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Iron in PDB 1h2r: Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution

Enzymatic activity of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution

All present enzymatic activity of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution:
1.12.2.1;

Protein crystallography data

The structure of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution, PDB code: 1h2r was solved by Y.Higuchi, H.Ogata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.440, 126.860, 66.680, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.4

Other elements in 1h2r:

The structure of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution 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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution (pdb code 1h2r). 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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution, PDB code: 1h2r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1h2r

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Iron binding site 1 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:10.2
occ:1.00
 FE1 S:SF41001 0.0 10.2 1.0
S4 S:SF41001 2.3 10.9 1.0
SG S:CYS17 2.3 10.4 1.0
S3 S:SF41001 2.3 12.6 1.0
S2 S:SF41001 2.3 11.3 1.0
FE3 S:SF41001 2.7 11.3 1.0
FE2 S:SF41001 2.7 11.0 1.0
FE4 S:SF41001 2.7 11.6 1.0
CB S:CYS17 3.4 11.9 1.0
N S:CYS17 3.8 10.7 1.0
S1 S:SF41001 3.9 11.2 1.0
CA S:CYS17 4.1 10.6 1.0
CE1 L:HIS235 4.2 8.3 1.0
N S:GLY19 4.3 9.8 1.0
O L:HOH3009 4.5 9.5 1.0
CG L:ARG79 4.6 15.9 1.0
CA S:GLY19 4.6 9.5 1.0
N S:THR18 4.6 10.8 1.0
C S:CYS17 4.6 10.9 1.0
N S:CYS20 4.7 10.2 1.0
SG S:CYS150 4.8 10.4 1.0
SG S:CYS114 4.8 10.3 1.0
SG S:CYS20 4.8 12.3 1.0
CD L:ARG79 4.9 19.3 1.0
C S:GLU16 4.9 11.0 1.0
ND1 L:HIS235 4.9 11.8 1.0
O L:ARG79 5.0 10.3 1.0

Iron binding site 2 out of 12 in 1h2r

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Iron binding site 2 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:11.0
occ:1.00
 FE2 S:SF41001 0.0 11.0 1.0
S4 S:SF41001 2.3 10.9 1.0
SG S:CYS114 2.3 10.3 1.0
S3 S:SF41001 2.3 12.6 1.0
S1 S:SF41001 2.3 11.2 1.0
FE3 S:SF41001 2.6 11.3 1.0
FE1 S:SF41001 2.7 10.2 1.0
FE4 S:SF41001 2.8 11.6 1.0
CB S:CYS114 3.2 9.8 1.0
S2 S:SF41001 3.9 11.3 1.0
O L:HOH3009 4.1 9.5 1.0
O S:HOH3425 4.1 10.4 1.0
N S:CYS114 4.1 10.4 1.0
O S:HOH3080 4.1 10.5 1.0
CA S:CYS114 4.2 11.0 1.0
O S:HOH3034 4.3 87.8 1.0
SG S:CYS150 4.5 10.4 1.0
SG S:CYS20 4.8 12.3 1.0
SG S:CYS17 4.9 10.4 1.0
N S:CYS17 4.9 10.7 1.0
CA S:GLU16 5.0 11.1 1.0

Iron binding site 3 out of 12 in 1h2r

Go back to Iron Binding Sites List in 1h2r
Iron binding site 3 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:11.3
occ:1.00
 FE3 S:SF41001 0.0 11.3 1.0
S4 S:SF41001 2.3 10.9 1.0
SG S:CYS150 2.3 10.4 1.0
S2 S:SF41001 2.3 11.3 1.0
S1 S:SF41001 2.3 11.2 1.0
FE2 S:SF41001 2.6 11.0 1.0
FE1 S:SF41001 2.7 10.2 1.0
FE4 S:SF41001 2.7 11.6 1.0
CB S:CYS150 3.5 9.6 1.0
CA S:CYS150 3.6 10.6 1.0
S3 S:SF41001 3.9 12.6 1.0
C S:CYS150 3.9 10.1 1.0
CD L:ARG79 4.0 19.3 1.0
CG L:ARG79 4.0 15.9 1.0
O S:HOH3425 4.0 10.4 1.0
O S:CYS150 4.3 9.9 1.0
N S:PRO151 4.4 9.9 1.0
SG S:CYS114 4.4 10.3 1.0
CE1 L:HIS235 4.6 8.3 1.0
SG S:CYS17 4.6 10.4 1.0
ND1 L:HIS235 4.7 11.8 1.0
O S:GLY149 4.7 8.6 1.0
CA S:PRO151 4.7 9.4 1.0
SG S:CYS20 4.8 12.3 1.0
N S:CYS150 4.9 9.5 1.0

