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Iron in PDB 6qii: Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri

Enzymatic activity of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri

All present enzymatic activity of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri:
1.12.98.1;

Protein crystallography data

The structure of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri, PDB code: 6qii 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) 45.55 / 2.28
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 236.705, 236.705, 236.705, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.7

Other elements in 6qii:

The structure of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom
Xenon (Xe) 7 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

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

Iron binding site 1 out of 19 in 6qii

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Iron binding site 1 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:58.6
occ:0.98
FE1 G:SF4301 0.0 58.6 1.0
SG G:CYS31 2.2 59.0 1.0
S2 G:SF4301 2.3 52.8 1.0
S4 G:SF4301 2.3 53.5 1.0
S3 G:SF4301 2.5 52.5 1.0
FE3 G:SF4301 2.7 58.8 1.0
FE4 G:SF4301 2.8 61.8 1.0
FE2 G:SF4301 2.9 56.4 1.0
CB G:CYS31 3.3 51.4 1.0
N G:CYS31 3.8 58.9 1.0
NE2 A:HIS162 3.9 48.4 1.0
S1 G:SF4301 3.9 56.2 1.0
CA G:CYS31 4.0 56.9 1.0
N G:GLY33 4.1 50.2 1.0
CA G:GLY33 4.3 48.7 1.0
N G:CYS34 4.5 48.7 1.0
C G:CYS31 4.5 56.0 1.0
N G:THR32 4.6 53.7 1.0
CE1 A:HIS162 4.7 52.5 1.0
OE2 G:GLU76 4.7 73.4 1.0
C G:GLY33 4.7 56.9 1.0
SG G:CYS106 4.8 53.6 1.0
C G:GLY30 4.9 54.6 1.0
SG G:CYS145 4.9 57.8 1.0
CD2 A:HIS162 4.9 45.7 1.0
O A:ARG61 4.9 53.3 1.0
SG G:CYS34 5.0 57.3 1.0

Iron binding site 2 out of 19 in 6qii

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Iron binding site 2 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:56.4
occ:0.98
FE2 G:SF4301 0.0 56.4 1.0
SG G:CYS106 2.1 53.6 1.0
S1 G:SF4301 2.3 56.2 1.0
S3 G:SF4301 2.4 52.5 1.0
S4 G:SF4301 2.5 53.5 1.0
FE4 G:SF4301 2.9 61.8 1.0
FE3 G:SF4301 2.9 58.8 1.0
FE1 G:SF4301 2.9 58.6 1.0
CB G:CYS106 3.1 61.4 1.0
N G:CYS106 3.8 54.0 1.0
CA G:CYS106 4.0 55.2 1.0
ND2 G:ASN111 4.1 53.9 1.0
S2 G:SF4301 4.1 52.8 1.0
O A:HOH689 4.3 53.2 1.0
SG G:CYS145 4.7 57.8 1.0
N G:CYS31 4.8 58.9 1.0
CA G:GLY30 4.8 56.9 1.0
SG G:CYS34 4.9 57.3 1.0
CG G:ASN111 4.9 58.3 1.0
SG G:CYS31 5.0 59.0 1.0
C G:SER105 5.0 51.2 1.0

Iron binding site 3 out of 19 in 6qii

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Iron binding site 3 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:58.8
occ:0.98
FE3 G:SF4301 0.0 58.8 1.0
SG G:CYS145 2.3 57.8 1.0
S4 G:SF4301 2.4 53.5 1.0
S2 G:SF4301 2.4 52.8 1.0
S1 G:SF4301 2.4 56.2 1.0
FE1 G:SF4301 2.7 58.6 1.0
FE2 G:SF4301 2.9 56.4 1.0
FE4 G:SF4301 3.0 61.8 1.0
CB G:CYS145 3.4 51.0 1.0
CA G:CYS145 3.8 56.5 1.0
NE2 A:HIS162 3.8 48.4 1.0
ND2 G:ASN111 3.9 53.9 1.0
S3 G:SF4301 4.1 52.5 1.0
CD2 A:HIS162 4.2 45.7 1.0
CG A:ARG61 4.3 51.4 1.0
C G:CYS145 4.4 60.9 1.0
SG G:CYS106 4.5 53.6 1.0
SG G:CYS31 4.7 59.0 1.0
CA G:PRO146 4.7 58.5 1.0
O G:GLY144 4.7 57.4 1.0
N G:PRO146 4.8 55.5 1.0
NE A:ARG61 4.9 52.4 1.0
CG G:ASN111 4.9 58.3 1.0
CE1 A:HIS162 5.0 52.5 1.0

