9 36.4 1.0
O G:LEU103 5.0 33.0 1.0

Iron binding site 5 out of 19 in 6qgt

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Iron binding site 5 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:35.0
occ:1.00
 FE1 G:SF4302 0.0 35.0 1.0
SG G:CYS234 2.2 34.8 1.0
S2 G:SF4302 2.3 34.6 1.0
S4 G:SF4302 2.3 32.5 1.0
S3 G:SF4302 2.4 38.2 1.0
FE3 G:SF4302 2.7 35.8 1.0
FE4 G:SF4302 2.8 35.7 1.0
FE2 G:SF4302 2.8 36.4 1.0
CB G:CYS234 3.1 32.6 1.0
CA G:CYS234 3.6 32.0 1.0
N G:PHE192 3.8 39.7 1.0
S1 G:SF4302 3.9 35.3 1.0
N G:LYS236 4.0 35.4 1.0
N G:ILE235 4.0 32.6 1.0
C G:CYS234 4.1 33.6 1.0
CA G:PHE192 4.3 37.9 1.0
C G:CYS191 4.4 38.5 1.0
CB G:PHE192 4.5 34.0 1.0
CA G:LYS236 4.5 36.5 1.0
N G:CYS237 4.6 33.2 1.0
CA G:CYS191 4.7 40.3 1.0
SG G:CYS215 4.8 33.4 1.0
N G:CYS234 4.9 35.2 1.0
C G:ILE235 4.9 38.2 1.0
SG G:CYS240 4.9 34.7 1.0
SG G:CYS237 5.0 36.4 1.0

Iron binding site 6 out of 19 in 6qgt

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Iron binding site 6 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:36.4
occ:1.00
 FE2 G:SF4302 0.0 36.4 1.0
SG G:CYS240 2.3 34.7 1.0
S1 G:SF4302 2.3 35.3 1.0
S3 G:SF4302 2.4 38.2 1.0
S4 G:SF4302 2.4 32.5 1.0
FE4 G:SF4302 2.8 35.7 1.0
FE1 G:SF4302 2.8 35.0 1.0
FE3 G:SF4302 2.9 35.8 1.0
CB G:CYS240 3.3 35.1 1.0
N G:CYS240 3.7 34.8 1.0
S2 G:SF4302 4.0 34.6 1.0
CA G:PHE192 4.0 37.9 1.0
N G:PHE192 4.1 39.7 1.0
CA G:CYS240 4.1 36.2 1.0
O G:HOH474 4.1 37.0 1.0
CD1 G:ILE220 4.2 33.5 1.0
C G:CYS191 4.3 38.5 1.0
O G:CYS191 4.4 38.0 1.0
N G:SER239 4.7 34.6 1.0
CB G:PHE192 4.7 34.0 1.0
SG G:CYS234 4.8 34.8 1.0
SG G:CYS237 4.8 36.4 1.0
SG G:CYS215 4.9 33.4 1.0
N G:GLY238 4.9 37.2 1.0
C G:SER239 4.9 38.0 1.0

Iron binding site 7 out of 19 in 6qgt

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Iron binding site 7 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:35.8
occ:1.00
 FE3 G:SF4302 0.0 35.8 1.0
S2 G:SF4302 2.2 34.6 1.0
SG G:CYS215 2.3 33.4 1.0
S4 G:SF4302 2.3 32.5 1.0
S1 G:SF4302 2.4 35.3 1.0
FE1 G:SF4302 2.7 35.0 1.0
FE4 G:SF4302 2.8 35.7 1.0
FE2 G:SF4302 2.9 36.4 1.0
CB G:CYS215 3.3 34.0 1.0
CA G:CYS215 3.9 34.0 1.0
CD G:PRO216 4.0 32.0 1.0
S3 G:SF4302 4.0 38.2 1.0
CB G:ALA219 4.3 33.3 1.0
CG2 G:VAL217 4.3 28.2 1.0
CD1 G:ILE220 4.5 33.5 1.0
C G:CYS215 4.6 34.4 1.0
N G:PRO216 4.6 32.4 1.0
CG1 G:ILE220 4.8 35.0 1.0
SG G:CYS237 4.8 36.4 1.0
SG G:CYS234 4.8 34.8 1.0
CA G:CYS234 4.9 32.0 1.0
SG G:CYS240 4.9 34.7 1.0
CB G:CYS234 4.9 32.6 1.0
CG G:PRO216 4.9 33.8 1.0
N G:ALA219 4.9 32.6 1.0

