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Iron in PDB 5y34: Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition

Enzymatic activity of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition

All present enzymatic activity of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition:
1.12.5.1;

Protein crystallography data

The structure of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition, PDB code: 5y34 was solved by Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.628, 116.943, 113.337, 90.00, 91.42, 90.00
R / Rfree (%) 13.1 / 15.8

Other elements in 5y34:

The structure of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iron atom in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition (pdb code 5y34). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 26 binding sites of Iron where determined in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition, PDB code: 5y34:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 26 in 5y34

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Iron binding site 1 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:11.0
occ:1.00
 FE A:FCO602 0.0 11.0 1.0
C1 A:FCO602 1.9 11.9 1.0
C2 A:FCO602 1.9 12.1 1.0
C3 A:FCO602 1.9 11.2 1.0
O A:O603 2.2 14.5 1.0
SG A:CYS79 2.3 11.8 1.0
SG A:CYS593 2.3 11.7 1.0
NI A:3NI601 2.8 15.4 1.0
O3 A:FCO602 3.0 12.1 1.0
N2 A:FCO602 3.0 10.5 1.0
N1 A:FCO602 3.0 11.1 1.0
CB A:CYS79 3.4 12.7 1.0
CB A:CYS593 3.4 11.6 1.0
CG1 A:VAL544 4.2 8.7 0.5
CD A:ARG523 4.2 10.2 1.0
SG A:CYS590 4.2 16.8 1.0
NE2 A:HIS83 4.2 10.5 1.0
CB A:CYS590 4.3 14.4 1.0
NH1 A:ARG523 4.3 12.4 1.0
SG A:CYS82 4.4 11.5 1.0
CD A:PRO545 4.7 10.0 1.0
SG A:CYS76 4.8 15.5 1.0
CA A:CYS593 4.8 10.0 1.0
CB A:CYS76 4.8 13.5 1.0
CA A:CYS79 4.8 12.6 1.0
NE A:ARG523 4.9 10.1 1.0
CZ A:ARG523 5.0 9.8 1.0
CD2 A:HIS83 5.0 10.2 1.0

Iron binding site 2 out of 26 in 5y34

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Iron binding site 2 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:11.2
occ:1.00
 FE1 B:SF3301 0.0 11.2 1.0
S2 B:SF3301 2.2 11.1 1.0
S1 B:SF3301 2.3 10.6 1.0
S3 B:SF3301 2.3 10.8 1.0
SG B:CYS121 2.3 10.7 1.0
FE4 B:SF3301 2.6 11.3 1.0
FE3 B:SF3301 2.7 10.2 1.0
CB B:CYS121 3.4 11.0 1.0
FE7 B:SF3301 3.7 11.4 0.5
O B:HOH423 3.7 13.6 1.0
FE7 B:SF3301 3.9 11.6 0.5
N B:CYS121 4.0 9.9 1.0
SG B:CYS25 4.1 12.1 1.0
O B:HOH455 4.2 10.9 1.0
CA B:CYS121 4.2 9.3 1.0
SG B:CYS126 4.4 10.7 1.0
CB B:CYS126 4.4 10.0 1.0
N B:CYS23 4.5 10.2 1.0
SG B:CYS26 4.6 10.6 1.0
SG B:CYS158 4.7 10.0 1.0
SG B:CYS23 4.7 10.8 1.0
CA B:GLU22 4.8 11.1 1.0
CB B:GLU22 5.0 12.7 1.0

