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Iron in PDB 7o26: Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)

Protein crystallography data

The structure of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine), PDB code: 7o26 was solved by R.Rohac, L.Martin, L.Liu, D.Basu, L.Tao, R.D.Britt, T.Rauchfuss, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.81 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.88, 79.84, 86.17, 90, 90, 90
R / Rfree (%) 17.8 / 21.7

Other elements in 7o26:

The structure of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Iodine (I) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) (pdb code 7o26). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine), PDB code: 7o26:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7o26

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Iron binding site 1 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:21.0
occ:0.76
 C A:CYN405 1.8 22.9 0.7
C A:CMO403 1.8 19.4 0.7
C A:CMO404 1.8 21.1 0.9
O A:CYS401 2.1 29.1 0.8
N A:CYS401 2.1 20.9 0.8
SG A:CYS401 2.2 26.4 0.8
CA A:CYS401 2.7 25.3 0.8
C A:CYS401 2.8 32.2 0.8
N A:CYN405 2.9 22.4 0.7
O A:CMO403 3.0 21.6 0.7
O A:CMO404 3.0 19.3 0.9
CB A:CYS401 3.0 28.0 0.8
NH2 A:ARG159 3.3 14.9 0.4
CL A:CL419 3.8 31.1 0.1
CL A:CL419 3.9 24.7 0.2
OXT A:CYS401 4.0 32.1 0.8
CZ A:ARG159 4.3 14.7 0.4
NH1 A:ARG159 4.4 29.3 0.6
SD A:MET291 4.5 23.9 0.6
CE A:MET291 4.6 14.2 0.6
OG1 A:THR269 4.7 24.6 0.8
CD1 A:ILE56 4.7 20.1 0.5
O A:HOH586 4.7 21.4 1.0
NE A:ARG159 4.8 16.4 0.4
CD2 A:LEU157 4.8 23.6 0.6
CG2 A:THR268 4.8 15.7 1.0
CB A:THR268 4.8 14.5 1.0
NE2 A:GLN107 4.9 17.4 1.0

Iron binding site 2 out of 9 in 7o26

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Iron binding site 2 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe410

b:21.4
occ:0.45
 FE1 A:FES410 0.0 21.4 0.5
FE1 A:FES410 1.0 28.6 0.3
SG A:CYS311 1.6 33.4 0.3
S2 A:FES410 2.0 28.5 0.3
S A:H2S407 2.1 18.1 0.5
SG A:CYS311 2.2 36.5 0.7
S1 A:FES410 2.2 26.8 0.5
S2 A:FES410 2.2 23.7 0.5
SG A:CYS319 2.2 16.2 0.1
FE2 A:FES410 2.6 25.1 0.5
S1 A:FES410 2.7 29.4 0.3
FE2 A:FES410 2.7 23.7 0.3
CB A:CYS311 2.8 42.2 0.3
SG A:CYS319 3.2 23.1 0.9
CB A:CYS311 3.3 27.9 0.7
CB A:CYS319 3.7 17.4 0.9
CB A:CYS319 3.8 23.2 0.1
SG A:CYS322 3.8 20.5 0.1
CA A:CYS311 4.0 24.1 0.7
CA A:CYS311 4.1 35.8 0.3
O A:HOH720 4.1 38.9 1.0
CA A:CYS319 4.2 21.5 0.1
CA A:CYS319 4.2 17.0 0.9
NH1 A:ARG279 4.5 24.2 1.0
N A:CYS311 4.5 27.9 0.7
NH2 A:ARG279 4.6 23.1 1.0
N A:CYS311 4.7 29.1 0.3
S A:H2S408 4.7 20.7 0.3
SG A:CYS322 4.8 19.5 0.5
CB A:CYS322 4.9 18.8 0.1
CB A:CYS322 4.9 18.8 0.4
CB A:CYS322 4.9 20.0 0.5

Iron binding site 3 out of 9 in 7o26

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Iron binding site 3 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe410

b:28.6
occ:0.30
 FE1 A:FES410 0.0 28.6 0.3
FE1 A:FES410 1.0 21.4 0.5
S A:H2S407 1.3 18.1 0.5
SG A:CYS319 1.9 16.2 0.1
S1 A:FES410 2.2 29.4 0.3
S2 A:FES410 2.2 28.5 0.3
SG A:CYS311 2.3 33.4 0.3
SG A:CYS319 2.5 23.1 0.9
S1 A:FES410 2.6 26.8 0.5
S2 A:FES410 2.7 23.7 0.5
FE2 A:FES410 2.8 23.7 0.3
SG A:CYS311 2.8 36.5 0.7
CB A:CYS311 3.0 42.2 0.3
CB A:CYS319 3.1 17.4 0.9
FE2 A:FES410 3.1 25.1 0.5
CB A:CYS319 3.2 23.2 0.1
CA A:CYS319 3.4 17.0 0.9
CA A:CYS319 3.4 21.5 0.1
CB A:CYS311 3.5 27.9 0.7
SG A:CYS322 3.6 20.5 0.1
CA A:CYS311 4.2 24.1 0.7
N A:CYS319 4.2 19.9 1.0
CA A:CYS311 4.2 35.8 0.3
CB A:CYS322 4.4 18.8 0.1
CB A:CYS322 4.4 18.8 0.4
CB A:CYS322 4.4 20.0 0.5
SG A:CYS322 4.5 19.5 0.5
CG A:GLU314 4.5 35.5 1.0
SG A:CYS322 4.6 26.7 0.4
C A:CYS319 4.6 15.4 1.0
O A:CYS319 4.7 18.3 1.0
C A:ALA318 4.8 22.3 1.0
O A:HOH720 4.9 38.9 1.0
N A:CYS311 4.9 27.9 0.7
S A:H2S408 4.9 20.7 0.3
CB A:GLU314 5.0 32.7 1.0

