Iron in PDB 8w6x: Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State

Enzymatic activity of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State

All present enzymatic activity of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State:
1.12.2.1;

Protein crystallography data

The structure of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State, PDB code: 8w6x was solved by T.Hiromoto, T.Tamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.705, 98.485, 126.86, 90, 90, 90
R / Rfree (%) 18.9 / 22

Other elements in 8w6x:

The structure of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State also contains other interesting chemical elements:

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

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State (pdb code 8w6x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State, PDB code: 8w6x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 8w6x

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Iron binding site 1 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe601

b:7.8
occ:1.00
FE L:NFU601 0.0 7.8 1.0
C3 L:NFU601 1.8 10.0 1.0
C1 L:NFU601 1.9 9.1 1.0
C2 L:NFU601 1.9 8.8 1.0
O L:OH608 2.1 8.1 0.7
OD L:CYS546 2.3 11.7 0.3
SG L:CYS84 2.3 9.3 1.0
SG L:CYS549 2.3 7.6 0.7
SG L:CYS549 2.6 12.9 0.3
O3 L:NFU601 2.9 10.6 1.0
NI L:NFU601 2.9 9.6 0.7
N1 L:NFU601 3.0 9.1 1.0
N2 L:NFU601 3.1 9.2 1.0
HD2 L:ARG479 3.2 3.0 1.0
HB3 L:CYS84 3.2 5.2 1.0
SG L:CYS546 3.3 10.7 0.3
CB L:CYS84 3.3 8.8 1.0
DE2 L:HIS88 3.4 20.5 0.1
HE2 L:HIS88 3.4 4.6 0.9
CB L:CYS549 3.4 9.3 0.7
HB3 L:CYS549 3.5 13.4 0.7
SG L:CYS81 3.5 10.4 0.3
HB3 L:CYS546 3.6 10.1 0.3
HB2 L:CYS84 3.7 10.5 1.0
HB2 L:CYS549 3.7 9.5 0.7
HH11 L:ARG479 3.7 9.1 0.2
DH11 L:ARG479 3.7 5.3 0.8
HB3 L:CYS546 3.8 7.5 0.7
CB L:CYS549 3.8 12.3 0.3
DG1 L:THR87 3.9 3.3 0.4
HG1 L:THR87 3.9 15.7 0.6
CB L:CYS546 3.9 8.7 0.3
HB3 L:CYS549 3.9 11.1 0.3
HB2 L:CYS549 4.0 12.6 0.3
NI L:NFU601 4.0 11.1 0.3
HB2 L:ARG479 4.0 4.6 1.0
HD2 L:PRO501 4.0 11.1 1.0
HB2 L:CYS546 4.0 8.7 0.3
HG12 L:VAL500 4.1 14.9 1.0
HG2 L:PRO501 4.1 8.5 1.0
HG13 L:VAL500 4.2 6.8 1.0
CD L:ARG479 4.2 9.3 1.0
NE2 L:HIS88 4.3 10.0 1.0
HG11 L:VAL500 4.3 10.7 1.0
CG1 L:VAL500 4.4 10.4 1.0
HB3 L:CYS81 4.4 7.1 0.7
SG L:CYS546 4.4 8.9 0.7
CB L:CYS546 4.4 8.7 0.7
HB2 L:CYS81 4.4 9.6 0.3
NH1 L:ARG479 4.4 9.4 1.0
H L:CYS84 4.5 4.5 0.8
D L:CYS84 4.5 13.9 0.2
HB2 L:CYS546 4.5 10.1 0.7
HD3 L:ARG479 4.5 21.1 1.0
CB L:CYS81 4.6 10.0 0.3
HB2 L:ALA477 4.7 6.7 1.0
OG1 L:THR87 4.7 9.2 1.0
CA L:CYS84 4.8 9.5 1.0
CA L:CYS549 4.8 8.0 0.7
HB2 L:CYS81 4.8 5.5 0.7
SG L:CYS81 4.8 10.3 0.7
D L:SER502 4.9 20.4 0.2
H L:SER502 4.9 4.2 0.8
HA L:CYS549 4.9 11.8 0.7
CD L:PRO501 4.9 10.4 1.0
CB L:CYS81 4.9 8.2 0.7
HB3 L:CYS81 4.9 11.8 0.3
HB3 L:ALA477 4.9 14.7 1.0
NE L:ARG479 5.0 9.1 1.0
HD2 L:HIS88 5.0 15.9 1.0
CB L:ARG479 5.0 7.5 1.0
DH12 L:ARG479 5.0 4.0 0.5
HH12 L:ARG479 5.0 15.2 0.5
CG L:PRO501 5.0 10.1 1.0
D L:ARG479 5.0 18.6 0.1
H L:ARG479 5.0 5.9 0.9

