Iron in PDB 2vkr: 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin

The structure of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin, PDB code: 2vkr was solved by C.Frazao, D.Aragao, R.Coelho, S.S.Leal, C.M.Gomes, M.Teixeira, M.A.Carrondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.48 / 2.01
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	117.500, 117.500, 50.900, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 27.3

The structure of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 49;

Binding sites:

The binding sites of Iron atom in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin (pdb code 2vkr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 49 binding sites of Iron where determined in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin, PDB code: 2vkr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe104 b:10.6 occ:1.00 FE1 A:F3S104 0.0 10.6 1.0 S3 A:F3S104 2.0 26.6 1.0 S2 A:F3S104 2.1 28.6 1.0 S1 A:F3S104 2.1 24.2 1.0 SG A:CYS45 2.2 26.7 1.0 FE3 A:F3S104 2.7 13.1 1.0 FE4 A:F3S104 2.8 13.9 1.0 CB A:CYS45 3.2 26.0 1.0 CA A:CYS45 3.7 25.8 1.0 N A:ALA47 3.8 31.0 1.0 S4 A:F3S104 3.9 29.8 1.0 N A:ILE46 4.0 29.0 1.0 C A:CYS45 4.2 27.6 1.0 N A:ASP48 4.2 34.0 1.0 CA A:ALA47 4.2 31.1 1.0 SG A:CYS93 4.6 29.9 1.0 CB A:ALA75 4.6 25.0 1.0 C A:ALA47 4.7 32.0 1.0 SG A:CYS51 4.7 30.4 1.0 N A:ALA75 4.8 23.2 1.0 C A:ILE46 4.8 30.4 1.0 N A:GLY49 5.0 35.8 1.0 N A:CYS45 5.0 25.1 1.0

Iron binding site 2 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe104 b:13.1 occ:1.00 FE3 A:F3S104 0.0 13.1 1.0 S1 A:F3S104 2.0 24.2 1.0 S3 A:F3S104 2.1 26.6 1.0 SG A:CYS93 2.2 29.9 1.0 S4 A:F3S104 2.2 29.8 1.0 FE1 A:F3S104 2.7 10.6 1.0 FE4 A:F3S104 2.7 13.9 1.0 CB A:CYS93 3.3 28.0 1.0 S2 A:F3S104 3.5 28.6 1.0 CD A:PRO94 3.8 33.1 1.0 CA A:CYS93 3.9 29.0 1.0 CG2 A:VAL95 4.3 23.6 1.0 N A:PRO94 4.5 31.1 1.0 C A:CYS93 4.6 30.4 1.0 CB A:ASP48 4.6 34.8 1.0 CG A:PRO94 4.6 33.4 1.0 SG A:CYS51 4.7 30.4 1.0 SG A:CYS45 4.7 26.7 1.0 CB A:ALA97 4.7 26.6 1.0 CD1 A:ILE98 4.8 20.7 1.0 CG1 A:ILE98 4.8 25.3 1.0 N A:ASP48 5.0 34.0 1.0 CA A:CYS45 5.0 25.8 1.0

Iron binding site 3 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe104 b:13.9 occ:1.00 FE4 A:F3S104 0.0 13.9 1.0 S2 A:F3S104 1.9 28.6 1.0 S4 A:F3S104 2.1 29.8 1.0 SG A:CYS51 2.2 30.4 1.0 S3 A:F3S104 2.2 26.6 1.0 FE3 A:F3S104 2.7 13.1 1.0 FE1 A:F3S104 2.8 10.6 1.0 CB A:CYS51 3.3 32.2 1.0 S1 A:F3S104 3.7 24.2 1.0 N A:CYS51 3.9 34.0 1.0 CB A:ALA75 4.1 25.0 1.0 CA A:CYS51 4.2 32.9 1.0 N A:GLY49 4.2 35.8 1.0 CD1 A:ILE98 4.3 20.7 1.0 N A:SER50 4.5 32.4 1.0 CA A:GLY49 4.6 33.6 1.0 SG A:CYS93 4.6 29.9 1.0 SG A:CYS45 4.7 26.7 1.0 C A:GLY49 4.7 34.5 1.0 N A:ILE52 4.9 33.2 1.0 CB A:CYS93 5.0 28.0 1.0

