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Iron in PDB 1cc1: Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum

Enzymatic activity of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum

All present enzymatic activity of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum:
1.18.99.1;

Protein crystallography data

The structure of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum, PDB code: 1cc1 was solved by E.Garcin, X.Vernede, E.C.Hatchikian, A.Volbeda, M.Frey, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.390, 63.700, 99.580, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.8

Other elements in 1cc1:

The structure of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum (pdb code 1cc1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum, PDB code: 1cc1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in 1cc1

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Iron binding site 1 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe284

b:24.7
occ:1.00
FE1 S:SF4284 0.0 24.7 1.0
SG S:CYS237 2.3 22.2 1.0
S3 S:SF4284 2.3 22.4 1.0
S4 S:SF4284 2.3 23.0 1.0
S2 S:SF4284 2.4 23.3 1.0
FE4 S:SF4284 2.8 23.1 1.0
FE2 S:SF4284 2.8 25.7 1.0
FE3 S:SF4284 2.9 26.0 1.0
CB S:CYS237 3.2 19.2 1.0
S1 S:SF4284 4.1 25.7 1.0
CG1 S:VAL259 4.3 27.5 1.0
CD S:PRO240 4.5 23.3 1.0
N S:GLY239 4.5 19.8 1.0
CA S:GLY239 4.6 21.0 1.0
CA S:CYS237 4.6 21.1 1.0
ND1 S:HIS208 4.7 25.6 1.0
N S:ALA233 4.7 23.2 1.0
CG2 S:VAL259 4.7 21.3 1.0
CB S:LYS232 4.8 21.7 1.0
C S:CYS237 4.8 21.2 1.0
SG S:CYS211 4.8 23.6 1.0
SG S:CYS231 4.9 24.9 1.0
N S:LYS232 4.9 23.4 1.0
C S:LYS232 4.9 23.5 1.0
O S:CYS237 5.0 22.8 1.0

Iron binding site 2 out of 14 in 1cc1

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Iron binding site 2 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe284

b:25.7
occ:1.00
FE2 S:SF4284 0.0 25.7 1.0
ND1 S:HIS208 2.0 25.6 1.0
S3 S:SF4284 2.3 22.4 1.0
S4 S:SF4284 2.3 23.0 1.0
S1 S:SF4284 2.4 25.7 1.0
FE3 S:SF4284 2.7 26.0 1.0
FE4 S:SF4284 2.7 23.1 1.0
CE1 S:HIS208 2.8 25.4 1.0
FE1 S:SF4284 2.8 24.7 1.0
CG S:HIS208 3.1 26.4 1.0
CB S:HIS208 3.6 26.2 1.0
CA S:HIS208 3.9 27.8 1.0
S2 S:SF4284 3.9 23.3 1.0
NE2 S:HIS208 4.0 25.4 1.0
CD2 S:HIS208 4.2 24.2 1.0
CG S:PRO240 4.2 23.5 1.0
CD S:PRO240 4.2 23.3 1.0
CB S:CYS211 4.6 24.8 1.0
O S:HIS208 4.6 28.2 1.0
CD1 S:TYR217 4.6 40.0 1.0
SG S:CYS231 4.6 24.9 1.0
C S:HIS208 4.7 27.8 1.0
SG S:CYS211 4.8 23.6 1.0
N S:PRO240 4.8 24.1 1.0
SG S:CYS237 4.9 22.2 1.0
N S:HIS208 4.9 27.2 1.0
CG S:TYR217 5.0 38.0 1.0

Iron binding site 3 out of 14 in 1cc1

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Iron binding site 3 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe284

b:26.0
occ:1.00
FE3 S:SF4284 0.0 26.0 1.0
S1 S:SF4284 2.3 25.7 1.0
SG S:CYS231 2.3 24.9 1.0
S2 S:SF4284 2.4 23.3 1.0
S4 S:SF4284 2.4 23.0 1.0
FE2 S:SF4284 2.7 25.7 1.0
FE4 S:SF4284 2.8 23.1 1.0
FE1 S:SF4284 2.9 24.7 1.0
CB S:CYS231 3.4 21.9 1.0
N S:LYS232 3.8 23.4 1.0
S3 S:SF4284 4.0 22.4 1.0
CA S:CYS231 4.0 25.6 1.0
N S:ALA233 4.0 23.2 1.0
C S:CYS231 4.2 24.5 1.0
CD1 S:TYR217 4.3 40.0 1.0
CB S:TYR213 4.3 30.6 1.0
ND1 S:HIS208 4.4 25.6 1.0
CB S:TYR217 4.4 35.6 1.0
CB S:ALA233 4.5 19.4 1.0
CE1 S:HIS208 4.6 25.4 1.0
CA S:ALA233 4.7 23.2 1.0
CA S:LYS232 4.7 22.2 1.0
CG S:TYR217 4.7 38.0 1.0
C S:LYS232 4.7 23.5 1.0
O S:TYR213 4.8 27.4 1.0
SG S:CYS211 4.9 23.6 1.0
C S:TYR213 5.0 28.3 1.0