Iron binding site 2 out of 12 in 8w6x

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Iron binding site 2 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:8.7
occ:1.00
FE1 S:SF41001 0.0 8.7 1.0
S4 S:SF41001 2.2 8.0 1.0
SG S:CYS17 2.3 8.0 1.0
S3 S:SF41001 2.3 8.2 1.0
S2 S:SF41001 2.3 7.8 1.0
FE2 S:SF41001 2.7 7.9 1.0
FE3 S:SF41001 2.7 7.7 1.0
FE4 S:SF41001 2.7 7.8 1.0
HG S:CYS17 2.8 8.5 0.5
D S:CYS17 3.0 20.3 0.3
H S:CYS17 3.0 4.8 0.7
HB3 S:CYS17 3.2 8.2 1.0
DE2 L:HIS235 3.3 15.4 0.2
HE2 L:HIS235 3.3 4.5 0.8
H S:GLY19 3.3 9.5 0.5
CB S:CYS17 3.4 8.3 1.0
D1 S:HOH1186 3.7 7.0 1.0
HG3 L:ARG79 3.7 7.7 1.0
N S:CYS17 3.8 9.0 1.0
S1 S:SF41001 3.8 7.8 1.0
HA3 S:GLY19 3.9 7.9 1.0
H S:CYS20 3.9 9.1 0.2
D S:CYS20 3.9 8.6 0.8
CA S:CYS17 4.1 7.9 1.0
N S:GLY19 4.2 9.5 1.0
NE2 L:HIS235 4.2 8.5 1.0
HB2 S:CYS17 4.3 5.9 1.0
D S:THR18 4.3 6.3 0.5
H S:THR18 4.3 11.4 0.5
CA S:GLY19 4.5 9.1 1.0
HB3 L:ARG79 4.5 12.8 1.0
C S:CYS17 4.5 8.3 1.0
O S:HOH1186 4.5 8.6 1.0
HA S:GLU16 4.5 10.3 1.0
N S:THR18 4.6 8.5 1.0
N S:CYS20 4.6 8.4 1.0
HA L:ARG79 4.6 4.0 1.0
HD2 L:HIS235 4.6 11.4 1.0
CG L:ARG79 4.7 7.7 1.0
SG S:CYS114 4.7 8.6 1.0
SG S:CYS150 4.7 7.7 1.0
HB2 S:GLU16 4.7 9.0 1.0
SG S:CYS20 4.8 8.3 1.0
CD2 L:HIS235 4.8 8.3 1.0
HG2 L:ARG79 4.9 7.5 1.0
HG13 S:VAL120 4.9 9.8 1.0
C S:GLU16 4.9 8.6 1.0
C S:GLY19 5.0 8.1 1.0
O L:ARG79 5.0 8.3 1.0

