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Iron in PDB 4omf: The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member

Enzymatic activity of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member

All present enzymatic activity of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member:
1.12.98.1;

Protein crystallography data

The structure of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member, PDB code: 4omf was solved by S.Vitt, K.Ma, E.Warkentin, J.Moll, A.Pierik, S.Shima, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.71
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 233.160, 233.160, 233.160, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.1

Other elements in 4omf:

The structure of The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Iron atom in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member (pdb code 4omf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 17 binding sites of Iron where determined in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member, PDB code: 4omf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 17 in 4omf

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Iron binding site 1 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:15.8
occ:1.00
FE1 G:SF4301 0.0 15.8 1.0
S4 G:SF4301 2.3 16.1 1.0
SG G:CYS57 2.3 15.6 1.0
S2 G:SF4301 2.3 16.2 1.0
S3 G:SF4301 2.3 16.5 1.0
FE4 G:SF4301 2.6 17.3 1.0
FE2 G:SF4301 2.6 16.8 1.0
FE3 G:SF4301 2.7 16.5 1.0
CB G:CYS57 3.3 12.7 1.0
N G:CYS57 3.8 16.8 1.0
S1 G:SF4301 3.8 16.5 1.0
NE2 A:HIS150 3.9 15.7 1.0
CA G:CYS57 4.1 15.4 1.0
OD2 G:ASP60 4.1 23.9 1.0
N G:GLY59 4.3 14.4 1.0
C G:CYS57 4.6 15.4 1.0
CA G:GLY59 4.6 13.2 1.0
SG G:CYS132 4.7 17.2 1.0
CD2 A:HIS150 4.7 16.4 1.0
N G:THR58 4.8 14.3 1.0
SG G:CYS171 4.8 15.8 1.0
CE1 A:HIS150 4.8 16.0 1.0
C G:GLY56 4.8 17.3 1.0
O G:HOH410 4.8 15.4 1.0
CG G:ASP60 5.0 24.2 1.0

Iron binding site 2 out of 17 in 4omf

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Iron binding site 2 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:16.8
occ:1.00
FE2 G:SF4301 0.0 16.8 1.0
S3 G:SF4301 2.3 16.5 1.0
S4 G:SF4301 2.3 16.1 1.0
S1 G:SF4301 2.3 16.5 1.0
SG G:CYS132 2.3 17.2 1.0
FE1 G:SF4301 2.6 15.8 1.0
FE3 G:SF4301 2.7 16.5 1.0
FE4 G:SF4301 2.8 17.3 1.0
CB G:CYS132 3.2 15.8 1.0
N G:CYS132 3.8 15.4 1.0
S2 G:SF4301 3.9 16.2 1.0
CA G:CYS132 4.0 13.2 1.0
O G:HOH422 4.1 14.7 1.0
O G:HOH410 4.1 15.4 1.0
SG G:CYS171 4.5 15.8 1.0
OD2 G:ASP60 4.6 23.9 1.0
SG G:CYS137 4.7 16.6 1.0
CE2 G:PHE138 4.7 16.2 1.0
CB G:CYS137 4.7 13.6 1.0
SG G:CYS57 4.8 15.6 1.0
CD2 G:PHE138 4.8 13.1 1.0
N G:CYS57 5.0 16.8 1.0

