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Iron in PDB 6qgr: The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State

Enzymatic activity of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State

All present enzymatic activity of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State:
1.12.98.1;

Protein crystallography data

The structure of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State, PDB code: 6qgr 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) 48.14 / 1.84
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 235.826, 235.826, 235.826, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.1

Other elements in 6qgr:

The structure of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State 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 F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State (pdb code 6qgr). 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 F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State, PDB code: 6qgr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 19 in 6qgr

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Iron binding site 1 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:32.7
occ:1.00
 FE1 G:SF4301 0.0 32.7 1.0
S2 G:SF4301 2.3 34.9 1.0
SG G:CYS31 2.3 34.5 1.0
S4 G:SF4301 2.3 34.4 1.0
S3 G:SF4301 2.4 35.0 1.0
FE3 G:SF4301 2.7 34.0 1.0
FE4 G:SF4301 2.7 35.6 1.0
FE2 G:SF4301 2.8 34.7 1.0
CB G:CYS31 3.2 26.9 1.0
N G:CYS31 3.8 33.5 1.0
S1 G:SF4301 3.9 36.2 1.0
NE2 A:HIS162 3.9 31.9 1.0
CA G:CYS31 4.0 32.7 1.0
N G:GLY33 4.2 32.8 1.0
CA G:GLY33 4.4 31.6 1.0
C G:CYS31 4.5 34.7 1.0
N G:CYS34 4.5 33.8 1.0
CE1 A:HIS162 4.6 33.8 1.0
N G:THR32 4.6 34.6 1.0
SG G:CYS106 4.7 34.9 1.0
C G:GLY33 4.8 34.4 1.0
SG G:CYS34 4.9 34.6 1.0
SG G:CYS145 4.9 34.3 1.0
C G:GLY30 4.9 35.8 1.0
O A:ARG61 4.9 31.9 1.0
CD2 A:HIS162 5.0 30.1 1.0

Iron binding site 2 out of 19 in 6qgr

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Iron binding site 2 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:34.7
occ:1.00
 FE2 G:SF4301 0.0 34.7 1.0
SG G:CYS106 2.2 34.9 1.0
S3 G:SF4301 2.4 35.0 1.0
S1 G:SF4301 2.4 36.2 1.0
S4 G:SF4301 2.5 34.4 1.0
FE3 G:SF4301 2.8 34.0 1.0
FE1 G:SF4301 2.8 32.7 1.0
FE4 G:SF4301 2.9 35.6 1.0
CB G:CYS106 3.2 35.8 1.0
O G:HOH448 3.7 33.0 1.0
N G:CYS106 3.8 30.9 1.0
ND2 G:ASN111 3.8 34.3 1.0
S2 G:SF4301 4.0 34.9 1.0
CA G:CYS106 4.1 33.5 1.0
O A:HOH797 4.5 33.8 1.0
SG G:CYS145 4.7 34.3 1.0
N G:CYS31 4.7 33.5 1.0
CG G:ASN111 4.8 37.6 1.0
SG G:CYS31 4.9 34.5 1.0
SG G:CYS34 4.9 34.6 1.0
CA G:GLY30 5.0 35.0 1.0
C G:SER105 5.0 33.5 1.0

Iron binding site 3 out of 19 in 6qgr

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Iron binding site 3 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:34.0
occ:1.00
 FE3 G:SF4301 0.0 34.0 1.0
S2 G:SF4301 2.3 34.9 1.0
SG G:CYS145 2.4 34.3 1.0
S4 G:SF4301 2.4 34.4 1.0
S1 G:SF4301 2.5 36.2 1.0
FE1 G:SF4301 2.7 32.7 1.0
FE2 G:SF4301 2.8 34.7 1.0
FE4 G:SF4301 2.9 35.6 1.0
CB G:CYS145 3.3 33.3 1.0
CA G:CYS145 3.7 31.1 1.0
ND2 G:ASN111 3.8 34.3 1.0
NE2 A:HIS162 3.8 31.9 1.0
S3 G:SF4301 4.0 35.0 1.0
CD2 A:HIS162 4.2 30.1 1.0
CG A:ARG61 4.3 35.3 1.0
C G:CYS145 4.4 36.4 1.0
SG G:CYS106 4.5 34.9 1.0
CA G:PRO146 4.6 34.8 1.0
O G:GLY144 4.7 34.1 1.0
SG G:CYS31 4.7 34.5 1.0
N G:PRO146 4.8 36.0 1.0
CG G:ASN111 4.8 37.6 1.0
NE A:ARG61 4.9 38.7 1.0
CE1 A:HIS162 4.9 33.8 1.0
N G:CYS145 4.9 33.3 1.0