Iron binding site 4 out of 12 in 1h2r

Go back to Iron Binding Sites List in 1h2r
Iron binding site 4 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:11.6
occ:1.00
 FE4 S:SF41001 0.0 11.6 1.0
SG S:CYS20 2.3 12.3 1.0
S2 S:SF41001 2.3 11.3 1.0
S1 S:SF41001 2.3 11.2 1.0
S3 S:SF41001 2.4 12.6 1.0
FE1 S:SF41001 2.7 10.2 1.0
FE3 S:SF41001 2.7 11.3 1.0
FE2 S:SF41001 2.8 11.0 1.0
CB S:CYS20 3.5 10.4 1.0
N S:CYS20 3.8 10.2 1.0
O S:HOH3080 4.0 10.5 1.0
S4 S:SF41001 4.0 10.9 1.0
CA S:CYS20 4.2 11.2 1.0
CA S:PRO151 4.4 9.4 1.0
CB S:PRO151 4.4 9.0 1.0
CA S:GLY112 4.6 10.1 1.0
C S:GLY19 4.6 9.3 1.0
OE2 S:GLU75 4.7 14.6 1.0
SG S:CYS17 4.7 10.4 1.0
O S:GLY149 4.8 8.6 1.0
CA S:CYS150 4.8 10.6 1.0
N S:PRO151 4.8 9.9 1.0
SG S:CYS150 4.9 10.4 1.0
SG S:CYS114 5.0 10.3 1.0
CA S:GLY19 5.0 9.5 1.0
N S:GLY19 5.0 9.8 1.0

Iron binding site 5 out of 12 in 1h2r

Go back to Iron Binding Sites List in 1h2r
Iron binding site 5 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:12.8
occ:1.00
 FE1 S:SF41002 0.0 12.8 1.0
ND1 S:HIS188 2.1 12.7 1.0
S4 S:SF41002 2.3 13.3 1.0
S3 S:SF41002 2.3 13.0 1.0
S2 S:SF41002 2.3 14.0 1.0
FE2 S:SF41002 2.7 12.1 1.0
FE4 S:SF41002 2.7 13.3 1.0
FE3 S:SF41002 2.7 11.9 1.0
CE1 S:HIS188 2.9 14.6 1.0
CG S:HIS188 3.2 13.2 1.0
CB S:HIS188 3.7 12.0 1.0
S1 S:SF41002 3.9 13.3 1.0
CA S:HIS188 3.9 13.4 1.0
NE2 S:HIS188 4.1 13.4 1.0
CD2 S:HIS188 4.3 12.6 1.0
CD S:PRO225 4.3 12.4 1.0
CG S:PRO225 4.3 13.1 1.0
O S:HIS188 4.5 13.9 1.0
CB S:CYS191 4.5 14.1 1.0
O S:HOH3338 4.7 80.0 1.0
C S:HIS188 4.7 13.1 1.0
SG S:CYS191 4.7 14.2 1.0
SG S:CYS216 4.7 13.9 1.0
CD2 S:PHE197 4.8 17.8 1.0
SG S:CYS222 4.8 11.6 1.0
O S:HOH3012 4.9 96.2 1.0
N S:PRO225 4.9 12.2 1.0
CA S:GLY224 5.0 11.1 1.0