Iron binding site 3 out of 26 in 5y34

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Iron binding site 3 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:10.2
occ:1.00
 FE3 B:SF3301 0.0 10.2 1.0
SG B:CYS158 2.2 10.0 1.0
S1 B:SF3301 2.3 10.6 1.0
S3 B:SF3301 2.3 10.8 1.0
SG B:CYS126 2.3 10.7 1.0
FE1 B:SF3301 2.7 11.2 1.0
CB B:CYS158 3.3 11.0 1.0
CB B:CYS126 3.4 10.0 1.0
FE4 B:SF3301 3.5 11.3 1.0
CA B:CYS158 3.9 8.9 1.0
SG B:CYS121 4.1 10.7 1.0
SG B:CYS25 4.3 12.1 1.0
CG A:ARG74 4.3 10.4 1.0
N B:CYS121 4.5 9.9 1.0
CB B:SER120 4.5 10.4 1.0
S2 B:SF3301 4.6 11.1 1.0
C B:CYS158 4.8 8.4 1.0
CA B:CYS126 4.9 9.6 1.0
O B:GLY157 4.9 9.4 1.0
N B:VAL127 4.9 9.4 1.0
N B:SER120 4.9 9.3 1.0
N B:CYS158 5.0 8.7 1.0

Iron binding site 4 out of 26 in 5y34

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Iron binding site 4 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:11.3
occ:1.00
 FE4 B:SF3301 0.0 11.3 1.0
SG B:CYS23 2.3 10.8 1.0
S3 B:SF3301 2.3 10.8 1.0
SG B:CYS25 2.3 12.1 1.0
S2 B:SF3301 2.3 11.1 1.0
FE1 B:SF3301 2.6 11.2 1.0
FE7 B:SF3301 2.9 11.4 0.5
FE7 B:SF3301 3.3 11.6 0.5
CB B:CYS25 3.4 10.5 1.0
CB B:CYS23 3.4 10.8 1.0
FE3 B:SF3301 3.5 10.2 1.0
N B:CYS25 3.7 10.2 1.0
S1 B:SF3301 3.7 10.6 1.0
N B:CYS23 3.8 10.2 1.0
CA B:CYS23 4.0 10.1 1.0
CA B:CYS25 4.1 9.5 1.0
NE2 A:HIS230 4.1 10.4 1.0
N B:THR24 4.1 10.4 1.0
C B:CYS23 4.3 9.8 1.0
SG B:CYS158 4.3 10.0 1.0
SG B:CYS121 4.7 10.7 1.0
N B:CYS26 4.7 9.6 1.0
O B:HOH455 4.7 10.9 1.0
CD2 A:HIS230 4.8 9.9 1.0
C B:THR24 4.8 10.2 1.0
C B:CYS25 4.9 8.8 1.0
SG B:CYS26 4.9 10.6 1.0
OE2 B:GLU82 5.0 10.7 0.5
C B:GLU22 5.0 9.5 1.0
CG A:ARG74 5.0 10.4 1.0

Iron binding site 5 out of 26 in 5y34

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Iron binding site 5 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:11.4
occ:0.50
 FE7 B:SF3301 0.0 11.4 0.5
FE7 B:SF3301 0.8 11.6 0.5
N B:CYS26 2.1 9.6 1.0
SG B:CYS25 2.2 12.1 1.0
SG B:CYS26 2.3 10.6 1.0
S2 B:SF3301 2.5 11.1 1.0
OE2 B:GLU82 2.9 10.7 0.5
FE4 B:SF3301 2.9 11.3 1.0
C B:CYS25 3.0 8.8 1.0
CA B:CYS26 3.1 9.0 1.0
CB B:CYS26 3.1 9.8 1.0
N B:CYS25 3.1 10.2 1.0
CA B:CYS25 3.2 9.5 1.0
CB B:CYS25 3.2 10.5 1.0
FE1 B:SF3301 3.7 11.2 1.0
S1 B:SF3301 3.8 10.6 1.0
CD B:GLU82 3.9 11.6 0.5
C B:THR24 4.0 10.2 1.0
OE2 B:GLU82 4.0 10.9 0.5
O B:CYS25 4.1 9.6 1.0
CB B:PRO159 4.1 9.1 1.0
CG B:GLU82 4.2 11.4 0.5
O B:HOH423 4.3 13.6 1.0
C B:CYS26 4.4 9.4 1.0
N B:THR24 4.5 10.4 1.0
SG B:CYS23 4.5 10.8 1.0
CG B:GLU82 4.5 11.4 0.5
CD B:GLU82 4.5 11.1 0.5
CA B:PRO159 4.6 8.8 1.0
O B:THR24 4.6 10.7 1.0
CA B:THR24 4.6 10.9 1.0
N B:SER27 4.7 9.5 1.0
S3 B:SF3301 4.9 10.8 1.0

