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Iron in PDB 1h2a: Single Crystals of Hydrogenase From Desulfovibrio Vulgaris

Enzymatic activity of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris

All present enzymatic activity of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris:
1.18.99.1;

Protein crystallography data

The structure of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris, PDB code: 1h2a was solved by Y.Higuchi, N.Yasuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.500, 126.500, 66.510, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.8

Other elements in 1h2a:

The structure of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris 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 Single Crystals of Hydrogenase From Desulfovibrio Vulgaris (pdb code 1h2a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris, PDB code: 1h2a:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1h2a

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Iron binding site 1 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:7.6
occ:1.00
 FE1 S:SF41001 0.0 7.6 1.0
SG S:CYS17 2.2 11.4 1.0
S4 S:SF41001 2.2 7.8 1.0
S2 S:SF41001 2.3 9.4 1.0
S3 S:SF41001 2.3 8.8 1.0
FE3 S:SF41001 2.4 5.3 1.0
FE4 S:SF41001 2.5 13.4 1.0
FE2 S:SF41001 2.7 10.3 1.0
CB S:CYS17 3.7 6.9 1.0
S1 S:SF41001 3.8 10.8 1.0
CE1 L:HIS235 4.1 7.9 1.0
N S:CYS17 4.1 10.8 1.0
N S:GLY19 4.2 13.5 1.0
CA S:CYS17 4.4 12.6 1.0
CA S:GLY19 4.4 10.1 1.0
SG S:CYS150 4.5 10.7 1.0
N S:CYS20 4.6 9.2 1.0
SG S:CYS20 4.7 16.2 1.0
C S:CYS17 4.7 13.1 1.0
N S:THR18 4.7 13.8 1.0
SG S:CYS114 4.8 17.5 1.0
ND1 L:HIS235 4.8 8.3 1.0
O L:HOH3011 4.8 7.8 1.0
C S:GLY19 4.9 11.6 1.0

Iron binding site 2 out of 12 in 1h2a

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Iron binding site 2 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:10.3
occ:1.00
 FE2 S:SF41001 0.0 10.3 1.0
S1 S:SF41001 2.2 10.8 1.0
S4 S:SF41001 2.3 7.8 1.0
SG S:CYS114 2.4 17.5 1.0
S3 S:SF41001 2.4 8.8 1.0
FE3 S:SF41001 2.5 5.3 1.0
FE4 S:SF41001 2.5 13.4 1.0
FE1 S:SF41001 2.7 7.6 1.0
CB S:CYS114 3.4 14.1 1.0
S2 S:SF41001 3.9 9.4 1.0
O S:HOH3364 4.1 29.4 1.0
N S:CYS114 4.1 11.1 1.0
O L:HOH3011 4.3 7.8 1.0
CA S:CYS114 4.4 13.6 1.0
SG S:CYS150 4.4 10.7 1.0
SG S:CYS20 4.5 16.2 1.0
SG S:CYS17 4.6 11.4 1.0

Iron binding site 3 out of 12 in 1h2a

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Iron binding site 3 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:5.3
occ:1.00
 FE3 S:SF41001 0.0 5.3 1.0
S4 S:SF41001 2.2 7.8 1.0
S1 S:SF41001 2.3 10.8 1.0
S2 S:SF41001 2.3 9.4 1.0
SG S:CYS150 2.3 10.7 1.0
FE1 S:SF41001 2.4 7.6 1.0
FE2 S:SF41001 2.5 10.3 1.0
FE4 S:SF41001 2.6 13.4 1.0
CB S:CYS150 3.6 9.0 1.0
S3 S:SF41001 3.8 8.8 1.0
CA S:CYS150 3.8 9.1 1.0
C S:CYS150 4.1 13.0 1.0
SG S:CYS17 4.3 11.4 1.0
CD L:ARG79 4.4 6.1 1.0
SG S:CYS114 4.4 17.5 1.0
O S:CYS150 4.5 7.8 1.0
CE1 L:HIS235 4.5 7.9 1.0
N S:PRO151 4.6 10.9 1.0
ND1 L:HIS235 4.7 8.3 1.0
SG S:CYS20 4.7 16.2 1.0
CA S:PRO151 4.9 9.0 1.0

