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Iron in PDB 1wuj: Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wuj 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 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.162, 125.924, 66.441, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 16.2

Other elements in 1wuj:

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

Iron binding site 1 out of 12 in 1wuj

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Iron binding site 1 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:9.0
occ:1.00
 FE1 S:SF41001 0.0 9.0 1.0
S4 S:SF41001 2.3 9.1 1.0
SG S:CYS17 2.3 9.8 1.0
S2 S:SF41001 2.3 9.0 1.0
S3 S:SF41001 2.3 9.9 1.0
FE2 S:SF41001 2.7 9.2 1.0
FE3 S:SF41001 2.7 8.9 1.0
FE4 S:SF41001 2.7 9.5 1.0
CB S:CYS17 3.4 9.5 1.0
N S:CYS17 3.8 8.4 1.0
S1 S:SF41001 3.9 9.2 1.0
CA S:CYS17 4.1 9.3 1.0
CE1 L:HIS235 4.2 6.4 1.0
N S:GLY19 4.2 8.3 1.0
CA S:GLY19 4.5 8.3 1.0
O S:HOH5007 4.5 9.0 1.0
C S:CYS17 4.5 10.0 1.0
N S:CYS20 4.6 9.4 1.0
N S:THR18 4.6 9.6 1.0
CG L:ARG79 4.7 8.5 1.0
SG S:CYS114 4.7 10.0 1.0
SG S:CYS150 4.7 9.3 1.0
ND1 L:HIS235 4.8 10.8 1.0
SG S:CYS20 4.8 9.9 1.0
C S:GLU16 4.9 9.3 1.0
C S:GLY19 4.9 8.6 1.0
O L:ARG79 5.0 8.5 1.0

Iron binding site 2 out of 12 in 1wuj

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Iron binding site 2 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:9.2
occ:1.00
 FE2 S:SF41001 0.0 9.2 1.0
S3 S:SF41001 2.3 9.9 1.0
S4 S:SF41001 2.3 9.1 1.0
S1 S:SF41001 2.3 9.2 1.0
SG S:CYS114 2.3 10.0 1.0
FE3 S:SF41001 2.6 8.9 1.0
FE1 S:SF41001 2.7 9.0 1.0
FE4 S:SF41001 2.7 9.5 1.0
CB S:CYS114 3.2 9.4 1.0
S2 S:SF41001 3.9 9.0 1.0
O S:HOH5060 4.0 10.5 1.0
O S:HOH5038 4.0 8.4 1.0
N S:CYS114 4.0 8.5 1.0
O S:HOH5007 4.2 9.0 1.0
CA S:CYS114 4.2 8.5 1.0
SG S:CYS150 4.5 9.3 1.0
SG S:CYS20 4.7 9.9 1.0
SG S:CYS17 4.9 9.8 1.0
N S:CYS17 4.9 8.4 1.0
CA S:GLU16 4.9 9.7 1.0

Iron binding site 3 out of 12 in 1wuj

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Iron binding site 3 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:8.9
occ:1.00
 FE3 S:SF41001 0.0 8.9 1.0
S2 S:SF41001 2.3 9.0 1.0
SG S:CYS150 2.3 9.3 1.0
S1 S:SF41001 2.3 9.2 1.0
S4 S:SF41001 2.4 9.1 1.0
FE2 S:SF41001 2.6 9.2 1.0
FE1 S:SF41001 2.7 9.0 1.0
FE4 S:SF41001 2.7 9.5 1.0
CB S:CYS150 3.4 9.2 1.0
CA S:CYS150 3.5 7.5 1.0
C S:CYS150 3.9 7.8 1.0
S3 S:SF41001 3.9 9.9 1.0
O S:HOH5060 3.9 10.5 1.0
CG L:ARG79 4.2 8.5 1.0
O S:CYS150 4.2 8.3 1.0
N S:PRO151 4.3 8.1 1.0
SG S:CYS114 4.4 10.0 1.0
ND1 L:HIS235 4.6 10.8 1.0
CE1 L:HIS235 4.6 6.4 1.0
SG S:CYS17 4.6 9.8 1.0
CA S:PRO151 4.7 7.9 1.0
NE L:ARG79 4.7 9.2 1.0
O S:GLY149 4.7 8.4 1.0
SG S:CYS20 4.7 9.9 1.0
N S:CYS150 4.8 8.6 1.0

