Atomistry » Iron » PDB 7ni3-7o4i » 7o26
Atomistry »
  Iron »
    PDB 7ni3-7o4i »
      7o26 »

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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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

Go back to Iron Binding Sites List in 7o26
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 8 10:25:39 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy