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Iron in PDB 4iud: Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State

Enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State

All present enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State:
1.12.5.1;

Protein crystallography data

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State, PDB code: 4iud was solved by M.Hammer, A.Schmidt, S.Frielingsdorf, J.Fritsch, O.Lenz, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.42 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.775, 95.795, 120.679, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 16.5

Other elements in 4iud:

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State (pdb code 4iud). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State, PDB code: 4iud:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 4iud

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Iron binding site 1 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe1001

b:10.4
occ:1.00
FE L:NFV1001 0.0 10.4 1.0
C1 L:NFV1001 1.8 10.3 1.0
C3 L:NFV1001 1.9 11.1 1.0
C2 L:NFV1001 1.9 10.5 1.0
O4 L:NFV1001 2.0 12.6 1.0
SG L:CYS78 2.4 10.9 1.0
SG L:CYS600 2.4 10.6 1.0
NI L:NFV1001 2.9 12.8 1.0
O1 L:NFV1001 3.0 11.8 1.0
N3 L:NFV1001 3.0 10.9 1.0
N2 L:NFV1001 3.1 10.1 1.0
CB L:CYS78 3.4 12.7 1.0
CB L:CYS600 3.5 9.6 1.0
NE2 L:HIS82 4.2 10.0 1.0
CG1 L:VAL551 4.2 11.5 1.0
CD L:ARG530 4.3 12.1 1.0
NH1 L:ARG530 4.3 13.8 1.0
SG L:CYS81 4.4 14.5 1.0
CB L:CSO597 4.4 11.3 0.5
CB L:CSO597 4.4 11.5 0.5
SG L:CSO597 4.4 12.6 0.5
SG L:CSO597 4.5 11.8 0.5
CD L:PRO552 4.7 9.4 1.0
SG L:CYS75 4.8 14.2 1.0
CA L:CYS78 4.8 12.8 1.0
CA L:CYS600 4.9 9.8 1.0
CB L:CYS75 4.9 12.1 1.0
CD2 L:HIS82 4.9 9.7 1.0
NE L:ARG530 4.9 12.4 1.0
CG L:PRO552 5.0 10.5 1.0
CZ L:ARG530 5.0 13.2 1.0

Iron binding site 2 out of 13 in 4iud

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Iron binding site 2 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:14.5
occ:1.00
FE1 S:SF41001 0.0 14.5 1.0
ND1 S:HIS187 2.0 16.9 1.0
S4 S:SF41001 2.2 13.7 1.0
S3 S:SF41001 2.3 13.7 1.0
S2 S:SF41001 2.3 14.6 1.0
FE3 S:SF41001 2.7 13.7 1.0
FE4 S:SF41001 2.8 13.7 1.0
FE2 S:SF41001 2.8 12.9 1.0
CE1 S:HIS187 2.8 17.4 1.0
CG S:HIS187 3.1 15.9 1.0
CB S:HIS187 3.6 14.7 1.0
S1 S:SF41001 3.8 13.0 1.0
CA S:HIS187 3.9 13.9 1.0
NE2 S:HIS187 4.0 18.8 1.0
CD2 S:HIS187 4.2 18.6 1.0
CG S:PRO224 4.2 13.1 1.0
CD S:PRO224 4.3 12.2 1.0
CB S:CYS190 4.6 13.8 1.0
SG S:CYS215 4.6 13.3 1.0
O S:HIS187 4.7 17.8 1.0
SG S:CYS190 4.7 14.2 1.0
N S:PRO224 4.8 12.7 1.0
SG S:CYS221 4.8 12.3 1.0
N S:HIS187 4.8 13.5 1.0
C S:HIS187 4.8 15.3 1.0
CD1 S:PHE196 4.9 17.1 1.0

