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Iron in PDB 4ko3: Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

Enzymatic activity of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

All present enzymatic activity of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air:
1.12.99.6; 1.18.99.1;

Protein crystallography data

The structure of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko3 was solved by A.Volbeda, C.Cavazza, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.200, 108.720, 136.620, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.1

Other elements in 4ko3:

The structure of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air also contains other interesting chemical elements:

Nickel (Ni) 6 atoms
Calcium (Ca) 8 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4ko3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 4ko3

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Iron binding site 1 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:10.0
occ:1.00
 FE1 S:SF4301 0.0 10.0 1.0
S4 S:SF4301 2.3 11.0 1.0
S3 S:SF4301 2.3 9.0 1.0
SG S:CYS231 2.3 11.3 1.0
S2 S:SF4301 2.3 10.0 1.0
FE3 S:SF4301 2.7 10.3 1.0
FE2 S:SF4301 2.7 9.6 1.0
FE4 S:SF4301 2.8 9.0 1.0
CB S:CYS231 3.4 11.1 1.0
N S:LYS232 3.7 8.2 1.0
S1 S:SF4301 3.9 9.1 1.0
CA S:CYS231 4.0 10.5 1.0
N S:ALA233 4.1 8.8 1.0
C S:CYS231 4.3 9.7 1.0
CB S:TYR213 4.3 9.6 1.0
ND1 S:HIS208 4.4 9.0 1.0
CD2 S:TYR217 4.4 9.2 1.0
CB S:TYR217 4.4 8.6 1.0
CB S:ALA233 4.6 9.3 1.0
CE1 S:HIS208 4.6 9.6 1.0
CA S:LYS232 4.7 8.5 1.0
CA S:ALA233 4.8 9.4 1.0
C S:LYS232 4.8 8.6 1.0
O S:TYR213 4.8 9.8 1.0
CG S:TYR217 4.8 11.1 1.0
SG S:CYS211 4.8 9.9 1.0
SG S:CYS237 4.9 8.1 1.0

Iron binding site 2 out of 28 in 4ko3

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Iron binding site 2 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:9.6
occ:1.00
 FE2 S:SF4301 0.0 9.6 1.0
S3 S:SF4301 2.3 9.0 1.0
S4 S:SF4301 2.3 11.0 1.0
SG S:CYS211 2.3 9.9 1.0
S1 S:SF4301 2.3 9.1 1.0
FE3 S:SF4301 2.7 10.3 1.0
FE1 S:SF4301 2.7 10.0 1.0
FE4 S:SF4301 2.7 9.0 1.0
CB S:CYS211 3.1 9.0 1.0
CB S:TYR213 3.8 9.6 1.0
S2 S:SF4301 3.9 10.0 1.0
CG1 S:VAL259 4.1 7.7 1.0
ND1 S:HIS208 4.5 9.0 1.0
CD1 S:TYR213 4.5 10.9 1.0
CG S:TYR213 4.5 11.6 1.0
CA S:CYS211 4.6 8.9 1.0
CA S:TYR213 4.6 10.2 1.0
N S:TYR213 4.6 9.4 1.0
C S:TYR213 4.7 9.9 1.0
SG S:CYS237 4.8 8.1 1.0
N S:LEU214 4.9 9.6 1.0
CA S:HIS208 4.9 8.2 1.0
SG S:CYS231 4.9 11.3 1.0

Iron binding site 3 out of 28 in 4ko3

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Iron binding site 3 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:10.3
occ:1.00
 FE3 S:SF4301 0.0 10.3 1.0
ND1 S:HIS208 2.1 9.0 1.0
S1 S:SF4301 2.3 9.1 1.0
S4 S:SF4301 2.3 11.0 1.0
S2 S:SF4301 2.3 10.0 1.0
FE2 S:SF4301 2.7 9.6 1.0
FE1 S:SF4301 2.7 10.0 1.0
FE4 S:SF4301 2.8 9.0 1.0
CE1 S:HIS208 3.0 9.6 1.0
CG S:HIS208 3.2 8.7 1.0
CB S:HIS208 3.6 6.8 1.0
S3 S:SF4301 3.8 9.0 1.0
CA S:HIS208 3.9 8.2 1.0
NE2 S:HIS208 4.1 9.3 1.0
CD S:PRO240 4.2 9.3 1.0
CD2 S:HIS208 4.2 9.2 1.0
CG S:PRO240 4.3 9.6 1.0
CB S:CYS211 4.5 9.0 1.0
SG S:CYS231 4.6 11.3 1.0
SG S:CYS211 4.6 9.9 1.0
O S:HIS208 4.6 9.5 1.0
C S:HIS208 4.7 8.6 1.0
CD2 S:TYR217 4.8 9.2 1.0
N S:PRO240 4.8 8.3 1.0
SG S:CYS237 4.8 8.1 1.0
N S:HIS208 4.9 8.2 1.0