Iron binding site 4 out of 12 in 1wuj

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Iron binding site 4 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:9.5
occ:1.00
 FE4 S:SF41001 0.0 9.5 1.0
SG S:CYS20 2.3 9.9 1.0
S1 S:SF41001 2.3 9.2 1.0
S3 S:SF41001 2.3 9.9 1.0
S2 S:SF41001 2.3 9.0 1.0
FE1 S:SF41001 2.7 9.0 1.0
FE2 S:SF41001 2.7 9.2 1.0
FE3 S:SF41001 2.7 8.9 1.0
CB S:CYS20 3.5 10.1 1.0
N S:CYS20 3.7 9.4 1.0
O S:HOH5038 3.9 8.4 1.0
S4 S:SF41001 4.0 9.1 1.0
CA S:CYS20 4.0 7.7 1.0
CB S:PRO151 4.4 8.7 1.0
CA S:PRO151 4.4 7.9 1.0
C S:GLY19 4.5 8.6 1.0
CA S:GLY112 4.6 8.1 1.0
OE1 S:GLU75 4.6 10.9 1.0
SG S:CYS17 4.7 9.8 1.0
O S:GLY149 4.8 8.4 1.0
CA S:CYS150 4.8 7.5 1.0
N S:PRO151 4.8 8.1 1.0
CA S:GLY19 4.9 8.3 1.0
SG S:CYS150 4.9 9.3 1.0
SG S:CYS114 4.9 10.0 1.0
N S:GLY19 4.9 8.3 1.0
CG S:GLU75 5.0 10.3 1.0

Iron binding site 5 out of 12 in 1wuj

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Iron binding site 5 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:10.7
occ:1.00
 FE1 S:SF41002 0.0 10.7 1.0
ND1 S:HIS188 2.1 10.5 1.0
S2 S:SF41002 2.3 10.9 1.0
S4 S:SF41002 2.3 10.3 1.0
S3 S:SF41002 2.3 10.4 1.0
FE3 S:SF41002 2.7 10.3 1.0
FE4 S:SF41002 2.7 10.4 1.0
FE2 S:SF41002 2.7 9.8 1.0
CE1 S:HIS188 3.0 14.5 1.0
CG S:HIS188 3.1 11.6 1.0
CB S:HIS188 3.6 11.0 1.0
S1 S:SF41002 3.9 10.1 1.0
CA S:HIS188 3.9 9.4 1.0
NE2 S:HIS188 4.1 13.0 1.0
CD2 S:HIS188 4.2 11.9 1.0
CD S:PRO225 4.3 10.8 1.0
CG S:PRO225 4.4 12.2 1.0
CB S:CYS191 4.5 12.1 1.0
O S:HIS188 4.5 10.7 1.0
SG S:CYS191 4.6 10.7 1.0
SG S:CYS216 4.6 11.2 1.0
C S:HIS188 4.6 10.2 1.0
CD2 S:PHE197 4.7 14.3 1.0
SG S:CYS222 4.7 10.1 1.0
N S:PRO225 4.8 10.7 1.0
CA S:GLY224 5.0 9.9 1.0
CG S:PHE197 5.0 12.7 1.0

Iron binding site 6 out of 12 in 1wuj

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Iron binding site 6 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:9.8
occ:1.00
 FE2 S:SF41002 0.0 9.8 1.0
SG S:CYS222 2.3 10.1 1.0
S4 S:SF41002 2.3 10.3 1.0
S1 S:SF41002 2.3 10.1 1.0
S3 S:SF41002 2.3 10.4 1.0
FE3 S:SF41002 2.7 10.3 1.0
FE1 S:SF41002 2.7 10.7 1.0
FE4 S:SF41002 2.8 10.4 1.0
CB S:CYS222 3.1 9.8 1.0
S2 S:SF41002 3.9 10.9 1.0
CG2 S:VAL243 4.3 11.2 1.0
CA S:CYS222 4.5 9.1 1.0
N S:GLY224 4.6 9.8 1.0
CA S:GLY224 4.6 9.9 1.0
CD S:PRO225 4.6 10.8 1.0
ND1 S:HIS188 4.7 10.5 1.0
SG S:CYS216 4.7 11.2 1.0
SG S:CYS191 4.8 10.7 1.0
CB S:LEU217 4.8 10.0 1.0
N S:TYR218 4.8 10.1 1.0
C S:CYS222 4.8 9.8 1.0
N S:LEU217 4.9 9.9 1.0
C S:LEU217 5.0 9.9 1.0

Iron binding site 7 out of 12 in 1wuj

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Iron binding site 7 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:10.3
occ:1.00
 FE3 S:SF41002 0.0 10.3 1.0
S1 S:SF41002 2.3 10.1 1.0
S2 S:SF41002 2.3 10.9 1.0
SG S:CYS191 2.3 10.7 1.0
S4 S:SF41002 2.3 10.3 1.0
FE1 S:SF41002 2.7 10.7 1.0
FE2 S:SF41002 2.7 9.8 1.0
FE4 S:SF41002 2.7 10.4 1.0
CB S:CYS191 3.1 12.1 1.0
S3 S:SF41002 3.9 10.4 1.0
CB S:ARG193 4.0 11.7 1.0
CG1 S:VAL243 4.3 10.0 1.0
ND1 S:HIS188 4.5 10.5 1.0
CA S:CYS191 4.6 9.8 1.0
CG2 S:VAL243 4.6 11.2 1.0
N S:ARG193 4.6 11.7 1.0
CA S:ARG193 4.6 11.6 1.0
C S:ARG193 4.7 10.3 1.0
CG S:ARG193 4.7 12.0 1.0
N S:LEU194 4.7 11.8 1.0
SG S:CYS222 4.8 10.1 1.0
SG S:CYS216 4.9 11.2 1.0
CB S:VAL243 5.0 9.0 1.0
CD S:ARG193 5.0 10.4 1.0