Iron binding site 3 out of 13 in 4iud

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Iron binding site 3 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:12.9
occ:1.00
FE2 S:SF41001 0.0 12.9 1.0
S3 S:SF41001 2.2 13.7 1.0
S1 S:SF41001 2.3 13.0 1.0
S4 S:SF41001 2.3 13.7 1.0
SG S:CYS221 2.3 12.3 1.0
FE4 S:SF41001 2.7 13.7 1.0
FE3 S:SF41001 2.7 13.7 1.0
FE1 S:SF41001 2.8 14.5 1.0
CB S:CYS221 3.3 11.4 1.0
S2 S:SF41001 3.9 14.6 1.0
CD1 S:ILE243 4.0 12.9 1.0
CG1 S:ILE243 4.4 12.3 1.0
CD S:PRO224 4.5 12.2 1.0
CA S:GLY223 4.5 12.4 1.0
N S:GLY223 4.5 11.8 1.0
CA S:CYS221 4.6 11.3 1.0
ND1 S:HIS187 4.6 16.9 1.0
SG S:CYS215 4.7 13.3 1.0
N S:TYR217 4.7 11.7 1.0
SG S:CYS190 4.7 14.2 1.0
N S:LEU216 4.8 12.8 1.0
C S:CYS221 4.8 11.6 1.0
C S:LEU216 4.9 11.3 1.0
CB S:LEU216 4.9 11.6 1.0
O S:CYS221 4.9 11.7 1.0

Iron binding site 4 out of 13 in 4iud

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Iron binding site 4 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:13.7
occ:1.00
FE3 S:SF41001 0.0 13.7 1.0
S1 S:SF41001 2.2 13.0 1.0
S2 S:SF41001 2.3 14.6 1.0
S4 S:SF41001 2.3 13.7 1.0
SG S:CYS190 2.3 14.2 1.0
FE4 S:SF41001 2.7 13.7 1.0
FE2 S:SF41001 2.7 12.9 1.0
FE1 S:SF41001 2.7 14.5 1.0
CB S:CYS190 3.1 13.8 1.0
S3 S:SF41001 3.8 13.7 1.0
CB S:ARG192 4.1 14.5 1.0
CD1 S:ILE243 4.1 12.9 1.0
CG2 S:ILE243 4.3 12.4 1.0
CA S:CYS190 4.5 14.3 1.0
ND1 S:HIS187 4.5 16.9 1.0
C S:ARG192 4.7 16.6 1.0
N S:ARG193 4.7 16.6 1.0
CA S:ARG192 4.7 15.4 1.0
CG1 S:ILE243 4.7 12.3 1.0
N S:ARG192 4.7 16.8 1.0
SG S:CYS221 4.8 12.3 1.0
C S:CYS190 4.9 15.2 1.0
CG S:ARG192 4.9 14.5 1.0
SG S:CYS215 5.0 13.3 1.0

Iron binding site 5 out of 13 in 4iud

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Iron binding site 5 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:13.7
occ:1.00
FE4 S:SF41001 0.0 13.7 1.0
S1 S:SF41001 2.2 13.0 1.0
S2 S:SF41001 2.3 14.6 1.0
S3 S:SF41001 2.3 13.7 1.0
SG S:CYS215 2.3 13.3 1.0
FE2 S:SF41001 2.7 12.9 1.0
FE3 S:SF41001 2.7 13.7 1.0
FE1 S:SF41001 2.8 14.5 1.0
CB S:CYS215 3.4 10.1 1.0
N S:LEU216 3.7 12.8 1.0
S4 S:SF41001 3.8 13.7 1.0
CA S:CYS215 3.9 12.6 1.0
N S:TYR217 4.2 11.7 1.0
C S:CYS215 4.2 12.7 1.0
CB S:PHE196 4.3 17.3 1.0
ND1 S:HIS187 4.4 16.9 1.0
CD1 S:PHE196 4.5 17.1 1.0
CB S:ARG192 4.6 14.5 1.0
CE1 S:HIS187 4.6 17.4 1.0
CB S:TYR217 4.7 13.2 1.0
CA S:LEU216 4.8 12.1 1.0
O S:ARG192 4.8 16.6 1.0
CG S:PHE196 4.8 15.1 1.0
C S:LEU216 4.8 11.3 1.0
SG S:CYS221 4.9 12.3 1.0
CA S:TYR217 4.9 12.1 1.0
SG S:CYS190 4.9 14.2 1.0
C S:ARG192 5.0 16.6 1.0

Iron binding site 6 out of 13 in 4iud

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Iron binding site 6 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:11.3
occ:1.00
FE1 S:F3S1002 0.0 11.3 1.0
S1 S:F3S1002 2.2 11.9 1.0
S2 S:F3S1002 2.3 11.5 1.0
S3 S:F3S1002 2.3 11.7 1.0
SG S:CYS249 2.3 10.9 1.0
FE3 S:F3S1002 2.6 11.2 1.0
FE4 S:F3S1002 2.7 11.4 1.0
CB S:CYS249 3.2 9.7 1.0
CA S:CYS249 3.7 9.9 1.0
S4 S:F3S1002 3.8 11.2 1.0
N S:ILE250 4.1 9.9 1.0
N S:GLY251 4.2 10.0 1.0
C S:CYS249 4.3 10.0 1.0
N S:CYS252 4.4 10.4 1.0
CG2 S:THR226 4.6 12.0 1.0
CG1 S:ILE186 4.6 16.9 1.0
O S:HOH1202 4.7 11.9 0.5
CA S:GLY251 4.7 10.6 1.0
SG S:CYS230 4.8 12.2 1.0
CG S:PRO242 4.8 11.4 1.0
SG S:CYS252 4.8 11.4 1.0
CD1 S:ILE186 4.9 17.2 1.0
O S:HOH1202 4.9 12.7 0.5
N S:CYS249 4.9 10.4 1.0

Iron binding site 7 out of 13 in 4iud

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Iron binding site 7 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:11.2
occ:1.00
FE3 S:F3S1002 0.0 11.2 1.0
S1 S:F3S1002 2.2 11.9 1.0
S3 S:F3S1002 2.2 11.7 1.0
S4 S:F3S1002 2.2 11.2 1.0
SG S:CYS230 2.3 12.2 1.0
FE1 S:F3S1002 2.6 11.3 1.0
FE4 S:F3S1002 2.7 11.4 1.0
CB S:CYS230 3.3 11.5 1.0
S2 S:F3S1002 3.9 11.5 1.0
ND2 S:ASN228 4.0 11.6 1.0
NE1 S:TRP235 4.3 9.4 1.0
CD1 S:ILE186 4.3 17.2 1.0
O S:HOH1128 4.4 12.4 1.0
CG S:PRO242 4.6 11.4 1.0
CD S:PRO242 4.6 10.5 1.0
CG S:ASN228 4.6 12.3 1.0
CB S:ASN228 4.6 12.3 1.0
SG S:CYS249 4.7 10.9 1.0
CA S:CYS230 4.8 12.0 1.0
SG S:CYS252 4.8 11.4 1.0
CG1 S:ILE186 4.9 16.9 1.0

Iron binding site 8 out of 13 in 4iud

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Iron binding site 8 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:11.4
occ:1.00
FE4 S:F3S1002 0.0 11.4 1.0
S4 S:F3S1002 2.2 11.2 1.0
S2 S:F3S1002 2.3 11.5 1.0
SG S:CYS252 2.3 11.4 1.0
S3 S:F3S1002 2.3 11.7 1.0
FE1 S:F3S1002 2.7 11.3 1.0
FE3 S:F3S1002 2.7 11.2 1.0
CB S:CYS252 3.4 11.9 1.0
N S:CYS252 3.8 10.4 1.0
O L:HOH1202 3.8 13.6 1.0
S1 S:F3S1002 3.9 11.9 1.0
O S:HOH1128 4.0 12.4 1.0
CA S:CYS252 4.0 10.7 1.0
NZ L:LYS226 4.0 12.3 1.0
N S:SER253 4.5 11.8 1.0
C S:CYS252 4.6 11.3 1.0
ND2 S:ASN228 4.6 11.6 1.0
O S:HOH1202 4.7 12.7 0.5
SG S:CYS249 4.7 10.9 1.0
SG S:CYS230 4.7 12.2 1.0
C S:GLY251 4.9 10.7 1.0