Iron binding site 3 out of 12 in 8w6x

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Iron binding site 3 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:7.9
occ:1.00
FE2 S:SF41001 0.0 7.9 1.0
S3 S:SF41001 2.2 8.2 1.0
S4 S:SF41001 2.3 8.0 1.0
SG S:CYS114 2.3 8.6 1.0
S1 S:SF41001 2.3 7.8 1.0
FE3 S:SF41001 2.6 7.7 1.0
FE1 S:SF41001 2.7 8.7 1.0
FE4 S:SF41001 2.7 7.8 1.0
HB2 S:CYS114 2.9 18.3 1.0
D S:CYS114 3.2 20.2 0.3
H S:CYS114 3.2 4.0 0.7
CB S:CYS114 3.2 9.8 1.0
D1 S:HOH1137 3.2 16.7 1.0
D1 S:HOH1186 3.3 7.0 1.0
D1 S:HOH1312 3.4 12.4 1.0
S2 S:SF41001 3.8 7.8 1.0
D2 S:HOH1312 3.9 17.4 1.0
HB3 S:CYS114 4.0 12.2 1.0
HA S:GLU16 4.0 10.3 1.0
D S:CYS17 4.0 20.3 0.3
H S:CYS17 4.0 4.8 0.7
N S:CYS114 4.0 9.1 1.0
O S:HOH1137 4.0 8.6 1.0
O S:HOH1312 4.1 9.2 1.0
O S:HOH1186 4.2 8.6 1.0
CA S:CYS114 4.2 8.3 1.0
D2 S:HOH1186 4.3 12.7 1.0
DE22 S:GLN121 4.4 21.9 0.2
HE22 S:GLN121 4.4 5.8 0.8
HG13 S:VAL120 4.4 9.8 1.0
HA2 S:GLY76 4.5 17.6 1.0
SG S:CYS150 4.5 7.7 1.0
D S:VAL120 4.5 8.8 0.6
H S:VAL120 4.5 8.4 0.4
SG S:CYS20 4.7 8.3 1.0
D2 S:HOH1137 4.7 28.4 1.0
HA3 S:GLY119 4.7 9.6 1.0
HA S:CYS114 4.7 4.4 1.0
HB3 S:CYS17 4.8 8.2 1.0
HA S:CYS150 4.8 4.1 1.0
HA3 S:GLY112 4.8 10.2 1.0
SG S:CYS17 4.8 8.0 1.0
N S:CYS17 4.9 9.0 1.0
HB3 S:GLU16 4.9 12.1 1.0
H S:GLY76 4.9 4.2 0.7
D S:GLY76 4.9 18.0 0.3
HB2 S:GLU16 5.0 9.0 1.0
HG3 L:ARG79 5.0 7.7 1.0
CA S:GLU16 5.0 9.0 1.0
HB S:THR113 5.0 7.2 1.0
H S:ALA115 5.0 4.5 0.6
D S:ALA115 5.0 16.2 0.4