Iron binding site 4 out of 19 in 6qgr

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Iron binding site 4 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:35.6
occ:1.00
 FE4 G:SF4301 0.0 35.6 1.0
S1 G:SF4301 2.2 36.2 1.0
SG G:CYS34 2.3 34.6 1.0
S3 G:SF4301 2.4 35.0 1.0
S2 G:SF4301 2.4 34.9 1.0
FE1 G:SF4301 2.7 32.7 1.0
FE3 G:SF4301 2.9 34.0 1.0
FE2 G:SF4301 2.9 34.7 1.0
CB G:CYS34 3.6 38.5 1.0
O G:HOH448 3.6 33.0 1.0
N G:CYS34 3.7 33.8 1.0
CA G:CYS34 4.0 38.4 1.0
S4 G:SF4301 4.1 34.4 1.0
CD G:PRO147 4.1 38.9 1.0
C G:GLY33 4.5 34.4 1.0
CA G:GLY104 4.5 33.0 1.0
SG G:CYS31 4.7 34.5 1.0
O G:GLY144 4.8 34.1 1.0
N G:SER105 4.9 36.4 1.0
CG G:PRO147 4.9 34.7 1.0
OE2 G:GLU76 4.9 42.5 1.0
CA G:GLY33 5.0 31.6 1.0
SG G:CYS106 5.0 34.9 1.0

Iron binding site 5 out of 19 in 6qgr

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Iron binding site 5 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:32.8
occ:1.00
 FE1 G:SF4302 0.0 32.8 1.0
S4 G:SF4302 2.3 33.3 1.0
SG G:CYS234 2.3 33.1 1.0
S2 G:SF4302 2.3 34.0 1.0
S3 G:SF4302 2.4 34.4 1.0
FE3 G:SF4302 2.7 33.4 1.0
FE4 G:SF4302 2.8 33.9 1.0
FE2 G:SF4302 2.8 34.5 1.0
CB G:CYS234 3.1 32.2 1.0
CA G:CYS234 3.6 33.4 1.0
N G:PHE192 3.7 33.8 1.0
S1 G:SF4302 3.9 33.2 1.0
N G:LYS236 4.0 36.8 1.0
N G:ILE235 4.1 28.6 1.0
C G:CYS234 4.2 31.8 1.0
CA G:PHE192 4.3 34.0 1.0
CB G:PHE192 4.5 28.9 1.0
C G:CYS191 4.5 38.6 1.0
CA G:LYS236 4.5 32.5 1.0
N G:CYS237 4.6 32.9 1.0
CA G:CYS191 4.8 33.9 1.0
SG G:CYS215 4.9 31.2 1.0
N G:CYS234 4.9 33.0 1.0
SG G:CYS240 4.9 32.4 1.0
C G:ILE235 5.0 35.9 1.0

Iron binding site 6 out of 19 in 6qgr

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Iron binding site 6 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:34.5
occ:1.00
 FE2 G:SF4302 0.0 34.5 1.0
S1 G:SF4302 2.3 33.2 1.0
SG G:CYS240 2.3 32.4 1.0
S3 G:SF4302 2.3 34.4 1.0
S4 G:SF4302 2.4 33.3 1.0
FE4 G:SF4302 2.8 33.9 1.0
FE1 G:SF4302 2.8 32.8 1.0
FE3 G:SF4302 2.9 33.4 1.0
CB G:CYS240 3.3 35.8 1.0
N G:CYS240 3.8 33.7 1.0
N G:PHE192 3.9 33.8 1.0
S2 G:SF4302 4.0 34.0 1.0
CA G:PHE192 4.1 34.0 1.0
CA G:CYS240 4.2 33.0 1.0
CD1 G:ILE220 4.2 28.4 1.0
O G:HOH477 4.2 35.8 1.0
C G:CYS191 4.3 38.6 1.0
O G:CYS191 4.6 34.9 1.0
N G:SER239 4.7 34.2 1.0
CB G:PHE192 4.8 28.9 1.0
SG G:CYS234 4.8 33.1 1.0
SG G:CYS237 4.8 33.2 1.0
SG G:CYS215 4.9 31.2 1.0
C G:SER239 5.0 35.7 1.0
N G:GLY238 5.0 34.5 1.0

Iron binding site 7 out of 19 in 6qgr

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Iron binding site 7 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:33.4
occ:1.00
 FE3 G:SF4302 0.0 33.4 1.0
SG G:CYS215 2.3 31.2 1.0
S4 G:SF4302 2.3 33.3 1.0
S2 G:SF4302 2.3 34.0 1.0
S1 G:SF4302 2.4 33.2 1.0
FE1 G:SF4302 2.7 32.8 1.0
FE4 G:SF4302 2.9 33.9 1.0
FE2 G:SF4302 2.9 34.5 1.0
CB G:CYS215 3.3 31.7 1.0
CA G:CYS215 3.8 33.2 1.0
CD G:PRO216 4.0 32.3 1.0
S3 G:SF4302 4.1 34.4 1.0
CB G:ALA219 4.3 34.0 1.0
CG2 G:VAL217 4.4 30.0 1.0
C G:CYS215 4.5 31.5 1.0
CD1 G:ILE220 4.5 28.4 1.0
N G:PRO216 4.6 33.6 1.0
CG1 G:ILE220 4.7 31.3 1.0
SG G:CYS237 4.8 33.2 1.0
SG G:CYS234 4.9 33.1 1.0
SG G:CYS240 4.9 32.4 1.0
CA G:CYS234 5.0 33.4 1.0
CB G:CYS234 5.0 32.2 1.0
CG G:PRO216 5.0 29.7 1.0
N G:ALA219 5.0 33.3 1.0