Iron binding site 4 out of 12 in 1h2a

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Iron binding site 4 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:13.4
occ:1.00
 FE4 S:SF41001 0.0 13.4 1.0
S3 S:SF41001 2.2 8.8 1.0
SG S:CYS20 2.3 16.2 1.0
S1 S:SF41001 2.3 10.8 1.0
S2 S:SF41001 2.4 9.4 1.0
FE2 S:SF41001 2.5 10.3 1.0
FE1 S:SF41001 2.5 7.6 1.0
FE3 S:SF41001 2.6 5.3 1.0
CB S:CYS20 3.7 15.8 1.0
S4 S:SF41001 3.8 7.8 1.0
N S:CYS20 3.9 9.2 1.0
O S:HOH3364 4.0 29.4 1.0
CA S:CYS20 4.3 13.6 1.0
CA S:PRO151 4.5 9.0 1.0
SG S:CYS17 4.5 11.4 1.0
C S:GLY19 4.6 11.6 1.0
SG S:CYS150 4.6 10.7 1.0
CB S:PRO151 4.7 7.9 1.0
CA S:GLY112 4.7 14.1 1.0
SG S:CYS114 4.8 17.5 1.0
OE2 S:GLU75 4.8 30.4 1.0
CA S:CYS150 4.8 9.1 1.0
N S:PRO151 4.9 10.9 1.0
CA S:GLY19 5.0 10.1 1.0
O S:GLY149 5.0 18.2 1.0
N S:GLY19 5.0 13.5 1.0

Iron binding site 5 out of 12 in 1h2a

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Iron binding site 5 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:18.4
occ:1.00
 FE1 S:SF41002 0.0 18.4 1.0
ND1 S:HIS188 2.0 20.5 1.0
S4 S:SF41002 2.3 19.0 1.0
S3 S:SF41002 2.3 18.9 1.0
S2 S:SF41002 2.4 18.2 1.0
FE2 S:SF41002 2.4 16.6 1.0
FE4 S:SF41002 2.6 16.7 1.0
FE3 S:SF41002 2.6 15.3 1.0
CE1 S:HIS188 2.8 27.6 1.0
CG S:HIS188 3.2 25.1 1.0
CB S:HIS188 3.8 27.0 1.0
S1 S:SF41002 3.8 20.0 1.0
CA S:HIS188 4.0 27.6 1.0
NE2 S:HIS188 4.0 28.9 1.0
CD2 S:HIS188 4.2 27.3 1.0
SG S:CYS216 4.4 22.3 1.0
CG S:PRO225 4.5 18.7 1.0
SG S:CYS222 4.5 14.3 1.0
O S:HIS188 4.5 30.0 1.0
CD S:PRO225 4.6 21.0 1.0
CB S:CYS191 4.6 12.9 1.0
SG S:CYS191 4.7 16.1 1.0
CD1 S:PHE197 4.7 17.5 1.0
C S:HIS188 4.7 29.2 1.0
CG S:PHE197 5.0 19.3 1.0

Iron binding site 6 out of 12 in 1h2a

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Iron binding site 6 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:16.6
occ:1.00
 FE2 S:SF41002 0.0 16.6 1.0
SG S:CYS222 2.2 14.3 1.0
S4 S:SF41002 2.2 19.0 1.0
S3 S:SF41002 2.2 18.9 1.0
S1 S:SF41002 2.3 20.0 1.0
FE1 S:SF41002 2.4 18.4 1.0
FE4 S:SF41002 2.5 16.7 1.0
FE3 S:SF41002 2.7 15.3 1.0
CB S:CYS222 3.2 18.2 1.0
S2 S:SF41002 3.8 18.2 1.0
ND1 S:HIS188 4.3 20.5 1.0
SG S:CYS216 4.4 22.3 1.0
CA S:CYS222 4.6 20.2 1.0
CA S:GLY224 4.7 20.8 1.0
SG S:CYS191 4.7 16.1 1.0
CD S:PRO225 4.8 21.0 1.0
N S:GLY224 4.8 24.6 1.0
N S:TYR218 4.9 20.3 1.0
CG1 S:VAL243 4.9 16.4 1.0
C S:CYS222 5.0 20.1 1.0
N S:LEU217 5.0 21.6 1.0
O S:CYS222 5.0 17.1 1.0

Iron binding site 7 out of 12 in 1h2a

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Iron binding site 7 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:15.3
occ:1.00
 FE3 S:SF41002 0.0 15.3 1.0
S2 S:SF41002 2.2 18.2 1.0
S1 S:SF41002 2.3 20.0 1.0
S4 S:SF41002 2.3 19.0 1.0
SG S:CYS191 2.3 16.1 1.0
FE4 S:SF41002 2.5 16.7 1.0
FE1 S:SF41002 2.6 18.4 1.0
FE2 S:SF41002 2.7 16.6 1.0
CB S:CYS191 3.2 12.9 1.0
S3 S:SF41002 3.9 18.9 1.0
CB S:ARG193 4.2 10.9 1.0
ND1 S:HIS188 4.3 20.5 1.0
C S:ARG193 4.6 20.4 1.0
CA S:CYS191 4.6 18.4 1.0
SG S:CYS216 4.6 22.3 1.0
SG S:CYS222 4.7 14.3 1.0
CA S:ARG193 4.7 15.9 1.0
N S:ARG193 4.7 15.4 1.0
N S:LEU194 4.8 23.7 1.0
CG2 S:VAL243 4.8 15.6 1.0
O S:ARG193 4.9 24.5 1.0
CG S:ARG193 4.9 8.8 1.0
O S:HIS188 4.9 30.0 1.0
CE1 S:HIS188 4.9 27.6 1.0
CG1 S:VAL243 5.0 16.4 1.0