Iron binding site 4 out of 12 in 8w6x

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Iron binding site 4 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:7.7
occ:1.00
FE3 S:SF41001 0.0 7.7 1.0
S2 S:SF41001 2.2 7.8 1.0
SG S:CYS150 2.3 7.7 1.0
S1 S:SF41001 2.3 7.8 1.0
S4 S:SF41001 2.3 8.0 1.0
FE2 S:SF41001 2.6 7.9 1.0
FE1 S:SF41001 2.7 8.7 1.0
FE4 S:SF41001 2.7 7.8 1.0
HA S:CYS150 2.8 4.1 1.0
D2 S:HOH1312 3.2 17.4 1.0
HG3 L:ARG79 3.4 7.7 1.0
CB S:CYS150 3.4 9.2 1.0
CA S:CYS150 3.5 8.3 1.0
D1 S:HOH1312 3.7 12.4 1.0
DE L:ARG79 3.8 19.6 0.4
HE L:ARG79 3.8 7.0 0.6
C S:CYS150 3.8 8.2 1.0
HD2 L:HIS235 3.8 11.4 1.0
S3 S:SF41001 3.8 8.2 1.0
HG2 L:ARG79 3.8 7.5 1.0
HB2 S:CYS150 3.9 14.6 1.0
O S:HOH1312 3.9 9.2 1.0
HA S:PRO151 4.0 11.8 1.0
DE2 L:HIS235 4.0 15.4 0.2
HE2 L:HIS235 4.0 4.5 0.8
CG L:ARG79 4.1 7.7 1.0
O S:CYS150 4.2 8.5 1.0
HB3 S:CYS150 4.3 10.0 1.0
N S:PRO151 4.3 7.3 1.0
SG S:CYS114 4.4 8.6 1.0
D S:CYS114 4.4 20.2 0.3
H S:CYS114 4.4 4.0 0.7
HB S:THR113 4.6 7.2 1.0
CD2 L:HIS235 4.6 8.3 1.0
HZ2 S:TRP258 4.6 6.4 1.0
SG S:CYS17 4.6 8.0 1.0
NE2 L:HIS235 4.7 8.5 1.0
CA S:PRO151 4.7 8.6 1.0
NE L:ARG79 4.7 8.9 1.0
HB3 S:PRO151 4.7 8.2 1.0
O S:GLY149 4.7 8.6 1.0
SG S:CYS20 4.7 8.3 1.0
D S:THR113 4.8 12.6 0.3
H S:THR113 4.8 4.0 0.7
N S:CYS150 4.8 8.2 1.0
HB3 L:ARG79 4.8 12.8 1.0
HD3 S:PRO151 4.8 10.8 1.0
D1 S:HOH1137 4.9 16.7 1.0
D1 S:HOH1186 5.0 7.0 1.0

Iron binding site 5 out of 12 in 8w6x

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Iron binding site 5 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:7.8
occ:1.00
FE4 S:SF41001 0.0 7.8 1.0
S1 S:SF41001 2.2 7.8 1.0
SG S:CYS20 2.2 8.3 1.0
S3 S:SF41001 2.3 8.2 1.0
S2 S:SF41001 2.3 7.8 1.0
FE2 S:SF41001 2.7 7.9 1.0
FE1 S:SF41001 2.7 8.7 1.0
FE3 S:SF41001 2.7 7.7 1.0
H S:CYS20 3.2 9.1 0.2
D S:CYS20 3.2 8.6 0.8
D1 S:HOH1137 3.2 16.7 1.0
CB S:CYS20 3.5 9.2 1.0
HB2 S:CYS20 3.5 13.7 1.0
HA S:PRO151 3.5 11.8 1.0
HB3 S:PRO151 3.6 8.2 1.0
HA3 S:GLY112 3.6 10.2 1.0
N S:CYS20 3.7 8.4 1.0
HA S:CYS150 3.7 4.1 1.0
S4 S:SF41001 3.9 8.0 1.0
O S:HOH1137 3.9 8.6 1.0
CA S:CYS20 4.1 8.7 1.0
D2 S:HOH1137 4.1 28.4 1.0
HG3 S:GLU75 4.1 6.2 1.0
HD3 S:PRO152 4.1 3.5 1.0
HA S:CYS20 4.2 15.5 1.0
D S:CYS114 4.3 20.2 0.3
H S:CYS114 4.3 4.0 0.7
CA S:PRO151 4.3 8.6 1.0
HB3 S:CYS20 4.4 9.4 1.0
CB S:PRO151 4.4 8.3 1.0
C S:GLY19 4.5 8.1 1.0
HB2 S:CYS114 4.5 18.3 1.0
HA3 S:GLY19 4.5 7.9 1.0
HG S:CYS17 4.5 8.5 0.5
CA S:GLY112 4.5 8.4 1.0
H S:GLY19 4.6 9.5 0.5
D S:CYS17 4.6 20.3 0.3
H S:CYS17 4.6 4.8 0.7
HA2 S:GLY112 4.6 9.7 1.0
OE2 S:GLU75 4.7 10.2 1.0
SG S:CYS17 4.7 8.0 1.0
D S:THR113 4.7 12.6 0.3
H S:THR113 4.7 4.0 0.7
O S:GLY149 4.7 8.6 1.0
CA S:CYS150 4.8 8.3 1.0
N S:PRO151 4.8 7.3 1.0
SG S:CYS150 4.9 7.7 1.0
SG S:CYS114 4.9 8.6 1.0
CA S:GLY19 4.9 9.1 1.0
HB2 S:PRO151 4.9 5.0 1.0
N S:GLY19 5.0 9.5 1.0