Iron binding site 4 out of 9 in 7o26

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Iron binding site 4 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe410

b:25.1
occ:0.45
 FE2 A:FES410 0.0 25.1 0.5
S2 A:FES410 1.5 28.5 0.3
FE2 A:FES410 1.7 23.7 0.3
S2 A:FES410 2.2 23.7 0.5
S1 A:FES410 2.2 26.8 0.5
S A:H2S408 2.2 20.7 0.3
SG A:CYS322 2.4 20.5 0.1
FE1 A:FES410 2.6 21.4 0.5
NH2 A:ARG279 2.6 23.1 1.0
NH1 A:ARG279 3.1 24.2 1.0
FE1 A:FES410 3.1 28.6 0.3
CZ A:ARG279 3.3 20.4 1.0
SG A:CYS322 3.4 19.5 0.5
SG A:CYS311 3.6 33.4 0.3
S1 A:FES410 3.6 29.4 0.3
CB A:CYS322 4.1 18.8 0.4
CB A:CYS322 4.1 20.0 0.5
CB A:CYS322 4.1 18.8 0.1
CG1 A:VAL323 4.1 14.8 1.0
O A:HOH790 4.2 44.5 1.0
SG A:CYS311 4.3 36.5 0.7
SG A:CYS319 4.3 16.2 0.1
S A:H2S407 4.4 18.1 0.5
CE A:MET326 4.6 20.9 1.0
NE A:ARG279 4.6 20.4 1.0
O A:HOH574 4.6 26.7 1.0
O A:CYS319 5.0 18.3 1.0
N A:VAL323 5.0 14.4 1.0
CD1 A:ILE310 5.0 35.0 1.0

Iron binding site 5 out of 9 in 7o26

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Iron binding site 5 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe410

b:23.7
occ:0.30
 FE2 A:FES410 0.0 23.7 0.3
FE2 A:FES410 1.7 25.1 0.5
S1 A:FES410 1.8 26.8 0.5
SG A:CYS322 1.8 20.5 0.1
S2 A:FES410 2.2 28.5 0.3
S1 A:FES410 2.2 29.4 0.3
SG A:CYS322 2.3 19.5 0.5
S A:H2S408 2.5 20.7 0.3
FE1 A:FES410 2.7 21.4 0.5
FE1 A:FES410 2.8 28.6 0.3
CB A:CYS322 3.2 18.8 0.4
CB A:CYS322 3.2 20.0 0.5
CB A:CYS322 3.2 18.8 0.1
S2 A:FES410 3.3 23.7 0.5
SG A:CYS311 3.6 33.4 0.3
SG A:CYS322 3.7 26.7 0.4
O A:HOH790 3.8 44.5 1.0
S A:H2S407 3.8 18.1 0.5
NH2 A:ARG279 3.9 23.1 1.0
SG A:CYS319 4.5 16.2 0.1
CA A:CYS322 4.5 16.0 0.1
CA A:CYS322 4.6 15.7 0.4
CA A:CYS322 4.6 15.7 0.5
SG A:CYS311 4.7 36.5 0.7
O A:HOH820 4.8 42.9 0.9
CZ A:ARG279 4.8 20.4 1.0
NH1 A:ARG279 4.8 24.2 1.0
C A:CYS322 4.8 16.5 1.0
O A:HOH574 4.9 26.7 1.0
CA A:CYS319 5.0 17.0 0.9
CA A:CYS319 5.0 21.5 0.1

Iron binding site 6 out of 9 in 7o26

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Iron binding site 6 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe417

b:21.1
occ:1.00
 FE1 A:SF4417 0.0 21.1 1.0
SG A:CYS70 2.3 19.5 1.0
S3 A:SF4417 2.3 19.4 1.0
S4 A:SF4417 2.3 20.7 1.0
S2 A:SF4417 2.3 20.4 1.0
FE3 A:SF4417 2.7 21.2 1.0
FE2 A:SF4417 2.7 20.2 1.0
FE4 A:SF4417 2.8 24.0 1.0
CB A:CYS70 3.0 18.5 1.0
S1 A:SF4417 3.8 21.6 1.0
SD A:MET406 4.2 33.2 1.0
CB A:LEU72 4.3 21.0 1.0
CA A:CYS70 4.5 20.6 1.0
CE A:MET406 4.6 31.4 1.0
CD2 A:LEU305 4.7 33.2 1.0
N A:ARG73 4.7 20.9 1.0
SG A:CYS67 4.7 21.8 1.0
C A:LEU72 4.8 20.7 1.0
CB A:CYS67 4.8 17.6 1.0
SG A:CYS63 4.8 20.5 1.0
OXT A:MET406 4.8 36.0 1.0
N A:LEU72 4.9 20.1 1.0
CG A:LEU72 4.9 22.0 1.0
CA A:LEU72 4.9 19.9 1.0
C A:CYS70 5.0 23.5 1.0