Iron binding site 3 out of 17 in 4omf

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Iron binding site 3 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:16.5
occ:1.00
FE3 G:SF4301 0.0 16.5 1.0
S2 G:SF4301 2.3 16.2 1.0
S4 G:SF4301 2.3 16.1 1.0
SG G:CYS171 2.3 15.8 1.0
S1 G:SF4301 2.3 16.5 1.0
FE1 G:SF4301 2.7 15.8 1.0
FE2 G:SF4301 2.7 16.8 1.0
FE4 G:SF4301 2.7 17.3 1.0
CB G:CYS171 3.4 13.1 1.0
CA G:CYS171 3.5 13.7 1.0
C G:CYS171 3.9 14.6 1.0
S3 G:SF4301 3.9 16.5 1.0
NE2 A:HIS150 4.1 15.7 1.0
CD2 A:HIS150 4.2 16.4 1.0
N G:PRO172 4.3 14.9 1.0
O G:CYS171 4.4 16.1 1.0
O G:GLY170 4.6 15.6 1.0
SG G:CYS137 4.6 16.6 1.0
SG G:CYS57 4.6 15.6 1.0
CA G:PRO172 4.6 15.5 1.0
SG G:CYS132 4.7 17.2 1.0
NE A:ARG61 4.7 15.2 1.0
N G:CYS171 4.8 15.8 1.0
OD1 G:ASP60 4.9 32.9 1.0
OD2 G:ASP60 4.9 23.9 1.0

Iron binding site 4 out of 17 in 4omf

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Iron binding site 4 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:17.3
occ:1.00
FE4 G:SF4301 0.0 17.3 1.0
OD2 G:ASP60 2.2 23.9 1.0
S1 G:SF4301 2.3 16.5 1.0
S2 G:SF4301 2.3 16.2 1.0
S3 G:SF4301 2.3 16.5 1.0
FE1 G:SF4301 2.6 15.8 1.0
OD1 G:ASP60 2.7 32.9 1.0
FE3 G:SF4301 2.7 16.5 1.0
FE2 G:SF4301 2.8 16.8 1.0
CG G:ASP60 2.8 24.2 1.0
O G:HOH422 3.7 14.7 1.0
S4 G:SF4301 3.9 16.1 1.0
N G:ASP60 4.1 16.0 1.0
CB G:ASP60 4.2 14.6 1.0
CA G:GLY130 4.5 16.6 1.0
SG G:CYS57 4.5 15.6 1.0
CA G:PRO172 4.6 15.5 1.0
O G:GLY170 4.6 15.6 1.0
CA G:ASP60 4.7 14.8 1.0
CB G:PRO172 4.7 13.6 1.0
CG G:GLU102 4.7 15.7 1.0
C G:GLY59 4.8 19.4 1.0
N G:SER131 4.9 15.3 1.0
CA G:CYS171 4.9 13.7 1.0
O G:PHE129 4.9 19.3 1.0
SG G:CYS171 4.9 15.8 1.0
N G:GLY59 4.9 14.4 1.0
C G:GLY130 4.9 13.6 1.0
SG G:CYS132 5.0 17.2 1.0
N G:CYS132 5.0 15.4 1.0
CA G:GLY59 5.0 13.2 1.0

Iron binding site 5 out of 17 in 4omf

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Iron binding site 5 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:15.8
occ:1.00
FE1 G:SF4302 0.0 15.8 1.0
S4 G:SF4302 2.3 15.1 1.0
S2 G:SF4302 2.3 13.6 1.0
S3 G:SF4302 2.3 17.0 1.0
SG G:CYS249 2.3 17.1 1.0
FE2 G:SF4302 2.7 15.3 1.0
FE3 G:SF4302 2.7 16.4 1.0
FE4 G:SF4302 2.7 16.1 1.0
CB G:CYS249 3.4 17.2 1.0
CA G:CYS249 3.7 14.5 1.0
S1 G:SF4302 3.9 15.4 1.0
N G:GLY207 3.9 18.9 1.0
N G:ILE250 4.0 16.1 1.0
CA G:GLY207 4.1 16.9 1.0
N G:LYS251 4.1 15.2 1.0
C G:CYS249 4.3 14.7 1.0
CD1 G:LEU244 4.6 16.8 1.0
CB G:ALA234 4.6 12.6 1.0
CA G:LYS251 4.7 16.3 1.0
C G:CYS206 4.8 20.6 1.0
N G:CYS252 4.9 14.7 1.0
SG G:CYS255 4.9 16.2 1.0
SG G:CYS230 4.9 16.2 1.0
N G:CYS249 5.0 13.4 1.0