Iron binding site 6 out of 12 in 8w6x

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Iron binding site 6 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:10.4
occ:1.00
FE1 S:SF41002 0.0 10.4 1.0
ND1 S:HIS188 2.0 12.4 1.0
S3 S:SF41002 2.2 10.9 1.0
S2 S:SF41002 2.3 11.8 1.0
S4 S:SF41002 2.3 10.3 1.0
FE4 S:SF41002 2.7 11.6 1.0
FE3 S:SF41002 2.7 11.8 1.0
FE2 S:SF41002 2.7 10.2 1.0
CE1 S:HIS188 2.9 13.6 1.0
HE1 S:HIS188 3.1 14.6 1.0
CG S:HIS188 3.1 12.2 1.0
HA S:HIS188 3.2 10.4 1.0
HB2 S:HIS188 3.4 14.3 1.0
HG3 S:PRO225 3.6 15.9 1.0
HD3 S:PRO225 3.6 8.3 1.0
CB S:HIS188 3.6 11.5 1.0
S1 S:SF41002 3.8 11.8 1.0
CA S:HIS188 3.9 10.5 1.0
HB3 S:CYS191 3.9 13.0 1.0
HA3 S:GLY224 4.0 13.7 1.0
NE2 S:HIS188 4.1 13.3 1.0
HB2 S:PHE197 4.2 16.7 0.6
HD2 S:PHE197 4.2 11.0 0.6
CD2 S:HIS188 4.2 14.4 1.0
HB2 S:CYS191 4.3 13.2 1.0
HB2 S:PHE197 4.3 12.4 0.4
HD12 S:LEU194 4.4 12.6 1.0
CG S:PRO225 4.4 11.9 1.0
CD S:PRO225 4.4 10.7 1.0
CB S:CYS191 4.5 12.3 1.0
O S:HIS188 4.5 12.2 1.0
HD2 S:PHE197 4.6 11.7 0.4
CD2 S:PHE197 4.6 13.5 0.6
SG S:CYS216 4.6 12.1 1.0
SG S:CYS191 4.6 10.7 1.0
HA S:LEU194 4.6 9.2 1.0
HB2 S:TYR218 4.6 15.2 0.6
HB3 S:HIS188 4.7 9.3 1.0
C S:HIS188 4.7 11.2 1.0
SG S:CYS222 4.8 9.6 1.0
HG2 S:PRO225 4.8 11.6 1.0
CD2 S:PHE197 4.8 12.1 0.4
HD1 S:TYR218 4.9 12.1 0.6
N S:PRO225 4.9 9.9 1.0
HB3 S:CYS222 4.9 13.1 1.0
CB S:PHE197 4.9 14.8 0.6
HD13 S:LEU194 4.9 16.0 1.0
CG S:PHE197 5.0 13.7 0.6
CA S:GLY224 5.0 10.4 1.0
HB2 S:ARG193 5.0 6.4 1.0
HE2 S:HIS188 5.0 19.1 0.4
DE2 S:HIS188 5.0 8.7 0.6