Iron binding site 8 out of 12 in 1h2a

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Iron binding site 8 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:16.7
occ:1.00
 FE4 S:SF41002 0.0 16.7 1.0
S1 S:SF41002 2.2 20.0 1.0
S2 S:SF41002 2.3 18.2 1.0
SG S:CYS216 2.3 22.3 1.0
S3 S:SF41002 2.3 18.9 1.0
FE3 S:SF41002 2.5 15.3 1.0
FE2 S:SF41002 2.5 16.6 1.0
FE1 S:SF41002 2.6 18.4 1.0
CB S:CYS216 3.5 23.1 1.0
S4 S:SF41002 3.7 19.0 1.0
N S:LEU217 3.9 21.6 1.0
CA S:CYS216 4.1 21.5 1.0
N S:TYR218 4.3 20.3 1.0
ND1 S:HIS188 4.4 20.5 1.0
C S:CYS216 4.4 21.9 1.0
CD1 S:PHE197 4.4 17.5 1.0
SG S:CYS222 4.5 14.3 1.0
CB S:PHE197 4.6 25.9 1.0
CE1 S:HIS188 4.6 27.6 1.0
SG S:CYS191 4.7 16.1 1.0
CB S:ARG193 4.7 10.9 1.0
O S:ARG193 4.8 24.5 1.0
CA S:LEU217 4.8 19.3 1.0
C S:LEU217 4.8 18.7 1.0
CB S:CYS222 4.9 18.2 1.0
CG S:PHE197 4.9 19.3 1.0
CB S:TYR218 4.9 23.0 1.0
CA S:TYR218 5.0 19.2 1.0

Iron binding site 9 out of 12 in 1h2a

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Iron binding site 9 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:13.5
occ:1.00
 FE1 S:F3S1003 0.0 13.5 1.0
S2 S:F3S1003 2.1 12.0 1.0
S1 S:F3S1003 2.2 16.9 1.0
S3 S:F3S1003 2.2 10.1 1.0
SG S:CYS249 2.3 12.7 1.0
FE3 S:F3S1003 2.4 11.6 1.0
FE4 S:F3S1003 2.5 9.3 1.0
CB S:CYS249 3.4 18.4 1.0
S4 S:F3S1003 3.8 11.4 1.0
CA S:CYS249 4.0 13.1 1.0
N S:GLY251 4.3 16.2 1.0
N S:ILE250 4.4 10.8 1.0
SG S:CYS231 4.5 20.7 1.0
C S:CYS249 4.5 13.9 1.0
N S:CYS252 4.6 20.0 1.0
SG S:CYS252 4.6 14.3 1.0
CA S:GLY251 4.7 17.6 1.0
CG2 S:THR227 4.7 15.8 1.0
CG1 S:VAL187 4.8 16.0 1.0

Iron binding site 10 out of 12 in 1h2a

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Iron binding site 10 out of 12 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:11.6
occ:1.00
 FE3 S:F3S1003 0.0 11.6 1.0
S4 S:F3S1003 2.2 11.4 1.0
S1 S:F3S1003 2.3 16.9 1.0
SG S:CYS231 2.3 20.7 1.0
S3 S:F3S1003 2.4 10.1 1.0
FE1 S:F3S1003 2.4 13.5 1.0
FE4 S:F3S1003 2.5 9.3 1.0
CB S:CYS231 3.5 19.5 1.0
S2 S:F3S1003 3.6 12.0 1.0
OD1 S:ASN229 4.2 13.2 1.0
O S:HOH3028 4.5 15.5 1.0
SG S:CYS252 4.5 14.3 1.0
SG S:CYS249 4.6 12.7 1.0
CE1 S:PHE236 4.7 24.6 1.0
CB S:ASN229 4.7 15.3 1.0
CG S:ASN229 4.8 11.3 1.0
CG S:PRO242 4.8 20.2 1.0
CA S:CYS231 4.9 20.8 1.0
CD1 S:TRP241 4.9 31.8 1.0
CZ S:PHE236 4.9 19.6 1.0

Reference:

Y.Higuchi, T.Yagi, N.Yasuoka. Unusual Ligand Structure in Ni-Fe Active Center and An Additional Mg Site in Hydrogenase Revealed By High Resolution X-Ray Structure Analysis. Structure V. 5 1671 1997.
ISSN: ISSN 0969-2126
PubMed: 9438867
DOI: 10.1016/S0969-2126(97)00313-4
Page generated: Sat Aug 3 06:48:40 2024

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