Iron binding site 4 out of 28 in 4ko3

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Iron binding site 4 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:9.0
occ:1.00
 FE4 S:SF4301 0.0 9.0 1.0
S2 S:SF4301 2.3 10.0 1.0
S1 S:SF4301 2.3 9.1 1.0
SG S:CYS237 2.3 8.1 1.0
S3 S:SF4301 2.3 9.0 1.0
FE2 S:SF4301 2.7 9.6 1.0
FE3 S:SF4301 2.8 10.3 1.0
FE1 S:SF4301 2.8 10.0 1.0
CB S:CYS237 3.2 7.8 1.0
S4 S:SF4301 4.0 11.0 1.0
CG1 S:VAL259 4.4 7.7 1.0
CD S:PRO240 4.5 9.3 1.0
N S:GLY239 4.5 7.0 1.0
CA S:GLY239 4.6 7.4 1.0
CA S:CYS237 4.6 6.7 1.0
CB S:LYS232 4.6 8.1 1.0
N S:ALA233 4.7 8.8 1.0
SG S:CYS231 4.7 11.3 1.0
ND1 S:HIS208 4.7 9.0 1.0
SG S:CYS211 4.8 9.9 1.0
N S:LYS232 4.8 8.2 1.0
CG2 S:VAL259 4.8 7.8 1.0
C S:CYS237 4.8 7.5 1.0
C S:LYS232 4.9 8.6 1.0
CA S:LYS232 5.0 8.5 1.0

Iron binding site 5 out of 28 in 4ko3

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Iron binding site 5 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:8.0
occ:1.00
 FE1 S:SF4302 0.0 8.0 1.0
S3 S:SF4302 2.3 7.7 1.0
SG S:CYS258 2.3 8.1 1.0
S4 S:SF4302 2.3 7.5 1.0
S2 S:SF4302 2.3 7.1 1.0
FE4 S:SF4302 2.7 7.5 1.0
FE2 S:SF4302 2.7 8.1 1.0
FE3 S:SF4302 2.7 7.7 1.0
CB S:CYS258 3.1 6.5 1.0
S1 S:SF4302 3.9 6.8 1.0
CZ L:ARG185 4.2 8.4 1.0
NE2 L:GLN190 4.2 7.5 1.0
NH1 L:ARG185 4.4 7.4 1.0
CA S:CYS258 4.4 7.3 1.0
NE L:ARG185 4.4 8.5 1.0
NH2 L:ARG185 4.4 8.0 1.0
N S:CYS258 4.5 6.7 1.0
NE1 S:TRP251 4.7 7.3 1.0
SG S:CYS267 4.7 7.1 1.0
SG S:CYS246 4.7 7.6 1.0
SG S:CYS264 4.8 7.5 1.0
CA S:CYS264 4.8 7.3 1.0
CD L:ARG185 4.8 8.0 1.0

Iron binding site 6 out of 28 in 4ko3

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Iron binding site 6 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:8.1
occ:1.00
 FE2 S:SF4302 0.0 8.1 1.0
S4 S:SF4302 2.3 7.5 1.0
S3 S:SF4302 2.3 7.7 1.0
SG S:CYS246 2.3 7.6 1.0
S1 S:SF4302 2.3 6.8 1.0
FE1 S:SF4302 2.7 8.0 1.0
FE3 S:SF4302 2.7 7.7 1.0
FE4 S:SF4302 2.8 7.5 1.0
CB S:CYS246 3.3 8.3 1.0
S2 S:SF4302 3.9 7.1 1.0
CD1 S:ILE207 4.1 16.6 1.0
NE1 S:TRP251 4.2 7.3 1.0
CB S:ALA244 4.6 8.0 1.0
CH2 S:TRP170 4.7 5.6 1.0
CA S:CYS246 4.7 8.3 1.0
SG S:CYS258 4.8 8.1 1.0
SG S:CYS267 4.8 7.1 1.0
SG S:CYS264 4.8 7.5 1.0
CE2 S:TRP251 5.0 6.6 1.0

Iron binding site 7 out of 28 in 4ko3

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Iron binding site 7 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:7.7
occ:1.00
 FE3 S:SF4302 0.0 7.7 1.0
S1 S:SF4302 2.3 6.8 1.0
SG S:CYS264 2.3 7.5 1.0
S4 S:SF4302 2.3 7.5 1.0
S2 S:SF4302 2.3 7.1 1.0
FE1 S:SF4302 2.7 8.0 1.0
FE2 S:SF4302 2.7 8.1 1.0
FE4 S:SF4302 2.7 7.5 1.0
CB S:CYS264 3.3 6.7 1.0
CA S:CYS264 3.8 7.3 1.0
S3 S:SF4302 3.9 7.7 1.0
N S:GLY266 4.1 5.8 1.0
N S:ILE265 4.1 7.1 1.0
C S:CYS264 4.3 7.0 1.0
CG2 S:THR242 4.4 6.9 1.0
CD1 S:ILE207 4.5 16.6 1.0
N S:CYS267 4.5 5.9 1.0
CA S:GLY266 4.6 6.2 1.0
CB S:CYS258 4.7 6.5 1.0
SG S:CYS258 4.7 8.1 1.0
SG S:CYS246 4.9 7.6 1.0
SG S:CYS267 4.9 7.1 1.0