Iron binding site 7 out of 9 in 7o26

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Iron binding site 7 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe417

b:20.2
occ:1.00
 FE2 A:SF4417 0.0 20.2 1.0
SG A:CYS63 2.2 20.5 1.0
S4 A:SF4417 2.3 20.7 1.0
S1 A:SF4417 2.3 21.6 1.0
S3 A:SF4417 2.3 19.4 1.0
FE1 A:SF4417 2.7 21.1 1.0
FE3 A:SF4417 2.7 21.2 1.0
FE4 A:SF4417 2.8 24.0 1.0
CB A:CYS63 3.3 22.6 1.0
S2 A:SF4417 3.9 20.4 1.0
CB A:LYS65 4.2 17.8 1.0
N A:MET406 4.2 33.2 1.0
N A:GLU110 4.4 18.7 1.0
CA A:GLY109 4.6 17.9 1.0
O A:LYS65 4.6 23.8 1.0
CA A:CYS63 4.7 19.4 1.0
SG A:CYS70 4.8 19.5 1.0
N A:LYS65 4.8 19.8 1.0
SG A:CYS67 4.8 21.8 1.0
C A:LYS65 4.8 20.3 1.0
CA A:LYS65 4.8 18.7 1.0
OXT A:MET406 4.8 36.0 1.0
O A:LEU72 4.9 22.3 1.0
CB A:LEU72 5.0 21.0 1.0

Iron binding site 8 out of 9 in 7o26

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Iron binding site 8 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe417

b:21.2
occ:1.00
 FE3 A:SF4417 0.0 21.2 1.0
S1 A:SF4417 2.3 21.6 1.0
S4 A:SF4417 2.3 20.7 1.0
S2 A:SF4417 2.3 20.4 1.0
SG A:CYS67 2.3 21.8 1.0
FE1 A:SF4417 2.7 21.1 1.0
FE2 A:SF4417 2.7 20.2 1.0
FE4 A:SF4417 2.9 24.0 1.0
CB A:CYS67 3.2 17.6 1.0
O A:HOH590 3.9 21.0 1.0
S3 A:SF4417 3.9 19.4 1.0
OXT A:MET406 4.2 36.0 1.0
N A:CYS67 4.3 19.4 1.0
CB A:LYS65 4.4 17.8 1.0
CA A:CYS67 4.4 18.7 1.0
CB A:CYS70 4.4 18.5 1.0
NH2 A:ARG172 4.5 22.6 1.0
SG A:CYS70 4.6 19.5 1.0
OH A:TYR69 4.7 19.0 1.0
SG A:CYS63 4.7 20.5 1.0
O A:HOH583 4.8 18.3 1.0
CE1 A:TYR69 4.9 17.4 1.0
CD A:LYS65 4.9 18.4 1.0
NE A:ARG172 5.0 21.3 1.0

Iron binding site 9 out of 9 in 7o26

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Iron binding site 9 out of 9 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (5'Da + Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe417

b:24.0
occ:1.00
 FE4 A:SF4417 0.0 24.0 1.0
OXT A:MET406 2.2 36.0 1.0
S2 A:SF4417 2.3 20.4 1.0
S3 A:SF4417 2.3 19.4 1.0
S1 A:SF4417 2.3 21.6 1.0
N A:MET406 2.5 33.2 1.0
FE1 A:SF4417 2.8 21.1 1.0
SD A:MET406 2.8 33.2 1.0
FE2 A:SF4417 2.8 20.2 1.0
FE3 A:SF4417 2.9 21.2 1.0
C A:MET406 3.1 36.5 1.0
CA A:MET406 3.3 34.4 1.0
CE A:MET406 3.8 31.4 1.0
CG A:MET406 3.9 33.7 1.0
S4 A:SF4417 4.0 20.7 1.0
CB A:MET406 4.1 33.0 1.0
O A:HOH590 4.1 21.0 1.0
O A:HOH583 4.2 18.3 1.0
O A:MET406 4.3 36.6 1.0
SG A:CYS63 4.7 20.5 1.0
SG A:CYS70 4.8 19.5 1.0

Reference:

Y.Nicolet, J.K.Rubach, M.C.Posewitz, P.Amara, C.Mathevon, M.Atta, M.Fontecave, J.C.Fontecilla-Camps. X-Ray Structure of the [Fefe]-Hydrogenase Maturase Hyde From Thermotoga Maritima* Journal of Biological V. 283 18861 2008CHEMISTRY.
DOI: 10.1074/JBC.M801161200
Page generated: Thu Aug 7 00:49:20 2025

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