Iron binding site 7 out of 12 in 8w6x

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Iron binding site 7 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:10.2
occ:1.00
FE2 S:SF41002 0.0 10.2 1.0
S4 S:SF41002 2.2 10.3 1.0
S1 S:SF41002 2.2 11.8 1.0
S3 S:SF41002 2.3 10.9 1.0
SG S:CYS222 2.3 9.6 1.0
FE3 S:SF41002 2.7 11.8 1.0
FE1 S:SF41002 2.7 10.4 1.0
FE4 S:SF41002 2.7 11.6 1.0
HB3 S:CYS222 3.0 13.1 1.0
CB S:CYS222 3.2 10.3 1.0
HG22 S:VAL243 3.4 10.1 1.0
HB2 S:CYS222 3.6 13.1 1.0
HD3 S:PRO225 3.7 8.3 1.0
HA3 S:GLY224 3.7 13.7 1.0
H S:GLY224 3.8 7.7 0.9
D S:GLY224 3.8 24.5 0.1
S2 S:SF41002 3.8 11.8 1.0
HB2 S:LEU217 3.9 16.6 1.0
D S:LEU217 3.9 25.7 0.0
H S:LEU217 3.9 6.3 1.0
HG11 S:VAL243 4.4 19.1 1.0
CG2 S:VAL243 4.4 13.6 1.0
HG21 S:VAL243 4.5 20.6 1.0
N S:GLY224 4.5 11.2 1.0
H S:CYS249 4.5 5.2 0.9
D S:CYS249 4.5 22.1 0.1
HB2 S:TYR218 4.5 15.2 0.6
HA S:TYR218 4.6 11.6 0.6
CA S:CYS222 4.6 9.5 1.0
CA S:GLY224 4.6 10.4 1.0
ND1 S:HIS188 4.6 12.4 1.0
SG S:CYS216 4.7 12.1 1.0
SG S:CYS191 4.7 10.7 1.0
HA S:HIS188 4.7 10.4 1.0
CD S:PRO225 4.7 10.7 1.0
H S:TYR218 4.8 9.3 0.9
HB3 S:CYS249 4.8 10.6 1.0
N S:TYR218 4.8 10.5 0.6
HD1 S:TYR218 4.8 12.1 0.6
C S:CYS222 4.8 9.6 1.0
N S:LEU217 4.8 12.4 1.0
HB2 S:HIS188 4.8 14.3 1.0
HG23 S:VAL243 4.9 17.1 1.0
CB S:LEU217 4.9 12.3 1.0
D S:TYR218 4.9 14.0 0.1
HA S:PRO248 4.9 7.0 1.0
HD1 S:TYR218 4.9 9.7 0.4
N S:TYR218 5.0 11.7 0.4
HB2 S:TYR218 5.0 13.9 0.4
O S:CYS222 5.0 10.5 1.0

Iron binding site 8 out of 12 in 8w6x

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Iron binding site 8 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:11.8
occ:1.00
FE3 S:SF41002 0.0 11.8 1.0
S1 S:SF41002 2.2 11.8 1.0
S2 S:SF41002 2.2 11.8 1.0
S4 S:SF41002 2.3 10.3 1.0
SG S:CYS191 2.3 10.7 1.0
FE2 S:SF41002 2.7 10.2 1.0
FE1 S:SF41002 2.7 10.4 1.0
FE4 S:SF41002 2.7 11.6 1.0
HB2 S:ARG193 2.9 6.4 1.0
HB3 S:CYS191 3.1 13.0 1.0
CB S:CYS191 3.1 12.3 1.0
HB2 S:CYS191 3.3 13.2 1.0
HG22 S:VAL243 3.7 10.1 1.0
HG11 S:VAL243 3.7 19.1 1.0
S3 S:SF41002 3.8 10.9 1.0
H S:ARG193 3.8 7.7 0.9
D S:ARG193 3.8 13.5 0.1
HG12 S:VAL243 3.9 8.7 1.0
HA S:HIS188 4.0 10.4 1.0
CB S:ARG193 4.0 12.2 1.0
HH2 S:TRP241 4.2 6.2 1.0
HD2 S:ARG193 4.2 16.5 1.0
CG1 S:VAL243 4.3 11.2 1.0
HG3 S:ARG193 4.3 5.5 1.0
ND1 S:HIS188 4.4 12.4 1.0
D S:LEU217 4.5 25.7 0.0
H S:LEU217 4.5 6.3 1.0
CA S:CYS191 4.6 13.5 1.0
HB3 S:ARG193 4.6 20.3 1.0
N S:ARG193 4.6 11.3 1.0
CG2 S:VAL243 4.6 13.6 1.0
CA S:ARG193 4.6 12.4 1.0
CG S:ARG193 4.6 12.3 1.0
C S:ARG193 4.7 13.7 1.0
HG21 S:VAL243 4.7 20.6 1.0
N S:LEU194 4.8 13.4 1.0
HA S:CYS216 4.8 14.4 1.0
SG S:CYS222 4.8 9.6 1.0
HA S:LEU194 4.8 9.2 1.0
D S:LEU194 4.8 11.6 0.4
H S:LEU194 4.8 15.9 0.6
SG S:CYS216 4.9 12.1 1.0
C S:CYS191 5.0 12.8 1.0
CD S:ARG193 5.0 15.7 1.0
CB S:VAL243 5.0 10.7 1.0
HA S:CYS191 5.0 23.7 1.0