Iron binding site 6 out of 12 in 1h2r

Go back to Iron Binding Sites List in 1h2r
Iron binding site 6 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:12.1
occ:1.00
 FE2 S:SF41002 0.0 12.1 1.0
S3 S:SF41002 2.3 13.0 1.0
S4 S:SF41002 2.3 13.3 1.0
SG S:CYS222 2.3 11.6 1.0
S1 S:SF41002 2.4 13.3 1.0
FE1 S:SF41002 2.7 12.8 1.0
FE3 S:SF41002 2.7 11.9 1.0
FE4 S:SF41002 2.7 13.3 1.0
O S:HOH3012 3.1 96.2 1.0
CB S:CYS222 3.3 11.4 1.0
S2 S:SF41002 3.9 14.0 1.0
CA S:GLY224 4.6 11.1 1.0
N S:GLY224 4.6 12.4 1.0
ND1 S:HIS188 4.6 12.7 1.0
CD S:PRO225 4.7 12.4 1.0
CG1 S:VAL243 4.7 19.0 1.0
CA S:CYS222 4.7 11.0 1.0
SG S:CYS216 4.7 13.9 1.0
O S:HOH3338 4.8 80.0 1.0
SG S:CYS191 4.8 14.2 1.0
N S:LEU217 4.8 13.8 1.0
N S:TYR218 4.9 13.3 1.0
C S:CYS222 5.0 10.5 1.0
CB S:LEU217 5.0 13.2 1.0
C S:LEU217 5.0 13.9 1.0

Iron binding site 7 out of 12 in 1h2r

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Iron binding site 7 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:11.9
occ:1.00
 FE3 S:SF41002 0.0 11.9 1.0
S1 S:SF41002 2.3 13.3 1.0
SG S:CYS191 2.3 14.2 1.0
S2 S:SF41002 2.3 14.0 1.0
S4 S:SF41002 2.3 13.3 1.0
FE2 S:SF41002 2.7 12.1 1.0
FE1 S:SF41002 2.7 12.8 1.0
FE4 S:SF41002 2.8 13.3 1.0
CB S:CYS191 3.1 14.1 1.0
O S:HOH3338 3.7 80.0 1.0
S3 S:SF41002 4.0 13.0 1.0
CB S:ARG193 4.1 15.7 1.0
O S:HOH3012 4.2 96.2 1.0
ND1 S:HIS188 4.5 12.7 1.0
CG2 S:VAL243 4.5 21.1 1.0
CA S:CYS191 4.6 14.7 1.0
C S:ARG193 4.7 17.1 1.0
CA S:ARG193 4.7 16.3 1.0
N S:ARG193 4.7 15.7 1.0
N S:LEU194 4.7 18.1 1.0
CG1 S:VAL243 4.8 19.0 1.0
CG S:ARG193 4.8 14.1 1.0
SG S:CYS222 4.8 11.6 1.0
CH2 S:TRP241 4.9 20.9 1.0
CD S:ARG193 5.0 14.3 1.0
SG S:CYS216 5.0 13.9 1.0

Iron binding site 8 out of 12 in 1h2r

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Iron binding site 8 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:13.3
occ:1.00
 FE4 S:SF41002 0.0 13.3 1.0
S2 S:SF41002 2.3 14.0 1.0
SG S:CYS216 2.3 13.9 1.0
S1 S:SF41002 2.3 13.3 1.0
S3 S:SF41002 2.4 13.0 1.0
FE1 S:SF41002 2.7 12.8 1.0
FE2 S:SF41002 2.7 12.1 1.0
FE3 S:SF41002 2.8 11.9 1.0
CB S:CYS216 3.4 13.1 1.0
N S:LEU217 3.8 13.8 1.0
CA S:CYS216 3.9 14.2 1.0
S4 S:SF41002 3.9 13.3 1.0
N S:TYR218 4.2 13.3 1.0
C S:CYS216 4.3 13.8 1.0
CB S:PHE197 4.4 20.3 1.0
ND1 S:HIS188 4.5 12.7 1.0
CD2 S:PHE197 4.5 17.8 1.0
CE1 S:HIS188 4.7 14.6 1.0
CB S:ARG193 4.7 15.7 1.0
CA S:LEU217 4.7 13.7 1.0
CB S:TYR218 4.7 14.9 1.0
C S:LEU217 4.8 13.9 1.0
CG S:PHE197 4.8 17.9 1.0
SG S:CYS222 4.9 11.6 1.0
O S:ARG193 4.9 16.3 1.0
SG S:CYS191 4.9 14.2 1.0
CA S:TYR218 4.9 14.7 1.0