Iron binding site 4 out of 14 in 1cc1

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Iron binding site 4 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe284

b:23.1
occ:1.00
FE4 S:SF4284 0.0 23.1 1.0
S2 S:SF4284 2.3 23.3 1.0
SG S:CYS211 2.3 23.6 1.0
S3 S:SF4284 2.3 22.4 1.0
S1 S:SF4284 2.4 25.7 1.0
FE2 S:SF4284 2.7 25.7 1.0
FE3 S:SF4284 2.8 26.0 1.0
FE1 S:SF4284 2.8 24.7 1.0
CB S:CYS211 3.1 24.8 1.0
CB S:TYR213 3.8 30.6 1.0
S4 S:SF4284 4.0 23.0 1.0
CG1 S:VAL259 4.0 27.5 1.0
ND1 S:HIS208 4.4 25.6 1.0
CD2 S:TYR213 4.5 35.0 1.0
CA S:CYS211 4.5 25.9 1.0
CG S:TYR213 4.6 34.0 1.0
CA S:TYR213 4.6 27.9 1.0
N S:TYR213 4.6 26.4 1.0
C S:TYR213 4.7 28.3 1.0
N S:LEU214 4.7 29.5 1.0
SG S:CYS237 4.9 22.2 1.0
CA S:HIS208 4.9 27.8 1.0
C S:CYS211 5.0 26.0 1.0
SG S:CYS231 5.0 24.9 1.0

Iron binding site 5 out of 14 in 1cc1

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Iron binding site 5 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe285

b:22.1
occ:1.00
FE1 S:SF4285 0.0 22.1 1.0
SG S:CYS267 2.3 18.2 1.0
S3 S:SF4285 2.3 19.2 1.0
S4 S:SF4285 2.3 20.0 1.0
S2 S:SF4285 2.3 19.8 1.0
FE2 S:SF4285 2.8 20.3 1.0
FE4 S:SF4285 2.8 23.6 1.0
FE3 S:SF4285 2.9 23.7 1.0
CB S:CYS267 3.3 18.1 1.0
N S:CYS267 3.7 18.7 1.0
CA S:CYS267 4.0 18.4 1.0
S1 S:SF4285 4.0 20.7 1.0
NH2 L:ARG185 4.1 24.6 1.0
NH1 L:ARG185 4.1 19.5 1.0
CZ L:ARG185 4.3 21.6 1.0
N S:VAL268 4.4 16.7 1.0
CG1 S:VAL268 4.4 18.4 1.0
C S:CYS267 4.5 19.5 1.0
C S:GLY266 4.8 18.8 1.0
SG S:CYS246 4.8 22.1 1.0
SG S:CYS264 4.9 18.7 1.0
SG S:CYS258 4.9 24.5 1.0
N S:GLY266 4.9 19.0 1.0

Iron binding site 6 out of 14 in 1cc1

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Iron binding site 6 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe285

b:20.3
occ:1.00
FE2 S:SF4285 0.0 20.3 1.0
S3 S:SF4285 2.3 19.2 1.0
SG S:CYS264 2.3 18.7 1.0
S4 S:SF4285 2.4 20.0 1.0
S1 S:SF4285 2.4 20.7 1.0
FE4 S:SF4285 2.7 23.6 1.0
FE3 S:SF4285 2.7 23.7 1.0
FE1 S:SF4285 2.8 22.1 1.0
CB S:CYS264 3.4 18.0 1.0
CA S:CYS264 3.8 20.2 1.0
S2 S:SF4285 3.9 19.8 1.0
N S:ILE265 4.0 19.8 1.0
N S:GLY266 4.0 19.0 1.0
C S:CYS264 4.3 21.5 1.0
CD1 S:ILE207 4.4 24.5 1.0
CG2 S:THR242 4.4 21.8 1.0
CA S:GLY266 4.5 18.6 1.0
N S:CYS267 4.6 18.7 1.0
SG S:CYS258 4.8 24.5 1.0
CB S:CYS258 4.8 22.5 1.0
SG S:CYS267 4.9 18.2 1.0
SG S:CYS246 4.9 22.1 1.0
C S:ILE265 5.0 20.4 1.0

Iron binding site 7 out of 14 in 1cc1

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Iron binding site 7 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe285

b:23.7
occ:1.00
FE3 S:SF4285 0.0 23.7 1.0
SG S:CYS258 2.3 24.5 1.0
S1 S:SF4285 2.3 20.7 1.0
S4 S:SF4285 2.3 20.0 1.0
S2 S:SF4285 2.4 19.8 1.0
FE4 S:SF4285 2.7 23.6 1.0
FE2 S:SF4285 2.7 20.3 1.0
FE1 S:SF4285 2.9 22.1 1.0
CB S:CYS258 3.1 22.5 1.0
S3 S:SF4285 3.9 19.2 1.0
NE2 L:GLN190 4.1 22.1 1.0
CZ L:ARG185 4.3 21.6 1.0
NH2 L:ARG185 4.4 24.6 1.0
CA S:CYS258 4.4 22.6 1.0
NE L:ARG185 4.4 23.1 1.0
NH1 L:ARG185 4.5 19.5 1.0
N S:CYS258 4.5 20.9 1.0
NE1 S:TRP251 4.6 19.1 1.0
SG S:CYS246 4.7 22.1 1.0
CA S:CYS264 4.8 20.2 1.0
SG S:CYS267 4.8 18.2 1.0
SG S:CYS264 4.8 18.7 1.0
CD L:ARG185 4.9 24.3 1.0

