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Iron in PDB 1wuk: High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wuk was solved by H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.291, 125.843, 66.440, 90.00, 90.00, 90.00
R / Rfree (%) 9.6 / 12.3

Other elements in 1wuk:

The structure of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F 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 - 12;

Binding sites:

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

Iron binding site 1 out of 12 in 1wuk

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Iron binding site 1 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:5.6
occ:1.00
 FE1 S:SF41001 0.0 5.6 1.0
S4 S:SF41001 2.2 6.0 1.0
SG S:CYS17 2.3 5.9 1.0
S2 S:SF41001 2.3 5.7 1.0
S3 S:SF41001 2.3 6.8 1.0
FE3 S:SF41001 2.7 5.5 1.0
FE2 S:SF41001 2.7 6.0 1.0
FE4 S:SF41001 2.7 6.0 1.0
CB S:CYS17 3.4 5.7 1.0
N S:CYS17 3.8 5.7 1.0
S1 S:SF41001 3.9 5.9 1.0
CA S:CYS17 4.1 5.9 1.0
CE1 L:HIS235 4.2 3.5 1.0
N S:GLY19 4.2 5.6 1.0
CA S:GLY19 4.5 5.7 1.0
O S:HOH5006 4.5 6.3 1.0
C S:CYS17 4.5 5.5 1.0
N S:THR18 4.6 6.3 1.0
N S:CYS20 4.6 5.2 1.0
CG L:ARG79 4.7 5.5 1.0
SG S:CYS114 4.7 6.3 1.0
SG S:CYS150 4.7 5.4 1.0
ND1 L:HIS235 4.8 7.2 1.0
SG S:CYS20 4.9 6.3 1.0
C S:GLU16 4.9 5.5 1.0
C S:GLY19 5.0 5.1 1.0

Iron binding site 2 out of 12 in 1wuk

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Iron binding site 2 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

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

b:6.0
occ:1.00
 FE2 S:SF41001 0.0 6.0 1.0
SG S:CYS114 2.3 6.3 1.0
S3 S:SF41001 2.3 6.8 1.0
S4 S:SF41001 2.3 6.0 1.0
S1 S:SF41001 2.3 5.9 1.0
FE3 S:SF41001 2.6 5.5 1.0
FE1 S:SF41001 2.7 5.6 1.0
FE4 S:SF41001 2.7 6.0 1.0
CB S:CYS114 3.3 5.9 1.0
S2 S:SF41001 3.9 5.7 1.0
O S:HOH5033 4.0 6.7 1.0
O S:HOH5026 4.0 6.9 1.0
N S:CYS114 4.0 5.5 1.0
O S:HOH5006 4.2 6.3 1.0
CA S:CYS114 4.2 5.7 1.0
SG S:CYS150 4.5 5.4 1.0
SG S:CYS20 4.7 6.3 1.0
SG S:CYS17 4.9 5.9 1.0
N S:CYS17 4.9 5.7 1.0
CA S:GLU16 4.9 6.6 1.0

Iron binding site 3 out of 12 in 1wuk

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Iron binding site 3 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

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

b:5.5
occ:1.00
 FE3 S:SF41001 0.0 5.5 1.0
S2 S:SF41001 2.3 5.7 1.0
SG S:CYS150 2.3 5.4 1.0
S1 S:SF41001 2.3 5.9 1.0
S4 S:SF41001 2.3 6.0 1.0
FE2 S:SF41001 2.6 6.0 1.0
FE1 S:SF41001 2.7 5.6 1.0
FE4 S:SF41001 2.8 6.0 1.0
CB S:CYS150 3.4 5.6 1.0
CA S:CYS150 3.4 4.8 1.0
C S:CYS150 3.8 4.8 1.0
S3 S:SF41001 3.9 6.8 1.0
O S:HOH5026 3.9 6.9 1.0
CG L:ARG79 4.1 5.5 1.0
O S:CYS150 4.2 5.3 1.0
N S:PRO151 4.4 4.8 1.0
SG S:CYS114 4.4 6.3 1.0
ND1 L:HIS235 4.6 7.2 1.0
SG S:CYS17 4.6 5.9 1.0
CE1 L:HIS235 4.7 3.5 1.0
CA S:PRO151 4.7 5.1 1.0
NE L:ARG79 4.7 5.4 1.0
O S:GLY149 4.7 5.3 1.0
SG S:CYS20 4.7 6.3 1.0
N S:CYS150 4.8 5.0 1.0

Iron binding site 4 out of 12 in 1wuk

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Iron binding site 4 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

