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Xenon 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
Iron (Fe) 19 atoms

Xenon Binding Sites:

The binding sites of Xenon 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 Xenon atom.
In total 7 binding sites of Xenon where determined in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri, PDB code: 6qii:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7;

Xenon binding site 1 out of 7 in 6qii

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Xenon binding site 1 out of 7 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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:Xe306

b:69.7
occ:0.00
CD2 G:LEU55 2.8 68.7 1.0
CD1 G:LEU55 3.3 56.4 1.0
CG G:LEU55 3.6 69.2 1.0
CD2 G:LEU38 3.6 52.3 1.0
XE G:XE307 4.0 89.8 0.2
CD1 G:LEU61 4.3 58.3 1.0
CB G:LEU55 4.4 70.5 1.0
CD1 G:LEU35 4.6 63.4 1.0
CG G:LEU38 4.7 59.0 1.0
CD1 G:LEU49 4.8 79.5 1.0
CD1 G:LEU45 4.9 61.6 1.0

Xenon binding site 2 out of 7 in 6qii

Go back to Xenon Binding Sites List in 6qii
Xenon binding site 2 out of 7 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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:Xe307

b:89.8
occ:0.21
CD2 G:LEU49 3.6 76.2 1.0
XE G:XE308 3.6 69.3 0.0
CD1 G:LEU45 3.8 61.6 1.0
XE G:XE306 4.0 69.7 0.0
CD1 G:ILE23 4.1 75.2 1.0
CG2 G:ILE23 4.2 75.8 1.0
CD2 G:LEU38 4.3 52.3 1.0
CG2 G:ILE48 4.4 64.2 1.0
CG G:LEU49 4.5 82.8 1.0
CB G:ILE23 4.6 71.8 1.0
CD1 G:LEU38 4.7 62.0 1.0
CD1 G:LEU55 4.7 56.4 1.0
CB G:ALA53 4.8 73.2 1.0
CG1 G:ILE23 5.0 74.2 1.0
CG G:LEU38 5.0 59.0 1.0
CD1 G:LEU49 5.0 79.5 1.0

Xenon binding site 3 out of 7 in 6qii

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Xenon binding site 3 out of 7 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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:Xe308

b:69.3
occ:0.01
CD1 G:LEU38 2.5 62.0 1.0
CD1 G:LEU45 3.4 61.6 1.0
XE G:XE307 3.6 89.8 0.2
CG G:LEU38 3.8 59.0 1.0
CD1 G:ILE48 3.9 60.7 1.0
CB G:ALA156 4.1 62.4 1.0
CD2 G:LEU38 4.2 52.3 1.0
CG2 G:ILE48 4.5 64.2 1.0
CA G:ARG153 4.6 64.6 1.0
CG2 G:ILE152 4.6 55.6 1.0
O G:ILE152 4.7 68.0 1.0
CG G:LEU45 4.8 56.5 1.0
N G:ARG153 4.8 57.9 1.0
ND2 G:ASN41 4.9 56.0 1.0
CB G:ILE48 4.9 70.6 1.0
C G:ILE152 4.9 68.1 1.0

Xenon binding site 4 out of 7 in 6qii

Go back to Xenon Binding Sites List in 6qii
Xenon binding site 4 out of 7 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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:Xe309

b:72.2
occ:0.08
CB G:ALA159 3.0 69.6 1.0
CA G:ALA159 3.9 70.0 1.0
O G:VAL155 3.9 65.1 1.0
CD1 G:LEU177 4.0 64.9 1.0
CG1 G:VAL155 4.1 64.1 1.0
CG2 G:ILE99 4.1 58.6 1.0
CD1 G:ILE99 4.2 58.3 1.0
CG2 G:VAL140 4.3 67.8 1.0
N G:ALA159 4.4 77.5 1.0
CD2 G:LEU177 4.5 65.3 1.0
CG2 G:VAL101 4.6 71.0 1.0
CG2 G:VAL72 4.7 66.3 1.0
CG1 G:VAL72 4.8 71.0 1.0
CB G:ILE99 4.8 63.1 1.0
XE G:XE310 4.9 0.8 0.4
CG G:LEU177 4.9 60.6 1.0
C G:VAL155 4.9 76.7 1.0

Xenon binding site 5 out of 7 in 6qii

Go back to Xenon Binding Sites List in 6qii
Xenon binding site 5 out of 7 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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:Xe310

b:0.8
occ:0.42
SD G:MET181 3.8 87.0 1.0
CG2 G:VAL140 3.9 67.8 1.0
CG2 G:ILE99 4.0 58.6 1.0
CD2 G:LEU162 4.2 66.9 1.0
CD1 G:ILE99 4.3 58.3 1.0
CG G:MET181 4.3 75.8 1.0
O G:HOH420 4.4 72.0 1.0
CB G:ASP139 4.5 67.3 1.0
CD1 G:LEU177 4.5 64.9 1.0
CE G:MET181 4.5 71.3 1.0
CG1 G:ILE99 4.6 66.0 1.0
XE G:XE309 4.9 72.2 0.1
CB G:ILE99 5.0 63.1 1.0

Xenon binding site 6 out of 7 in 6qii

Go back to Xenon Binding Sites List in 6qii
Xenon binding site 6 out of 7 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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:Xe314

b:72.2
occ:0.20
CD1 A:LEU108 3.6 44.8 1.0
CG G:LEU35 3.9 62.2 1.0
CD2 G:LEU35 4.0 60.3 1.0
CD2 A:LEU108 4.0 53.4 1.0
CB G:ALA39 4.1 53.3 1.0
XE A:XE501 4.2 0.0 0.3
CG A:LEU108 4.4 57.0 1.0
CD2 G:LEU61 4.5 58.0 1.0
CA G:VAL36 4.5 55.9 1.0
O G:LEU35 4.5 57.2 1.0
C G:LEU35 4.7 48.0 1.0
N G:VAL36 4.7 59.0 1.0
CG2 G:VAL36 4.8 48.4 1.0
CB G:LEU35 4.8 54.2 1.0
CD1 G:LEU35 4.8 63.4 1.0
CG2 G:THR60 4.9 46.7 1.0
CG G:LEU61 4.9 68.9 1.0
CD1 G:LEU61 5.0 58.3 1.0

Xenon binding site 7 out of 7 in 6qii

Go back to Xenon Binding Sites List in 6qii
Xenon binding site 7 out of 7 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe 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
A:Xe501

b:0.0
occ:0.34
CD1 A:ILE111 3.7 44.7 1.0
CD2 G:LEU61 3.9 58.0 1.0
CB G:ALA39 4.0 53.3 1.0
XE G:XE314 4.2 72.2 0.2
CD1 G:LEU61 4.2 58.3 1.0
CG2 A:ILE111 4.3 44.8 1.0
CD1 A:LEU108 4.6 44.8 1.0
CG G:LEU61 4.7 68.9 1.0
CG1 A:ILE111 4.9 45.4 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 Dec 16 02:40:29 2020

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