Iron binding site 4 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:17.3 occ:1.00 FE1 A:SF4105 0.0 17.3 1.0 S3 A:SF4105 2.0 31.4 1.0 S4 A:SF4105 2.0 31.9 1.0 SG A:CYS55 2.2 34.6 1.0 S2 A:SF4105 2.2 30.9 1.0 FE3 A:SF4105 2.7 24.5 1.0 FE4 A:SF4105 2.7 17.7 1.0 FE2 A:SF4105 2.8 15.7 1.0 CB A:CYS55 3.3 35.1 1.0 S1 A:SF4105 3.7 33.3 1.0 CA A:CYS55 3.8 37.4 1.0 CG2 A:VAL59 3.9 31.7 1.0 CD A:PRO56 4.0 38.9 1.0 CB A:VAL59 4.3 31.8 1.0 CE2 A:PHE60 4.4 27.5 1.0 SG A:CYS86 4.5 42.9 1.0 C A:CYS55 4.6 37.4 1.0 N A:PRO56 4.6 37.3 1.0 SG A:CYS89 4.7 33.6 1.0 SG A:CYS83 4.8 33.4 1.0 CG A:PRO56 4.8 38.7 1.0 N A:CYS55 4.9 36.7 1.0 N A:VAL57 5.0 37.6 1.0

Iron binding site 5 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:15.7 occ:1.00 FE2 A:SF4105 0.0 15.7 1.0 S3 A:SF4105 2.1 31.4 1.0 SG A:CYS83 2.2 33.4 1.0 S1 A:SF4105 2.2 33.3 1.0 S4 A:SF4105 2.2 31.9 1.0 FE1 A:SF4105 2.8 17.3 1.0 FE4 A:SF4105 2.8 17.7 1.0 FE3 A:SF4105 2.8 24.5 1.0 CB A:CYS83 3.2 35.1 1.0 CA A:CYS83 3.7 37.0 1.0 S2 A:SF4105 3.8 30.9 1.0 N A:PHE85 3.9 39.9 1.0 N A:ILE84 4.0 37.2 1.0 C A:CYS83 4.2 37.1 1.0 CA A:PHE85 4.3 39.7 1.0 CG2 A:VAL38 4.4 24.3 1.0 CG2 A:VAL59 4.4 31.7 1.0 N A:CYS86 4.6 40.2 1.0 CG1 A:VAL100 4.7 37.0 1.0 SG A:CYS55 4.7 34.6 1.0 SG A:CYS89 4.8 33.6 1.0 C A:ILE84 4.8 41.5 1.0 N A:CYS83 4.9 36.2 1.0 SG A:CYS86 5.0 42.9 1.0 CG2 A:VAL100 5.0 12.3 1.0 C A:PHE85 5.0 40.1 1.0 CA A:ILE84 5.0 40.5 1.0

Iron binding site 6 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:24.5 occ:1.00 FE3 A:SF4105 0.0 24.5 1.0 S4 A:SF4105 2.2 31.9 1.0 S2 A:SF4105 2.2 30.9 1.0 SG A:CYS86 2.2 42.9 1.0 S1 A:SF4105 2.2 33.3 1.0 FE1 A:SF4105 2.7 17.3 1.0 FE4 A:SF4105 2.7 17.7 1.0 FE2 A:SF4105 2.8 15.7 1.0 N A:CYS86 3.4 40.2 1.0 CB A:CYS86 3.4 40.1 1.0 S3 A:SF4105 3.5 31.4 1.0 N A:MET87 3.6 41.1 1.0 CA A:CYS86 3.8 38.0 1.0 C A:CYS86 4.1 40.2 1.0 CD A:PRO56 4.1 38.9 1.0 N A:ALA88 4.1 38.9 1.0 C A:PHE85 4.4 40.1 1.0 CA A:MET87 4.4 38.6 1.0 N A:PHE85 4.5 39.9 1.0 CD1 A:ILE84 4.6 43.4 1.0 SG A:CYS55 4.6 34.6 1.0 CG A:PRO56 4.6 38.7 1.0 SG A:CYS89 4.7 33.6 1.0 CA A:PHE85 4.7 39.7 1.0 SG A:CYS83 4.7 33.4 1.0 C A:MET87 4.7 37.6 1.0 CB A:ALA88 4.8 36.7 1.0 N A:CYS89 4.9 37.7 1.0

Iron binding site 7 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:17.7 occ:1.00 FE4 A:SF4105 0.0 17.7 1.0 S3 A:SF4105 2.1 31.4 1.0 S1 A:SF4105 2.1 33.3 1.0 S2 A:SF4105 2.2 30.9 1.0 SG A:CYS89 2.2 33.6 1.0 FE3 A:SF4105 2.7 24.5 1.0 FE1 A:SF4105 2.7 17.3 1.0 FE2 A:SF4105 2.8 15.7 1.0 CB A:CYS89 3.3 34.0 1.0 S4 A:SF4105 3.6 31.9 1.0 N A:CYS89 3.9 37.7 1.0 CA A:CYS89 4.2 36.3 1.0 CE2 A:PHE60 4.3 27.5 1.0 CG2 A:VAL100 4.4 12.3 1.0 CZ A:PHE60 4.4 26.8 1.0 SG A:CYS86 4.5 42.9 1.0 N A:MET87 4.6 41.1 1.0 N A:ALA88 4.6 38.9 1.0 SG A:CYS55 4.6 34.6 1.0 SG A:CYS83 4.7 33.4 1.0 CA A:MET87 4.7 38.6 1.0 C A:MET87 4.9 37.6 1.0 N A:VAL90 5.0 33.8 1.0