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

b:6.0
occ:1.00
 FE4 S:SF41001 0.0 6.0 1.0
SG S:CYS20 2.2 6.3 1.0
S1 S:SF41001 2.3 5.9 1.0
S2 S:SF41001 2.3 5.7 1.0
S3 S:SF41001 2.3 6.8 1.0
FE1 S:SF41001 2.7 5.6 1.0
FE2 S:SF41001 2.7 6.0 1.0
FE3 S:SF41001 2.8 5.5 1.0
CB S:CYS20 3.5 5.9 1.0
N S:CYS20 3.6 5.2 1.0
S4 S:SF41001 3.9 6.0 1.0
O S:HOH5033 4.0 6.7 1.0
CA S:CYS20 4.0 5.5 1.0
CA S:PRO151 4.4 5.1 1.0
CB S:PRO151 4.4 5.3 1.0
C S:GLY19 4.5 5.1 1.0
CA S:GLY112 4.6 5.5 1.0
SG S:CYS17 4.7 5.9 1.0
OE1 S:GLU75 4.7 9.3 1.0
CA S:CYS150 4.8 4.8 1.0
O S:GLY149 4.8 5.3 1.0
N S:PRO151 4.8 4.8 1.0
CA S:GLY19 4.9 5.7 1.0
SG S:CYS150 4.9 5.4 1.0
SG S:CYS114 4.9 6.3 1.0
N S:GLY19 4.9 5.6 1.0

Iron binding site 5 out of 12 in 1wuk

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Iron binding site 5 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:7.0
occ:1.00
 FE1 S:SF41002 0.0 7.0 1.0
ND1 S:HIS188 2.1 7.5 1.0
S3 S:SF41002 2.3 7.0 1.0
S4 S:SF41002 2.3 6.8 1.0
S2 S:SF41002 2.3 7.3 1.0
FE3 S:SF41002 2.7 6.8 1.0
FE4 S:SF41002 2.7 6.8 1.0
FE2 S:SF41002 2.7 6.4 1.0
CE1 S:HIS188 3.0 9.2 1.0
CG S:HIS188 3.1 7.2 1.0
CB S:HIS188 3.6 7.8 1.0
S1 S:SF41002 3.9 6.7 1.0
CA S:HIS188 3.9 6.8 1.0
NE2 S:HIS188 4.1 9.2 1.0
CD2 S:HIS188 4.2 8.7 1.0
CD S:PRO225 4.3 7.4 1.0
CG S:PRO225 4.3 9.1 1.0
CB S:CYS191 4.4 7.5 1.0
O S:HIS188 4.5 7.5 1.0
SG S:CYS191 4.6 7.0 1.0
SG S:CYS216 4.6 7.2 1.0
C S:HIS188 4.7 7.0 1.0
SG S:CYS222 4.7 6.2 1.0
CD2 S:PHE197 4.7 10.5 1.0
N S:PRO225 4.9 6.6 1.0
CA S:GLY224 5.0 6.7 1.0

Iron binding site 6 out of 12 in 1wuk

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Iron binding site 6 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

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

b:6.4
occ:1.00
 FE2 S:SF41002 0.0 6.4 1.0
S4 S:SF41002 2.3 6.8 1.0
SG S:CYS222 2.3 6.2 1.0
S3 S:SF41002 2.3 7.0 1.0
S1 S:SF41002 2.3 6.7 1.0
FE1 S:SF41002 2.7 7.0 1.0
FE3 S:SF41002 2.7 6.8 1.0
FE4 S:SF41002 2.8 6.8 1.0
CB S:CYS222 3.2 6.0 1.0
S2 S:SF41002 3.9 7.3 1.0
CG2 S:VAL243 4.4 7.4 1.0
N S:GLY224 4.5 6.5 1.0
CA S:CYS222 4.6 5.9 1.0
CA S:GLY224 4.6 6.7 1.0
ND1 S:HIS188 4.6 7.5 1.0
CD S:PRO225 4.7 7.4 1.0
SG S:CYS216 4.7 7.2 1.0
SG S:CYS191 4.8 7.0 1.0
N S:TYR218 4.8 6.6 1.0
N S:LEU217 4.9 6.5 1.0
C S:CYS222 4.9 5.7 1.0
CB S:LEU217 4.9 6.2 1.0

Iron binding site 7 out of 12 in 1wuk

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Iron binding site 7 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

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

b:6.8
occ:1.00
 FE3 S:SF41002 0.0 6.8 1.0
S1 S:SF41002 2.3 6.7 1.0
SG S:CYS191 2.3 7.0 1.0
S2 S:SF41002 2.3 7.3 1.0
S4 S:SF41002 2.3 6.8 1.0
FE1 S:SF41002 2.7 7.0 1.0
FE2 S:SF41002 2.7 6.4 1.0
FE4 S:SF41002 2.7 6.8 1.0
CB S:CYS191 3.1 7.5 1.0
S3 S:SF41002 3.9 7.0 1.0
CB S:ARG193 4.0 7.7 1.0
CG1 S:VAL243 4.3 7.3 1.0
ND1 S:HIS188 4.5 7.5 1.0
CA S:CYS191 4.6 7.0 1.0
CG2 S:VAL243 4.6 7.4 1.0
N S:ARG193 4.6 7.7 1.0
CA S:ARG193 4.6 7.8 1.0
CG S:ARG193 4.6 7.9 1.0
C S:ARG193 4.7 8.2 1.0
N S:LEU194 4.7 8.4 1.0
SG S:CYS222 4.8 6.2 1.0
CD S:ARG193 4.9 7.4 1.0
SG S:CYS216 5.0 7.2 1.0
CB S:VAL243 5.0 6.1 1.0
C S:CYS191 5.0 7.3 1.0