Iron binding site 9 out of 13 in 4iud

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Iron binding site 9 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:13.7
occ:1.00
FE2 S:S3F1003 0.0 13.7 1.0
S3 S:S3F1003 2.2 13.1 1.0
S2 S:S3F1003 2.3 12.9 1.0
SG S:CYS115 2.3 13.3 1.0
S1 S:S3F1003 2.3 14.2 1.0
FE1 S:S3F1003 2.6 14.9 1.0
FE3 S:S3F1003 2.7 12.3 1.0
FE4 S:S3F1003 2.8 14.8 0.5
CB S:CYS115 3.3 12.4 1.0
O S:HOH1121 3.8 15.2 1.0
FE4 S:S3F1003 3.8 16.7 0.5
O1 S:S3F1003 4.0 12.7 0.3
N S:CYS115 4.0 11.8 1.0
O S:HOH1110 4.2 11.9 1.0
SG S:CYS19 4.2 12.6 1.0
CA S:CYS115 4.2 11.9 1.0
SG S:CYS120 4.4 12.9 1.0
CB S:CYS120 4.4 12.0 1.0
N S:CYS17 4.5 11.8 1.0
SG S:CYS20 4.6 13.8 1.0
SG S:CYS17 4.7 12.2 1.0
SG S:CYS149 4.7 11.3 1.0
CA S:GLU16 4.8 13.1 0.5
CA S:GLU16 4.8 12.9 0.5

Iron binding site 10 out of 13 in 4iud

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Iron binding site 10 out of 13 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:12.3
occ:1.00
FE3 S:S3F1003 0.0 12.3 1.0
S2 S:S3F1003 2.3 12.9 1.0
S3 S:S3F1003 2.3 13.1 1.0
SG S:CYS149 2.3 11.3 1.0
SG S:CYS120 2.4 12.9 1.0
FE2 S:S3F1003 2.7 13.7 1.0
CB S:CYS149 3.3 10.6 1.0
FE1 S:S3F1003 3.5 14.9 1.0
CB S:CYS120 3.5 12.0 1.0
O1 S:S3F1003 3.7 12.7 0.3
CA S:CYS149 4.0 10.3 1.0
FE4 S:S3F1003 4.0 14.8 0.5
SG S:CYS115 4.1 13.3 1.0
SG S:CYS19 4.3 12.6 1.0
CG L:ARG73 4.3 10.1 1.0
CB S:SER114 4.5 11.3 1.0
N S:CYS115 4.5 11.8 1.0
S1 S:S3F1003 4.6 14.2 1.0
C S:CYS149 4.8 10.1 1.0
CA S:CYS120 4.9 12.4 1.0
O S:GLY148 4.9 10.7 1.0
N S:VAL121 5.0 10.7 1.0
N S:SER114 5.0 12.0 1.0

Reference:

S.Frielingsdorf, J.Fritsch, A.Schmidt, M.Hammer, J.Lowenstein, E.Siebert, V.Pelmenschikov, T.Jaenicke, J.Kalms, Y.Rippers, F.Lendzian, I.Zebger, C.Teutloff, M.Kaupp, R.Bittl, P.Hildebrandt, B.Friedrich, O.Lenz, P.Scheerer. Reversible [4FE-3S] Cluster Morphing in An O2-Tolerant [Nife] Hydrogenase. Nat.Chem.Biol. V. 10 378 2014.
ISSN: ISSN 1552-4450
PubMed: 24705592
DOI: 10.1038/NCHEMBIO.1500
Page generated: Sun Dec 13 15:37:57 2020

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