Iron binding site 8 out of 28 in 4ko3

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Iron binding site 8 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:7.5
occ:1.00
 FE4 S:SF4302 0.0 7.5 1.0
S1 S:SF4302 2.3 6.8 1.0
S2 S:SF4302 2.3 7.1 1.0
S3 S:SF4302 2.3 7.7 1.0
SG S:CYS267 2.3 7.1 1.0
FE1 S:SF4302 2.7 8.0 1.0
FE3 S:SF4302 2.7 7.7 1.0
FE2 S:SF4302 2.8 8.1 1.0
CB S:CYS267 3.4 6.2 1.0
N S:CYS267 3.7 5.9 1.0
S4 S:SF4302 3.9 7.5 1.0
CA S:CYS267 4.0 5.9 1.0
NH1 L:ARG185 4.0 7.4 1.0
NH2 L:ARG185 4.2 8.0 1.0
CZ L:ARG185 4.3 8.4 1.0
N S:VAL268 4.4 6.1 1.0
C S:CYS267 4.5 6.4 1.0
CG1 S:VAL268 4.6 5.8 1.0
C S:GLY266 4.8 6.4 1.0
SG S:CYS246 4.8 7.6 1.0
SG S:CYS258 4.8 8.1 1.0
SG S:CYS264 4.8 7.5 1.0
N S:GLY266 4.9 5.8 1.0

Iron binding site 9 out of 28 in 4ko3

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Iron binding site 9 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:6.8
occ:1.00
 FE1 S:SF4303 0.0 6.8 1.0
S3 S:SF4303 2.3 5.9 1.0
SG S:CYS164 2.3 6.7 1.0
S4 S:SF4303 2.3 6.6 1.0
S2 S:SF4303 2.3 6.2 1.0
FE3 S:SF4303 2.7 7.4 1.0
FE4 S:SF4303 2.7 6.8 1.0
FE2 S:SF4303 2.8 7.7 1.0
CB S:CYS164 3.4 5.7 1.0
CA S:CYS164 3.5 6.5 1.0
S1 S:SF4303 3.9 7.7 1.0
O S:HOH439 3.9 7.6 1.0
C S:CYS164 4.0 6.0 1.0
CG L:ARG68 4.2 7.5 1.0
CE1 L:HIS188 4.3 5.9 1.0
SG S:CYS126 4.4 7.2 1.0
N S:PRO165 4.4 5.3 1.0
O S:GLY163 4.5 6.0 1.0
ND1 L:HIS188 4.5 9.8 1.0
CA S:PRO165 4.6 5.4 1.0
O S:CYS164 4.6 7.3 1.0
SG S:CYS18 4.6 6.7 1.0
N S:CYS164 4.7 5.9 1.0
SG S:CYS21 4.9 8.1 1.0
NE L:ARG68 4.9 6.0 1.0

Iron binding site 10 out of 28 in 4ko3

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Iron binding site 10 out of 28 in the Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:7.7
occ:1.00
 FE2 S:SF4303 0.0 7.7 1.0
S4 S:SF4303 2.3 6.6 1.0
SG S:CYS21 2.3 8.1 1.0
S3 S:SF4303 2.3 5.9 1.0
S1 S:SF4303 2.3 7.7 1.0
FE4 S:SF4303 2.7 6.8 1.0
FE3 S:SF4303 2.8 7.4 1.0
FE1 S:SF4303 2.8 6.8 1.0
N S:CYS21 3.6 5.6 1.0
CB S:CYS21 3.6 6.8 1.0
O S:HOH409 3.9 6.2 1.0
S2 S:SF4303 4.0 6.2 1.0
CA S:CYS21 4.1 5.7 1.0
CA S:GLY124 4.4 5.0 1.0
C S:GLY20 4.4 4.8 1.0
CA S:PRO165 4.5 5.4 1.0
SG S:CYS18 4.6 6.7 1.0
O S:GLY163 4.7 6.0 1.0
OE1 S:GLU77 4.7 7.3 1.0
CB S:PRO165 4.7 5.3 1.0
CA S:GLY20 4.8 4.6 1.0
CD S:PRO166 4.8 6.8 1.0
N S:GLY20 4.8 5.2 1.0
CG S:GLU77 4.9 6.2 1.0
CA S:CYS164 4.9 6.5 1.0
SG S:CYS126 5.0 7.2 1.0
SG S:CYS164 5.0 6.7 1.0

Reference:

A.Volbeda, P.Amara, M.Iannello, A.L.De Lacey, C.Cavazza, J.C.Fontecilla-Camps. Structural Foundations For the O2 Resistance of Desulfomicrobium Baculatum [Nifese]-Hydrogenase. Chem.Commun.(Camb.) V. 49 7061 2013.
ISSN: ISSN 1359-7345
PubMed: 23811828
DOI: 10.1039/C3CC43619E
Page generated: Mon Aug 5 05:32:09 2024

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