Iron binding site 8 out of 12 in 1wuk

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Iron binding site 8 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

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

b:6.8
occ:1.00
 FE4 S:SF41002 0.0 6.8 1.0
S2 S:SF41002 2.3 7.3 1.0
SG S:CYS216 2.3 7.2 1.0
S1 S:SF41002 2.3 6.7 1.0
S3 S:SF41002 2.3 7.0 1.0
FE1 S:SF41002 2.7 7.0 1.0
FE3 S:SF41002 2.7 6.8 1.0
FE2 S:SF41002 2.8 6.4 1.0
CB S:CYS216 3.4 7.8 1.0
N S:LEU217 3.8 6.5 1.0
CA S:CYS216 3.9 7.3 1.0
S4 S:SF41002 4.0 6.8 1.0
N S:TYR218 4.2 6.6 1.0
C S:CYS216 4.3 6.8 1.0
ND1 S:HIS188 4.4 7.5 1.0
CB S:PHE197 4.4 9.4 1.0
CD2 S:PHE197 4.4 10.5 1.0
CB S:ARG193 4.5 7.7 1.0
CB S:TYR218 4.7 7.8 1.0
CE1 S:HIS188 4.7 9.2 1.0
CA S:LEU217 4.8 6.5 1.0
C S:LEU217 4.8 6.7 1.0
CG S:PHE197 4.8 9.8 1.0
O S:ARG193 4.9 9.4 1.0
SG S:CYS222 4.9 6.2 1.0
SG S:CYS191 4.9 7.0 1.0
CA S:TYR218 4.9 7.2 1.0
CB S:CYS222 5.0 6.0 1.0

Iron binding site 9 out of 12 in 1wuk

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Iron binding site 9 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:5.7
occ:1.00
 FE1 S:F3S1003 0.0 5.7 1.0
S1 S:F3S1003 2.2 6.5 1.0
S2 S:F3S1003 2.3 5.9 1.0
S3 S:F3S1003 2.3 5.8 1.0
SG S:CYS249 2.3 5.8 1.0
FE4 S:F3S1003 2.7 5.5 1.0
FE3 S:F3S1003 2.7 6.0 1.0
CB S:CYS249 3.3 6.1 1.0
CA S:CYS249 3.7 5.4 1.0
S4 S:F3S1003 4.0 6.1 1.0
N S:ILE250 4.1 5.3 1.0
N S:GLY251 4.2 5.5 1.0
C S:CYS249 4.3 5.4 1.0
N S:CYS252 4.5 5.6 1.0
CG2 S:THR227 4.6 7.5 1.0
CG2 S:VAL187 4.7 6.9 1.0
CA S:GLY251 4.8 5.6 1.0
SG S:CYS231 4.8 6.3 1.0
SG S:CYS252 4.8 5.8 1.0
NE2 L:GLN237 4.8 6.2 1.0
N S:CYS249 5.0 5.7 1.0

Iron binding site 10 out of 12 in 1wuk

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Iron binding site 10 out of 12 in the High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

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

b:6.0
occ:1.00
 FE3 S:F3S1003 0.0 6.0 1.0
S1 S:F3S1003 2.2 6.5 1.0
S4 S:F3S1003 2.3 6.1 1.0
SG S:CYS231 2.3 6.3 1.0
S3 S:F3S1003 2.3 5.8 1.0
FE1 S:F3S1003 2.7 5.7 1.0
FE4 S:F3S1003 2.7 5.5 1.0
CB S:CYS231 3.3 6.6 1.0
OD1 S:ASN229 3.9 8.1 1.0
S2 S:F3S1003 4.0 5.9 1.0
CE2 S:PHE236 4.4 6.8 1.0
O S:HOH5024 4.4 7.7 1.0
CG S:ASN229 4.5 6.0 1.0
CZ S:PHE236 4.5 6.7 1.0
CG2 S:VAL187 4.6 6.9 1.0
CB S:ASN229 4.6 6.1 1.0
CA S:CYS231 4.8 5.9 1.0
CD S:PRO242 4.8 6.3 1.0
SG S:CYS252 4.8 5.8 1.0
SG S:CYS249 4.8 5.8 1.0
CG S:PRO242 4.8 6.1 1.0

Reference:

H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, Y.Higuchi. Activation Process of [Nife] Hydrogenase Elucidated By High-Resolution X-Ray Analyses: Conversion of the Ready to the Unready State Structure V. 13 1635 2005.
ISSN: ISSN 0969-2126
PubMed: 16271886
DOI: 10.1016/J.STR.2005.07.018
Page generated: Sat Aug 3 16:37:37 2024

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