Iron binding site 4 out of 19 in 6qii

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Iron binding site 4 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:61.8
occ:0.98
FE4 G:SF4301 0.0 61.8 1.0
S1 G:SF4301 2.3 56.2 1.0
SG G:CYS34 2.4 57.3 1.0
S3 G:SF4301 2.4 52.5 1.0
S2 G:SF4301 2.4 52.8 1.0
FE1 G:SF4301 2.8 58.6 1.0
FE2 G:SF4301 2.9 56.4 1.0
FE3 G:SF4301 3.0 58.8 1.0
CB G:CYS34 3.5 63.0 1.0
N G:CYS34 3.7 48.7 1.0
CA G:CYS34 4.0 57.2 1.0
S4 G:SF4301 4.1 53.5 1.0
CD G:PRO147 4.2 58.0 1.0
OE2 G:GLU76 4.3 73.4 1.0
C G:GLY33 4.5 56.9 1.0
CA G:GLY104 4.6 61.0 1.0
SG G:CYS31 4.7 59.0 1.0
O G:GLY144 4.9 57.4 1.0
SG G:CYS106 4.9 53.6 1.0
CG G:PRO147 4.9 63.9 1.0
O G:LEU103 4.9 62.5 1.0
N G:SER105 4.9 60.6 1.0
CA G:GLY33 5.0 48.7 1.0

Iron binding site 5 out of 19 in 6qii

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Iron binding site 5 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:56.4
occ:0.98
FE1 G:SF4302 0.0 56.4 1.0
SG G:CYS234 2.3 50.1 1.0
S4 G:SF4302 2.3 44.5 1.0
S2 G:SF4302 2.3 49.5 1.0
S3 G:SF4302 2.5 48.8 1.0
FE3 G:SF4302 2.8 53.8 1.0
FE4 G:SF4302 2.9 55.7 1.0
FE2 G:SF4302 3.0 55.2 1.0
CB G:CYS234 3.0 51.5 1.0
CA G:CYS234 3.5 42.8 1.0
N G:PHE192 3.8 57.0 1.0
N G:LYS236 3.9 53.7 1.0
N G:ILE235 4.0 47.2 1.0
C G:CYS234 4.1 45.5 1.0
S1 G:SF4302 4.1 45.5 1.0
CB G:PHE192 4.3 48.0 1.0
CA G:PHE192 4.3 52.2 1.0
CA G:LYS236 4.5 52.3 1.0
C G:CYS191 4.6 51.4 1.0
N G:CYS237 4.6 52.9 1.0
N G:CYS234 4.8 58.3 1.0
CA G:CYS191 4.8 55.7 1.0
C G:ILE235 4.9 57.3 1.0
SG G:CYS215 5.0 46.0 1.0
SG G:CYS237 5.0 52.3 1.0

Iron binding site 6 out of 19 in 6qii

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Iron binding site 6 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:55.2
occ:0.98
FE2 G:SF4302 0.0 55.2 1.0
SG G:CYS240 2.3 49.3 1.0
S3 G:SF4302 2.3 48.8 1.0
S1 G:SF4302 2.4 45.5 1.0
S4 G:SF4302 2.5 44.5 1.0
FE4 G:SF4302 2.7 55.7 1.0
FE1 G:SF4302 3.0 56.4 1.0
FE3 G:SF4302 3.1 53.8 1.0
CB G:CYS240 3.3 51.4 1.0
N G:CYS240 3.8 52.6 1.0
S2 G:SF4302 4.0 49.5 1.0
CA G:PHE192 4.0 52.2 1.0
N G:PHE192 4.1 57.0 1.0
CA G:CYS240 4.2 56.5 1.0
CD1 G:ILE220 4.3 46.0 1.0
C G:CYS191 4.4 51.4 1.0
CB G:PHE192 4.5 48.0 1.0
O G:CYS191 4.5 52.5 1.0
N G:SER239 4.6 56.7 1.0
SG G:CYS237 4.8 52.3 1.0
C G:SER239 4.9 53.5 1.0
SG G:CYS234 4.9 50.1 1.0
N G:GLY238 4.9 51.0 1.0
SG G:CYS215 5.0 46.0 1.0

Iron binding site 7 out of 19 in 6qii

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Iron binding site 7 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:53.8
occ:0.98
FE3 G:SF4302 0.0 53.8 1.0
S2 G:SF4302 2.3 49.5 1.0
SG G:CYS215 2.3 46.0 1.0
S4 G:SF4302 2.3 44.5 1.0
S1 G:SF4302 2.5 45.5 1.0
FE1 G:SF4302 2.8 56.4 1.0
FE4 G:SF4302 2.8 55.7 1.0
FE2 G:SF4302 3.1 55.2 1.0
CB G:CYS215 3.3 46.2 1.0
CA G:CYS215 3.9 55.6 1.0
CD G:PRO216 3.9 46.7 1.0
CB G:ALA219 4.1 46.9 1.0
S3 G:SF4302 4.2 48.8 1.0
CG2 G:VAL217 4.3 45.7 1.0
CD1 G:ILE220 4.5 46.0 1.0
N G:PRO216 4.5 51.9 1.0
C G:CYS215 4.6 50.4 1.0
CG1 G:ILE220 4.6 49.8 1.0
SG G:CYS237 4.8 52.3 1.0
CA G:CYS234 4.8 42.8 1.0
CB G:CYS234 4.8 51.5 1.0
SG G:CYS234 4.9 50.1 1.0
CG G:PRO216 5.0 48.4 1.0
N G:ALA219 5.0 51.2 1.0
N G:VAL217 5.0 46.1 1.0

Iron binding site 8 out of 19 in 6qii

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Iron binding site 8 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:55.7
occ:0.98
FE4 G:SF4302 0.0 55.7 1.0
S1 G:SF4302 2.3 45.5 1.0
SG G:CYS237 2.3 52.3 1.0
S2 G:SF4302 2.4 49.5 1.0
S3 G:SF4302 2.4 48.8 1.0
FE2 G:SF4302 2.7 55.2 1.0
FE3 G:SF4302 2.8 53.8 1.0
FE1 G:SF4302 2.9 56.4 1.0
CB G:CYS237 3.7 41.2 1.0
N G:CYS237 3.7 52.9 1.0
S4 G:SF4302 3.9 44.5 1.0
N G:GLY238 4.0 51.0 1.0
N G:SER239 4.0 56.7 1.0
CA G:CYS237 4.1 55.8 1.0
CD G:PRO216 4.2 46.7 1.0
C G:CYS237 4.3 51.2 1.0
CB G:SER239 4.3 51.5 1.0
N G:CYS240 4.6 52.6 1.0
OG G:SER239 4.7 52.1 1.0
CA G:SER239 4.7 47.8 1.0
N G:LYS236 4.7 53.7 1.0
SG G:CYS240 4.8 49.3 1.0
SG G:CYS215 4.8 46.0 1.0
CG G:PRO216 4.8 48.4 1.0
C G:GLY238 4.8 61.4 1.0
CA G:GLY238 4.9 52.2 1.0
SG G:CYS234 4.9 50.1 1.0
C G:LYS236 4.9 52.4 1.0

Iron binding site 9 out of 19 in 6qii

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Iron binding site 9 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:59.0
occ:1.00
FE1 G:SF4303 0.0 59.0 1.0
SG G:CYS211 2.3 54.0 1.0
S2 G:SF4303 2.3 54.5 1.0
S4 G:SF4303 2.3 54.8 1.0
S3 G:SF4303 2.5 56.6 1.0
FE2 G:SF4303 2.8 60.6 1.0
FE4 G:SF4303 2.8 65.4 1.0
FE3 G:SF4303 3.0 58.4 1.0
CB G:CYS211 3.4 51.3 1.0
CG G:PRO227 3.9 45.9 1.0
N G:CYS211 3.9 47.6 1.0
S1 G:SF4303 4.0 56.6 1.0
CA G:CYS211 4.3 43.7 1.0
CD1 G:LEU195 4.6 43.6 1.0
N G:THR210 4.6 52.0 1.0
N G:GLY209 4.7 55.4 1.0
SG G:CYS208 4.8 50.0 1.0
SG G:CYS205 4.8 52.5 1.0
CD G:PRO227 4.9 48.9 1.0
CA G:GLY209 4.9 58.0 1.0
C G:GLY209 4.9 58.5 1.0
SG G:CYS244 4.9 57.7 1.0
CB G:PRO227 5.0 51.3 1.0

Iron binding site 10 out of 19 in 6qii

Go back to Iron Binding Sites List in 6qii
Iron binding site 10 out of 19 in the Xenon Derivatization of the 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:60.6
occ:1.00
FE2 G:SF4303 0.0 60.6 1.0
SG G:CYS205 2.3 52.5 1.0
S3 G:SF4303 2.4 56.6 1.0
S4 G:SF4303 2.4 54.8 1.0
S1 G:SF4303 2.5 56.6 1.0
FE1 G:SF4303 2.8 59.0 1.0
FE4 G:SF4303 2.8 65.4 1.0
FE3 G:SF4303 3.0 58.4 1.0
CB G:CYS205 3.3 60.3 1.0
CA G:CYS205 3.8 51.9 1.0
N G:GLY207 3.9 54.5 1.0
S2 G:SF4303 4.0 54.5 1.0
N G:MET206 4.0 49.6 1.0
CG G:PRO227 4.1 45.9 1.0
CD G:PRO227 4.3 48.9 1.0
C G:CYS205 4.3 51.7 1.0
CA G:GLY207 4.4 56.4 1.0
CG1 G:VAL199 4.4 51.2 1.0
N G:CYS208 4.8 59.9 1.0
C G:MET206 4.9 55.2 1.0
SG G:CYS211 5.0 54.0 1.0
SG G:CYS244 5.0 57.7 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 Oct 28 18:32:09 2020

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