Iron binding site 8 out of 19 in 6qgt

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Iron binding site 8 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:35.7
occ:1.00
 FE4 G:SF4302 0.0 35.7 1.0
S1 G:SF4302 2.3 35.3 1.0
SG G:CYS237 2.3 36.4 1.0
S3 G:SF4302 2.3 38.2 1.0
S2 G:SF4302 2.4 34.6 1.0
FE2 G:SF4302 2.8 36.4 1.0
FE1 G:SF4302 2.8 35.0 1.0
FE3 G:SF4302 2.8 35.8 1.0
CB G:CYS237 3.5 31.1 1.0
N G:CYS237 3.6 33.2 1.0
N G:GLY238 3.8 37.2 1.0
CA G:CYS237 4.0 38.6 1.0
N G:SER239 4.0 34.6 1.0
S4 G:SF4302 4.0 32.5 1.0
CD G:PRO216 4.1 32.0 1.0
C G:CYS237 4.2 40.7 1.0
CB G:SER239 4.4 36.0 1.0
OG G:SER239 4.6 37.7 1.0
CG G:PRO216 4.6 33.8 1.0
N G:CYS240 4.6 34.8 1.0
CA G:SER239 4.7 32.9 1.0
CD1 G:ILE235 4.7 37.0 1.0
N G:LYS236 4.7 35.4 1.0
SG G:CYS234 4.8 34.8 1.0
SG G:CYS215 4.8 33.4 1.0
C G:LYS236 4.8 37.7 1.0
CA G:GLY238 4.8 33.4 1.0
C G:GLY238 4.8 37.0 1.0
SG G:CYS240 4.8 34.7 1.0
CA G:LYS236 5.0 36.5 1.0

Iron binding site 9 out of 19 in 6qgt

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Iron binding site 9 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:36.7
occ:1.00
 FE1 G:SF4303 0.0 36.7 1.0
S4 G:SF4303 2.3 36.8 1.0
SG G:CYS211 2.3 36.8 1.0
S2 G:SF4303 2.3 37.4 1.0
S3 G:SF4303 2.4 39.0 1.0
FE4 G:SF4303 2.8 39.1 1.0
FE2 G:SF4303 2.8 38.1 1.0
FE3 G:SF4303 2.9 37.2 1.0
CB G:CYS211 3.3 33.6 1.0
CG G:PRO227 3.8 36.2 1.0
N G:CYS211 3.9 31.8 1.0
S1 G:SF4303 4.0 38.2 1.0
CA G:CYS211 4.2 32.1 1.0
N G:THR210 4.5 36.9 1.0
N G:GLY209 4.6 31.4 1.0
CD1 G:LEU195 4.6 31.4 1.0
SG G:CYS208 4.7 37.7 1.0
CA G:GLY209 4.8 38.5 1.0
C G:GLY209 4.8 41.5 1.0
SG G:CYS205 4.8 35.2 1.0
SG G:CYS244 4.9 37.7 1.0
CD2 G:LEU195 4.9 39.9 1.0
CB G:PRO227 4.9 34.5 1.0
CD G:PRO227 5.0 35.1 1.0

Iron binding site 10 out of 19 in 6qgt

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Iron binding site 10 out of 19 in the The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Carbon Monoxide Inhibition of F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:38.1
occ:1.00
 FE2 G:SF4303 0.0 38.1 1.0
SG G:CYS205 2.3 35.2 1.0
S3 G:SF4303 2.3 39.0 1.0
S4 G:SF4303 2.4 36.8 1.0
S1 G:SF4303 2.5 38.2 1.0
FE4 G:SF4303 2.8 39.1 1.0
FE1 G:SF4303 2.8 36.7 1.0
FE3 G:SF4303 2.9 37.2 1.0
CB G:CYS205 3.2 34.6 1.0
CA G:CYS205 3.7 36.0 1.0
N G:GLY207 3.9 35.1 1.0
N G:MET206 4.0 31.3 1.0
CG G:PRO227 4.0 36.2 1.0
S2 G:SF4303 4.0 37.4 1.0
C G:CYS205 4.2 35.5 1.0
CG1 G:VAL199 4.3 34.5 1.0
CD G:PRO227 4.4 35.1 1.0
CA G:GLY207 4.5 35.1 1.0
N G:CYS208 4.9 35.8 1.0
C G:MET206 4.9 30.9 1.0
SG G:CYS244 4.9 37.7 1.0
N G:CYS205 5.0 37.6 1.0
SG G:CYS211 5.0 36.8 1.0

Reference:

Y.Ilina, C.Lorent, S.Katz, J.H.Jeoung, S.Shima, M.Horch, I.Zebger, H.Dobbek. X-Ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling By [Nife] Hydrogenases. Angew.Chem.Int.Ed.Engl. 2019.
ISSN: ESSN 1521-3773
PubMed: 31591784
DOI: 10.1002/ANIE.201908258
Page generated: Wed Aug 7 07:53:11 2024

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