Iron binding site 6 out of 26 in 5y34

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Iron binding site 6 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:11.6
occ:0.50
 FE7 B:SF3301 0.0 11.6 0.5
FE7 B:SF3301 0.8 11.4 0.5
N B:CYS26 2.0 9.6 1.0
OE2 B:GLU82 2.1 10.7 0.5
S2 B:SF3301 2.3 11.1 1.0
SG B:CYS26 2.4 10.6 1.0
N B:CYS25 2.9 10.2 1.0
SG B:CYS25 2.9 12.1 1.0
CB B:CYS26 2.9 9.8 1.0
CA B:CYS26 3.0 9.0 1.0
C B:CYS25 3.0 8.8 1.0
CD B:GLU82 3.2 11.6 0.5
OE2 B:GLU82 3.2 10.9 0.5
CA B:CYS25 3.3 9.5 1.0
FE4 B:SF3301 3.3 11.3 1.0
C B:THR24 3.5 10.2 1.0
CG B:GLU82 3.6 11.4 0.5
CB B:CYS25 3.6 10.5 1.0
CD B:GLU82 3.8 11.1 0.5
CG B:GLU82 3.9 11.4 0.5
FE1 B:SF3301 3.9 11.2 1.0
CA B:THR24 4.0 10.9 1.0
N B:THR24 4.0 10.4 1.0
C B:CYS26 4.1 9.4 1.0
O B:THR24 4.1 10.7 1.0
O B:CYS25 4.2 9.6 1.0
N B:SER27 4.2 9.5 1.0
O B:HOH423 4.2 13.6 1.0
OE1 B:GLU82 4.3 12.5 0.5
S1 B:SF3301 4.3 10.6 1.0
SG B:CYS23 4.7 10.8 1.0
CB B:PRO159 4.8 9.1 1.0
OE1 B:GLU82 4.8 13.0 0.5

Iron binding site 7 out of 26 in 5y34

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Iron binding site 7 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:10.2
occ:1.00
 FE1 B:F3S302 0.0 10.2 1.0
S2 B:F3S302 2.2 10.6 1.0
SG B:CYS258 2.2 10.2 1.0
S3 B:F3S302 2.3 10.5 1.0
S1 B:F3S302 2.3 10.2 1.0
FE4 B:F3S302 2.7 9.8 1.0
FE3 B:F3S302 2.7 10.0 1.0
CB B:CYS258 3.2 10.1 1.0
CA B:CYS258 3.6 9.5 1.0
CD1 B:ILE195 3.7 16.1 0.5
S4 B:F3S302 3.8 10.3 1.0
N B:ILE259 4.1 9.5 1.0
N B:GLY260 4.1 9.7 1.0
C B:CYS258 4.3 9.2 1.0
N B:CYS261 4.4 10.4 1.0
CG2 B:THR235 4.5 12.2 1.0
O B:HOH623 4.6 22.1 1.0
CA B:GLY260 4.7 9.6 1.0
CG1 B:ILE195 4.7 10.7 0.5
SG B:CYS239 4.8 9.7 1.0
SG B:CYS261 4.8 10.2 1.0
N B:CYS258 4.8 9.5 1.0
CG B:PRO251 4.9 10.0 1.0
CD1 B:ILE195 4.9 12.5 0.5
C B:GLY260 5.0 9.8 1.0