Iron binding site 9 out of 12 in 8w6x

Go back to Iron Binding Sites List in 8w6x
Iron binding site 9 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:11.6
occ:1.00
FE4 S:SF41002 0.0 11.6 1.0
S2 S:SF41002 2.2 11.8 1.0
S3 S:SF41002 2.3 10.9 1.0
S1 S:SF41002 2.3 11.8 1.0
SG S:CYS216 2.3 12.1 1.0
FE1 S:SF41002 2.7 10.4 1.0
FE3 S:SF41002 2.7 11.8 1.0
FE2 S:SF41002 2.7 10.2 1.0
D S:LEU217 3.0 25.7 0.0
H S:LEU217 3.0 6.3 1.0
HB2 S:PHE197 3.1 12.4 0.4
HB2 S:CYS216 3.4 23.0 1.0
CB S:CYS216 3.4 14.6 1.0
HB2 S:PHE197 3.4 16.7 0.6
HA S:CYS216 3.5 14.4 1.0
HB2 S:TYR218 3.6 15.2 0.6
HD2 S:PHE197 3.6 11.7 0.4
HB2 S:ARG193 3.6 6.4 1.0
H S:TYR218 3.6 9.3 0.9
HD2 S:PHE197 3.7 11.0 0.6
D S:TYR218 3.7 14.0 0.1
HB2 S:TYR218 3.8 13.9 0.4
N S:LEU217 3.8 12.4 1.0
S4 S:SF41002 3.8 10.3 1.0
CA S:CYS216 3.9 13.1 1.0
HE1 S:HIS188 4.2 14.6 1.0
CB S:PHE197 4.2 13.5 0.4
N S:TYR218 4.2 10.5 0.6
C S:CYS216 4.3 12.6 1.0
N S:TYR218 4.3 11.7 0.4
HB3 S:CYS216 4.3 11.9 1.0
HB3 S:CYS222 4.3 13.1 1.0
CD2 S:PHE197 4.3 12.1 0.4
ND1 S:HIS188 4.4 12.4 1.0
HB3 S:ARG193 4.4 20.3 1.0
CB S:PHE197 4.5 14.8 0.6
CB S:ARG193 4.5 12.2 1.0
CD2 S:PHE197 4.5 13.5 0.6
CB S:TYR218 4.6 10.7 0.6
HB2 S:LEU217 4.6 16.6 1.0
H S:PHE197 4.6 17.4 0.2
HB3 S:PHE197 4.6 17.6 0.4
CE1 S:HIS188 4.7 13.6 1.0
CG S:PHE197 4.7 12.4 0.4
HD2 S:ARG193 4.7 16.5 1.0
HA S:LEU194 4.7 9.2 1.0
O S:ARG193 4.8 14.2 1.0
CB S:TYR218 4.8 10.7 0.4
CA S:LEU217 4.8 11.4 1.0
CA S:TYR218 4.8 10.4 0.6
SG S:CYS222 4.8 9.6 1.0
HA S:TYR218 4.8 11.6 0.6
SG S:CYS191 4.9 10.7 1.0
C S:LEU217 4.9 11.1 1.0
HB3 S:TYR218 4.9 10.7 0.6
HB3 S:PHE197 4.9 16.6 0.6
HD1 S:TYR218 4.9 9.7 0.4
CG S:PHE197 4.9 13.7 0.6
CB S:CYS222 5.0 10.3 1.0
HE1 S:PHE202 5.0 14.0 1.0
C S:ARG193 5.0 13.7 1.0