Iron binding site 6 out of 17 in 4omf

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Iron binding site 6 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:15.3
occ:1.00
FE2 G:SF4302 0.0 15.3 1.0
S1 G:SF4302 2.3 15.4 1.0
S3 G:SF4302 2.3 17.0 1.0
S4 G:SF4302 2.3 15.1 1.0
SG G:CYS255 2.4 16.2 1.0
FE4 G:SF4302 2.7 16.1 1.0
FE3 G:SF4302 2.7 16.4 1.0
FE1 G:SF4302 2.7 15.8 1.0
CB G:CYS255 3.3 15.1 1.0
N G:CYS255 3.8 14.9 1.0
S2 G:SF4302 3.9 13.6 1.0
CA G:GLY207 4.0 16.9 1.0
CA G:CYS255 4.2 13.0 1.0
N G:GLY207 4.3 18.9 1.0
CD1 G:LEU235 4.5 13.6 1.0
N G:ILE254 4.6 14.7 1.0
SG G:CYS252 4.7 16.3 1.0
SG G:CYS249 4.8 17.1 1.0
N G:GLY253 4.8 14.7 1.0
C G:CYS206 4.8 20.6 1.0
SG G:CYS230 4.8 16.2 1.0
C G:GLY253 4.9 16.9 1.0
C G:ILE254 5.0 13.7 1.0
O G:CYS206 5.0 18.4 1.0

Iron binding site 7 out of 17 in 4omf

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Iron binding site 7 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:16.4
occ:1.00
FE3 G:SF4302 0.0 16.4 1.0
S2 G:SF4302 2.3 13.6 1.0
S4 G:SF4302 2.3 15.1 1.0
S1 G:SF4302 2.3 15.4 1.0
SG G:CYS230 2.4 16.2 1.0
FE2 G:SF4302 2.7 15.3 1.0
FE1 G:SF4302 2.7 15.8 1.0
FE4 G:SF4302 2.7 16.1 1.0
CB G:CYS230 3.3 15.7 1.0
S3 G:SF4302 3.9 17.0 1.0
CA G:CYS230 4.0 13.5 1.0
CB G:ALA234 4.1 12.6 1.0
OG1 G:THR232 4.1 14.2 1.0
CD1 G:LEU235 4.6 13.6 1.0
CG G:LEU235 4.7 14.1 1.0
O G:HOH414 4.7 14.7 1.0
C G:CYS230 4.7 14.8 1.0
SG G:CYS252 4.8 16.3 1.0
SG G:CYS255 4.8 16.2 1.0
N G:GLN231 4.8 13.1 1.0
N G:ALA234 4.8 14.1 1.0
CB G:CYS255 4.9 15.1 1.0
SG G:CYS249 5.0 17.1 1.0
CA G:ALA234 5.0 16.9 1.0

Iron binding site 8 out of 17 in 4omf

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Iron binding site 8 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe302

b:16.1
occ:1.00
FE4 G:SF4302 0.0 16.1 1.0
S1 G:SF4302 2.3 15.4 1.0
S2 G:SF4302 2.3 13.6 1.0
S3 G:SF4302 2.3 17.0 1.0
SG G:CYS252 2.4 16.3 1.0
FE2 G:SF4302 2.7 15.3 1.0
FE3 G:SF4302 2.7 16.4 1.0
FE1 G:SF4302 2.7 15.8 1.0
N G:CYS252 3.7 14.7 1.0
CB G:CYS252 3.7 12.6 1.0
N G:GLY253 3.9 14.7 1.0
S4 G:SF4302 3.9 15.1 1.0
CA G:CYS252 4.1 17.6 1.0
O G:HOH414 4.1 14.7 1.0
N G:ILE254 4.2 14.7 1.0
CG1 G:ILE250 4.2 12.2 1.0
C G:CYS252 4.3 14.7 1.0
N G:LYS251 4.5 15.2 1.0
SG G:CYS249 4.7 17.1 1.0
SG G:CYS230 4.7 16.2 1.0
CA G:GLY253 4.8 14.8 1.0
C G:LYS251 4.8 18.6 1.0
CB G:ILE254 4.8 14.7 1.0
SG G:CYS255 4.8 16.2 1.0
N G:ILE250 4.8 16.1 1.0
N G:CYS255 4.8 14.9 1.0
CD1 G:ILE250 4.9 14.5 1.0
C G:GLY253 4.9 16.9 1.0
CA G:LYS251 5.0 16.3 1.0
CA G:ILE254 5.0 15.5 1.0