Iron binding site 8 out of 26 in 5y34

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Iron binding site 8 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:10.0
occ:1.00
 FE3 B:F3S302 0.0 10.0 1.0
S4 B:F3S302 2.2 10.3 1.0
S1 B:F3S302 2.3 10.2 1.0
SG B:CYS261 2.3 10.2 1.0
S3 B:F3S302 2.3 10.5 1.0
FE4 B:F3S302 2.7 9.8 1.0
FE1 B:F3S302 2.7 10.2 1.0
CB B:CYS261 3.4 10.5 1.0
N B:CYS261 3.7 10.4 1.0
O A:HOH853 3.8 13.3 1.0
S2 B:F3S302 3.9 10.6 1.0
NZ A:LYS227 3.9 10.2 0.5
O B:HOH504 4.0 10.9 1.0
CA B:CYS261 4.0 10.5 1.0
C B:CYS261 4.6 9.4 1.0
N B:SER262 4.6 9.7 1.0
SG B:CYS258 4.7 10.2 1.0
SG B:CYS239 4.7 9.7 1.0
ND2 B:ASN237 4.7 10.2 1.0
C B:GLY260 4.9 9.8 1.0

Iron binding site 9 out of 26 in 5y34

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Iron binding site 9 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:9.8
occ:1.00
 FE4 B:F3S302 0.0 9.8 1.0
S2 B:F3S302 2.2 10.6 1.0
S4 B:F3S302 2.2 10.3 1.0
S3 B:F3S302 2.3 10.5 1.0
SG B:CYS239 2.3 9.7 1.0
FE1 B:F3S302 2.7 10.2 1.0
FE3 B:F3S302 2.7 10.0 1.0
CB B:CYS239 3.2 9.6 1.0
CD1 B:ILE195 3.9 16.1 0.5
S1 B:F3S302 3.9 10.2 1.0
ND2 B:ASN237 4.1 10.2 1.0
NE1 B:TRP244 4.2 8.8 1.0
O B:HOH504 4.3 10.9 1.0
CD1 B:ILE195 4.3 12.5 0.5
CD B:PRO251 4.5 9.3 1.0
CG B:PRO251 4.6 10.0 1.0
CG B:ASN237 4.6 9.8 1.0
CA B:CYS239 4.6 9.1 1.0
SG B:CYS258 4.7 10.2 1.0
CB B:ASN237 4.7 10.6 1.0
SG B:CYS261 4.8 10.2 1.0
CG1 B:ILE195 4.9 13.5 0.5

Iron binding site 10 out of 26 in 5y34

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Iron binding site 10 out of 26 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:10.8
occ:1.00
 FE1 B:SF4303 0.0 10.8 1.0
S3 B:SF4303 2.2 11.6 1.0
SG B:CYS199 2.3 10.8 1.0
S4 B:SF4303 2.3 10.6 1.0
S2 B:SF4303 2.3 10.9 1.0
FE4 B:SF4303 2.7 11.3 1.0
FE2 B:SF4303 2.7 11.0 1.0
FE3 B:SF4303 2.7 10.6 1.0
CB B:CYS199 3.1 10.8 1.0
S1 B:SF4303 3.9 10.5 1.0
CB B:ARG201 4.2 9.2 1.0
CD1 B:ILE252 4.4 13.0 1.0
CG2 B:ILE252 4.4 11.2 1.0
ND1 B:HIS196 4.5 11.5 1.0
N B:ARG202 4.6 10.2 1.0
CA B:CYS199 4.6 9.7 1.0
C B:ARG201 4.6 10.3 1.0
CA B:ARG201 4.7 9.3 1.0
N B:ARG201 4.7 9.7 1.0
SG B:CYS230 4.8 10.1 1.0
SG B:CYS224 4.9 11.3 1.0
C B:CYS199 4.9 9.9 1.0
CG1 B:ILE252 4.9 11.3 1.0
CA B:HIS196 5.0 11.4 1.0

Reference:

Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi. Structural Basis For A [4FE-3S] Cluster in the Oxygen-Tolerant Membrane-Bound [Nife]-Hydrogenase Nature V. 479 253 2011.
ISSN: ESSN 1476-4687
PubMed: 22002607
DOI: 10.1038/NATURE10504
Page generated: Tue Aug 6 12:36:36 2024

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