Iron binding site 8 out of 19 in 6qgr

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Iron binding site 8 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:33.9
occ:1.00
 FE4 G:SF4302 0.0 33.9 1.0
S1 G:SF4302 2.3 33.2 1.0
SG G:CYS237 2.3 33.2 1.0
S3 G:SF4302 2.3 34.4 1.0
S2 G:SF4302 2.4 34.0 1.0
FE1 G:SF4302 2.8 32.8 1.0
FE2 G:SF4302 2.8 34.5 1.0
FE3 G:SF4302 2.9 33.4 1.0
CB G:CYS237 3.5 29.1 1.0
N G:CYS237 3.6 32.9 1.0
N G:GLY238 3.9 34.5 1.0
CA G:CYS237 3.9 35.0 1.0
S4 G:SF4302 4.0 33.3 1.0
N G:SER239 4.0 34.2 1.0
CD G:PRO216 4.1 32.3 1.0
C G:CYS237 4.2 35.0 1.0
CB G:SER239 4.4 36.3 1.0
OG G:SER239 4.6 35.2 1.0
N G:LYS236 4.7 36.8 1.0
C G:LYS236 4.7 37.4 1.0
N G:CYS240 4.7 33.7 1.0
CG G:PRO216 4.7 29.7 1.0
CA G:SER239 4.8 29.5 1.0
SG G:CYS234 4.8 33.1 1.0
CA G:GLY238 4.8 31.3 1.0
SG G:CYS215 4.8 31.2 1.0
C G:GLY238 4.9 35.8 1.0
SG G:CYS240 4.9 32.4 1.0
CG1 G:ILE235 4.9 31.0 1.0
CA G:LYS236 4.9 32.5 1.0

Iron binding site 9 out of 19 in 6qgr

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Iron binding site 9 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:34.3
occ:1.00
 FE1 G:SF4303 0.0 34.3 1.0
SG G:CYS211 2.3 34.8 1.0
S4 G:SF4303 2.3 35.9 1.0
S2 G:SF4303 2.3 35.9 1.0
S3 G:SF4303 2.4 39.1 1.0
FE4 G:SF4303 2.8 35.4 1.0
FE3 G:SF4303 2.9 35.9 1.0
FE2 G:SF4303 2.9 35.5 1.0
CB G:CYS211 3.3 32.9 1.0
CG G:PRO227 3.8 33.7 1.0
N G:CYS211 3.9 31.2 1.0
S1 G:SF4303 4.1 36.2 1.0
CA G:CYS211 4.2 31.6 1.0
N G:THR210 4.5 35.4 1.0
N G:GLY209 4.5 30.1 1.0
CA G:GLY209 4.6 39.3 1.0
CD1 G:LEU195 4.7 29.0 1.0
SG G:CYS208 4.7 37.1 1.0
C G:GLY209 4.7 38.6 1.0
SG G:CYS205 4.9 34.7 1.0
SG G:CYS244 4.9 35.4 1.0
CB G:PRO227 4.9 33.9 1.0
CD G:PRO227 4.9 35.6 1.0
CD2 G:LEU195 5.0 36.5 1.0

Iron binding site 10 out of 19 in 6qgr

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Iron binding site 10 out of 19 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

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

b:35.5
occ:1.00
 FE2 G:SF4303 0.0 35.5 1.0
SG G:CYS205 2.3 34.7 1.0
S3 G:SF4303 2.3 39.1 1.0
S4 G:SF4303 2.4 35.9 1.0
S1 G:SF4303 2.4 36.2 1.0
FE4 G:SF4303 2.8 35.4 1.0
FE1 G:SF4303 2.9 34.3 1.0
FE3 G:SF4303 2.9 35.9 1.0
CB G:CYS205 3.3 38.6 1.0
CA G:CYS205 3.7 35.2 1.0
N G:GLY207 3.9 37.4 1.0
N G:MET206 4.0 30.8 1.0
CG G:PRO227 4.1 33.7 1.0
S2 G:SF4303 4.1 35.9 1.0
C G:CYS205 4.2 33.9 1.0
CG1 G:VAL199 4.4 33.0 1.0
CD G:PRO227 4.4 35.6 1.0
CA G:GLY207 4.6 33.6 1.0
N G:CYS208 4.9 33.0 1.0
C G:MET206 4.9 29.9 1.0
SG G:CYS244 5.0 35.4 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 Aug 7 07:53:12 2024

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