Iron binding site 9 out of 17 in 4omf

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Iron binding site 9 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:17.0
occ:1.00
FE1 G:SF4303 0.0 17.0 1.0
S2 G:SF4303 2.3 15.5 1.0
S4 G:SF4303 2.3 16.2 1.0
S3 G:SF4303 2.3 15.6 1.0
SG G:CYS226 2.3 16.0 1.0
FE2 G:SF4303 2.7 16.4 1.0
FE4 G:SF4303 2.7 17.7 1.0
FE3 G:SF4303 2.8 17.0 1.0
CB G:CYS226 3.2 15.7 1.0
N G:CYS226 3.9 14.7 1.0
S1 G:SF4303 3.9 15.8 1.0
CA G:CYS226 4.2 16.5 1.0
CG G:PRO242 4.5 16.5 1.0
CD G:PRO242 4.6 18.4 1.0
N G:THR225 4.7 17.2 1.0
SG G:CYS223 4.7 16.6 1.0
N G:GLY224 4.7 15.1 1.0
CB G:PRO242 4.8 15.1 1.0
SG G:CYS220 4.8 16.4 1.0
CD1 G:LEU210 4.8 19.2 1.0
SG G:CYS259 4.9 17.3 1.0
CD2 G:LEU210 4.9 14.5 1.0

Iron binding site 10 out of 17 in 4omf

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Iron binding site 10 out of 17 in the The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member


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 Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe303

b:16.4
occ:1.00
FE2 G:SF4303 0.0 16.4 1.0
S3 G:SF4303 2.3 15.6 1.0
S4 G:SF4303 2.3 16.2 1.0
S1 G:SF4303 2.3 15.8 1.0
SG G:CYS220 2.4 16.4 1.0
FE4 G:SF4303 2.7 17.7 1.0
FE1 G:SF4303 2.7 17.0 1.0
FE3 G:SF4303 2.7 17.0 1.0
CB G:CYS220 3.4 14.3 1.0
CA G:CYS220 3.8 15.0 1.0
S2 G:SF4303 3.9 15.5 1.0
N G:ILE221 4.0 15.9 1.0
N G:GLY222 4.1 17.5 1.0
CG1 G:VAL214 4.3 16.4 1.0
C G:CYS220 4.4 14.6 1.0
CD G:PRO242 4.5 18.4 1.0
CA G:GLY222 4.7 18.1 1.0
CG G:PRO242 4.8 16.5 1.0
SG G:CYS259 4.9 17.3 1.0
N G:CYS223 4.9 15.9 1.0
SG G:CYS226 4.9 16.0 1.0

Reference:

S.Vitt, K.Ma, E.Warkentin, J.Moll, A.J.Pierik, S.Shima, U.Ermler. The F420-Reducing [Nife]-Hydrogenase Complex From Methanothermobacter Marburgensis, the First X-Ray Structure of A Group 3 Family Member. J.Mol.Biol. V. 426 2813 2014.
ISSN: ISSN 0022-2836
PubMed: 24887099
DOI: 10.1016/J.JMB.2014.05.024
Page generated: Sun Dec 13 15:43:41 2020

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