Iron binding site 8 out of 14 in 1cc1

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Iron binding site 8 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe285

b:23.6
occ:1.00
FE4 S:SF4285 0.0 23.6 1.0
S1 S:SF4285 2.3 20.7 1.0
S2 S:SF4285 2.3 19.8 1.0
SG S:CYS246 2.3 22.1 1.0
S3 S:SF4285 2.4 19.2 1.0
FE2 S:SF4285 2.7 20.3 1.0
FE3 S:SF4285 2.7 23.7 1.0
FE1 S:SF4285 2.8 22.1 1.0
CB S:CYS246 3.3 18.7 1.0
S4 S:SF4285 3.9 20.0 1.0
CD1 S:ILE207 4.0 24.5 1.0
NE1 S:TRP251 4.3 19.1 1.0
CB S:ALA244 4.6 15.7 1.0
CA S:CYS246 4.7 23.3 1.0
SG S:CYS258 4.8 24.5 1.0
CH2 S:TRP170 4.8 21.6 1.0
SG S:CYS264 4.8 18.7 1.0
SG S:CYS267 4.8 18.2 1.0

Iron binding site 9 out of 14 in 1cc1

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Iron binding site 9 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe286

b:20.5
occ:1.00
FE1 S:SF4286 0.0 20.5 1.0
SG S:CYS18 2.3 16.4 1.0
S4 S:SF4286 2.3 15.6 1.0
S3 S:SF4286 2.3 17.6 1.0
S2 S:SF4286 2.3 17.9 1.0
FE3 S:SF4286 2.7 19.0 1.0
FE2 S:SF4286 2.8 22.3 1.0
FE4 S:SF4286 2.8 18.4 1.0
CB S:CYS18 3.3 15.3 1.0
N S:CYS18 3.6 16.5 1.0
S1 S:SF4286 3.9 14.6 1.0
CA S:CYS18 4.0 16.4 1.0
CE1 L:HIS188 4.1 14.7 1.0
N S:GLY20 4.1 16.9 1.0
CA S:GLY20 4.3 14.4 1.0
O S:HOH289 4.4 16.0 1.0
C S:CYS18 4.5 18.2 1.0
N S:THR19 4.5 17.8 1.0
N S:CYS21 4.7 17.1 1.0
O L:ARG68 4.7 18.6 1.0
C S:GLY17 4.7 18.5 1.0
SG S:CYS126 4.8 19.5 1.0
CG L:ARG68 4.8 17.9 1.0
SG S:CYS164 4.8 16.8 1.0
C S:GLY20 4.9 16.1 1.0
NE2 L:HIS188 4.9 19.3 1.0
SG S:CYS21 4.9 20.9 1.0
ND1 L:HIS188 5.0 17.7 1.0

Iron binding site 10 out of 14 in 1cc1

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Iron binding site 10 out of 14 in the Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of A Reduced, Active Form of the Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe286

b:22.3
occ:1.00
FE2 S:SF4286 0.0 22.3 1.0
SG S:CYS126 2.3 19.5 1.0
S3 S:SF4286 2.3 17.6 1.0
S1 S:SF4286 2.4 14.6 1.0
S4 S:SF4286 2.4 15.6 1.0
FE3 S:SF4286 2.7 19.0 1.0
FE1 S:SF4286 2.8 20.5 1.0
FE4 S:SF4286 2.9 18.4 1.0
CB S:CYS126 3.2 18.3 1.0
O S:HOH288 3.8 11.7 1.0
O S:HOH289 3.9 16.0 1.0
S2 S:SF4286 3.9 17.9 1.0
O S:HOH312 4.0 15.3 1.0
N S:CYS126 4.1 17.5 1.0
CA S:CYS126 4.2 19.8 1.0
SG S:CYS164 4.6 16.8 1.0
N S:CYS18 4.8 16.5 1.0
SG S:CYS21 4.8 20.9 1.0
CA S:GLY17 4.8 20.2 1.0
SG S:CYS18 4.9 16.4 1.0
CA S:GLY78 5.0 21.0 1.0

Reference:

E.Garcin, X.Vernede, E.C.Hatchikian, A.Volbeda, M.Frey, J.C.Fontecilla-Camps. The Crystal Structure of A Reduced [Nifese] Hydrogenase Provides An Image of the Activated Catalytic Center Structure Fold.Des. V. 7 557 1999.
ISSN: ISSN 0969-2126
PubMed: 10378275
DOI: 10.1016/S0969-2126(99)80072-0
Page generated: Sun Dec 13 14:08:41 2020

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