Iron binding site 8 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe104 b:10.4 occ:1.00 FE1 B:F3S104 0.0 10.4 1.0 S3 B:F3S104 2.0 26.6 1.0 S2 B:F3S104 2.1 28.6 1.0 S1 B:F3S104 2.1 24.3 1.0 SG B:CYS45 2.2 26.6 1.0 FE3 B:F3S104 2.7 12.7 1.0 FE4 B:F3S104 2.8 13.8 1.0 CB B:CYS45 3.2 25.9 1.0 N B:ALA47 3.6 31.0 1.0 CA B:CYS45 3.7 25.8 1.0 S4 B:F3S104 3.9 29.8 1.0 CA B:ALA47 3.9 31.1 1.0 N B:ILE46 3.9 28.9 1.0 N B:ASP48 4.1 34.0 1.0 C B:CYS45 4.2 27.6 1.0 C B:ALA47 4.5 32.0 1.0 SG B:CYS93 4.6 29.8 1.0 CB B:ALA75 4.6 25.0 1.0 SG B:CYS51 4.7 30.4 1.0 C B:ILE46 4.7 30.4 1.0 N B:ALA75 4.8 23.2 1.0 N B:GLY49 4.9 35.8 1.0 N B:CYS45 5.0 25.0 1.0 CA B:ILE46 5.0 28.7 1.0

Iron binding site 9 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe104 b:12.7 occ:1.00 FE3 B:F3S104 0.0 12.7 1.0 S1 B:F3S104 2.1 24.3 1.0 S3 B:F3S104 2.1 26.6 1.0 SG B:CYS93 2.2 29.8 1.0 S4 B:F3S104 2.2 29.8 1.0 FE1 B:F3S104 2.7 10.4 1.0 FE4 B:F3S104 2.7 13.8 1.0 CB B:CYS93 3.3 28.0 1.0 S2 B:F3S104 3.5 28.6 1.0 CD B:PRO94 3.9 33.1 1.0 CA B:CYS93 3.9 29.0 1.0 CG1 B:VAL95 4.3 25.6 1.0 CB B:ASP48 4.6 34.8 1.0 N B:PRO94 4.6 31.1 1.0 C B:CYS93 4.7 30.4 1.0 SG B:CYS51 4.7 30.4 1.0 SG B:CYS45 4.7 26.6 1.0 CB B:ALA97 4.7 26.6 1.0 CG B:PRO94 4.8 33.3 1.0 N B:ASP48 4.9 34.0 1.0 CG1 B:ILE98 4.9 25.3 1.0 CD1 B:ILE98 5.0 20.7 1.0

Iron binding site 10 out of 49 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe104 b:13.8 occ:1.00 FE4 B:F3S104 0.0 13.8 1.0 S2 B:F3S104 1.9 28.6 1.0 S4 B:F3S104 2.1 29.8 1.0 SG B:CYS51 2.1 30.4 1.0 S3 B:F3S104 2.2 26.6 1.0 FE3 B:F3S104 2.7 12.7 1.0 FE1 B:F3S104 2.8 10.4 1.0 CB B:CYS51 3.3 32.2 1.0 S1 B:F3S104 3.7 24.3 1.0 N B:CYS51 3.9 34.0 1.0 N B:GLY49 4.0 35.8 1.0 CB B:ALA75 4.1 25.0 1.0 CA B:CYS51 4.2 32.9 1.0 CA B:GLY49 4.4 33.6 1.0 CD1 B:ILE98 4.4 20.7 1.0 N B:SER50 4.4 32.4 1.0 SG B:CYS93 4.6 29.8 1.0 C B:GLY49 4.6 34.5 1.0 SG B:CYS45 4.7 26.6 1.0 N B:ILE52 4.9 33.2 1.0 N B:ASP48 4.9 34.0 1.0

C.Frazao, D.Aragao, R.Coelho, S.S.Leal, C.M.Gomes, M.Teixeira, M.A.Carrondo. Crystallographic Analysis of the Intact Metal Centres [3FE-4S](1+/0) and [4FE-4S](2+/1+) in A Zn(2+) -Containing Ferredoxin. Febs Lett. V. 582 763 2008.
ISSN: ISSN 0014-5793
PubMed: 18258200
DOI: 10.1016/J.FEBSLET.2008.01.041