Iron binding site 8 out of 12 in 1wuj

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Iron binding site 8 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:10.4
occ:1.00
 FE4 S:SF41002 0.0 10.4 1.0
S2 S:SF41002 2.3 10.9 1.0
SG S:CYS216 2.3 11.2 1.0
S1 S:SF41002 2.3 10.1 1.0
S3 S:SF41002 2.4 10.4 1.0
FE1 S:SF41002 2.7 10.7 1.0
FE3 S:SF41002 2.7 10.3 1.0
FE2 S:SF41002 2.8 9.8 1.0
CB S:CYS216 3.4 10.7 1.0
N S:LEU217 3.8 9.9 1.0
CA S:CYS216 3.9 9.7 1.0
S4 S:SF41002 3.9 10.3 1.0
N S:TYR218 4.2 10.1 1.0
C S:CYS216 4.3 10.3 1.0
CB S:PHE197 4.4 13.8 1.0
ND1 S:HIS188 4.4 10.5 1.0
CD2 S:PHE197 4.4 14.3 1.0
CB S:ARG193 4.5 11.7 1.0
CB S:TYR218 4.7 10.9 1.0
CE1 S:HIS188 4.7 14.5 1.0
CA S:LEU217 4.8 9.6 1.0
CG S:PHE197 4.8 12.7 1.0
O S:ARG193 4.8 12.6 1.0
SG S:CYS222 4.8 10.1 1.0
C S:LEU217 4.9 9.9 1.0
SG S:CYS191 4.9 10.7 1.0
CA S:TYR218 4.9 9.9 1.0
CB S:CYS222 4.9 9.8 1.0
C S:ARG193 5.0 10.3 1.0

Iron binding site 9 out of 12 in 1wuj

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Iron binding site 9 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:9.2
occ:1.00
 FE1 S:F3S1003 0.0 9.2 1.0
S1 S:F3S1003 2.2 9.8 1.0
S2 S:F3S1003 2.3 9.6 1.0
S3 S:F3S1003 2.3 9.4 1.0
SG S:CYS249 2.4 9.7 1.0
FE4 S:F3S1003 2.7 9.2 1.0
FE3 S:F3S1003 2.7 9.6 1.0
CB S:CYS249 3.2 9.1 1.0
CA S:CYS249 3.7 8.7 1.0
S4 S:F3S1003 3.9 9.5 1.0
N S:ILE250 4.1 8.7 1.0
N S:GLY251 4.2 8.3 1.0
C S:CYS249 4.3 8.6 1.0
N S:CYS252 4.5 7.9 1.0
CG2 S:THR227 4.6 9.6 1.0
CG2 S:VAL187 4.7 11.5 1.0
CA S:GLY251 4.8 9.5 1.0
SG S:CYS231 4.8 10.3 1.0
NE2 L:GLN237 4.8 9.8 1.0
SG S:CYS252 4.8 9.8 1.0
N S:CYS249 5.0 9.0 1.0

Iron binding site 10 out of 12 in 1wuj

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Iron binding site 10 out of 12 in the Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:9.6
occ:1.00
 FE3 S:F3S1003 0.0 9.6 1.0
S1 S:F3S1003 2.2 9.8 1.0
S4 S:F3S1003 2.3 9.5 1.0
SG S:CYS231 2.3 10.3 1.0
S3 S:F3S1003 2.3 9.4 1.0
FE4 S:F3S1003 2.7 9.2 1.0
FE1 S:F3S1003 2.7 9.2 1.0
CB S:CYS231 3.3 11.4 1.0
OD1 S:ASN229 3.9 12.4 1.0
S2 S:F3S1003 3.9 9.6 1.0
CE2 S:PHE236 4.3 10.5 1.0
O S:HOH5020 4.4 10.3 1.0
CG S:ASN229 4.5 8.7 1.0
CZ S:PHE236 4.5 9.6 1.0
CG2 S:VAL187 4.6 11.5 1.0
CB S:ASN229 4.7 8.6 1.0
CA S:CYS231 4.7 10.7 1.0
CD S:PRO242 4.8 9.4 1.0
SG S:CYS252 4.8 9.8 1.0
SG S:CYS249 4.8 9.7 1.0
CG S:PRO242 4.9 9.0 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 16:36:23 2024

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