Iron binding site 10 out of 12 in 8w6x

Go back to Iron Binding Sites List in 8w6x
Iron binding site 10 out of 12 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:8.5
occ:1.00
FE1 S:F3S1003 0.0 8.5 1.0
S1 S:F3S1003 2.2 9.3 1.0
S2 S:F3S1003 2.3 8.7 1.0
S3 S:F3S1003 2.3 8.6 1.0
SG S:CYS249 2.3 9.0 1.0
FE4 S:F3S1003 2.7 8.1 1.0
FE3 S:F3S1003 2.7 8.3 1.0
HA S:CYS249 3.1 13.9 1.0
HB2 S:CYS249 3.2 16.6 1.0
H S:GLY251 3.2 4.6 0.7
D S:GLY251 3.2 20.2 0.3
CB S:CYS249 3.2 9.9 1.0
H S:ILE250 3.5 5.9 0.9
D S:ILE250 3.5 19.3 0.1
HG21 S:THR227 3.5 10.2 1.0
H S:CYS252 3.5 5.6 0.9
D S:CYS252 3.5 23.3 0.1
CA S:CYS249 3.7 9.3 1.0
S4 S:F3S1003 3.9 8.4 1.0
DE22 L:GLN237 3.9 6.6 0.7
HE22 L:GLN237 3.9 11.4 0.3
HG23 S:VAL187 4.0 14.1 1.0
HG2 S:PRO242 4.0 8.9 1.0
N S:ILE250 4.1 9.5 1.0
N S:GLY251 4.2 9.5 1.0
HB3 S:CYS249 4.2 10.6 1.0
C S:CYS249 4.3 9.0 1.0
HG22 S:VAL187 4.4 17.0 1.0
N S:CYS252 4.5 9.4 1.0
HA2 S:GLY251 4.6 6.5 1.0
HG11 S:VAL187 4.6 7.2 1.0
CG2 S:THR227 4.6 11.4 1.0
CG2 S:VAL187 4.7 10.9 1.0
HB2 S:PRO242 4.7 10.0 1.0
HZ3 S:TRP241 4.7 16.1 1.0
HG13 S:VAL187 4.8 10.4 1.0
HD21 S:ASN229 4.8 15.5 0.1
DD21 S:ASN229 4.8 3.4 0.9
SG S:CYS231 4.8 9.3 1.0
SG S:CYS252 4.8 8.8 1.0
CA S:GLY251 4.8 8.7 1.0
NE2 L:GLN237 4.9 9.6 1.0
D1 L:HOH931 4.9 8.5 1.0
HG12 S:ILE250 4.9 9.4 1.0
HD2 S:PRO242 5.0 9.3 1.0
N S:CYS249 5.0 9.7 1.0
HE3 S:TRP241 5.0 16.0 1.0
HB3 S:CYS252 5.0 17.4 1.0

Reference:

T.Hiromoto, K.Nishikawa, S.Inoue, H.Ogata, Y.Hori, K.Kusaka, Y.Hirano, K.Kurihara, Y.Shigeta, T.Tamada, Y.Higuchi. New Insights Into the Oxidation Process From Neutron and X-Ray Crystal Structures of An O2-Sensitive [Nife]-Hydrogenase. Chemical Science 2023.
DOI: 10.1039/D3SC02156D
Page generated: Sat Aug 10 18:53:37 2024

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