Iron binding site 9 out of 12 in 1h2r

Go back to Iron Binding Sites List in 1h2r
Iron binding site 9 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:11.2
occ:1.00
 FE1 S:F3S1003 0.0 11.2 1.0
S3 S:F3S1003 2.3 12.6 1.0
S1 S:F3S1003 2.3 12.8 1.0
S2 S:F3S1003 2.3 12.3 1.0
SG S:CYS249 2.4 11.5 1.0
FE4 S:F3S1003 2.7 11.1 1.0
FE3 S:F3S1003 2.7 11.8 1.0
CB S:CYS249 3.4 11.5 1.0
O S:HOH3184 3.4 0.0 1.0
CA S:CYS249 3.8 10.9 1.0
S4 S:F3S1003 4.0 10.8 1.0
N S:ILE250 4.1 10.8 1.0
N S:GLY251 4.2 10.4 1.0
C S:CYS249 4.3 10.7 1.0
N S:CYS252 4.6 11.7 1.0
O S:HOH3067 4.7 58.8 1.0
CA S:GLY251 4.8 10.6 1.0
SG S:CYS252 4.8 12.0 1.0
CG2 S:THR227 4.8 10.9 1.0
SG S:CYS231 4.9 13.1 1.0
O S:HOH3237 4.9 98.9 1.0
NE2 L:GLN237 4.9 12.0 1.0
NE1 S:TRP241 5.0 26.0 1.0

Iron binding site 10 out of 12 in 1h2r

Go back to Iron Binding Sites List in 1h2r
Iron binding site 10 out of 12 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:11.8
occ:1.00
 FE3 S:F3S1003 0.0 11.8 1.0
S1 S:F3S1003 2.3 12.8 1.0
S4 S:F3S1003 2.3 10.8 1.0
SG S:CYS231 2.3 13.1 1.0
S3 S:F3S1003 2.4 12.6 1.0
FE4 S:F3S1003 2.7 11.1 1.0
FE1 S:F3S1003 2.7 11.2 1.0
CB S:CYS231 3.4 12.9 1.0
O S:HOH3067 3.5 58.8 1.0
O S:HOH3184 3.8 0.0 1.0
OD1 S:ASN229 4.0 13.5 1.0
S2 S:F3S1003 4.0 12.3 1.0
NE1 S:TRP241 4.0 26.0 1.0
O S:HOH3237 4.2 98.9 1.0
O S:HOH3043 4.4 9.7 1.0
CD1 S:TRP241 4.4 25.6 1.0
CG S:ASN229 4.5 12.3 1.0
CE2 S:PHE236 4.6 12.0 1.0
CB S:ASN229 4.6 10.7 1.0
CZ S:PHE236 4.7 13.5 1.0
SG S:CYS252 4.8 12.0 1.0
CA S:CYS231 4.8 13.7 1.0
CG S:PRO242 4.8 13.9 1.0
SG S:CYS249 4.9 11.5 1.0
CD S:PRO242 5.0 14.2 1.0

Reference:

Y.Higuchi, H.Ogata, K.Miki, N.Yasuoka, T.Yagi. Removal of the Bridging Ligand Atom at the Ni-Fe Active Site of [Nife] Hydrogenase Upon Reduction with H2, As Revealed By X-Ray Structure Analysis at 1.4 A Resolution. Structure Fold.Des. V. 7 549 1999.
ISSN: ISSN 0969-2126
PubMed: 10378274
DOI: 10.1016/S0969-2126(99)80071-9
Page generated: Sat Aug 3 06:52:26 2024

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