Iron in PDB 2v2k: The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis

The structure of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis, PDB code: 2v2k was solved by S.Ricagno, M.De Rosa, A.Aliverti, G.Zanetti, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.73 / 1.6
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	54.581, 54.526, 135.382, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis (pdb code 2v2k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis, PDB code: 2v2k:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:14.2 occ:1.00 FE1 A:F3S107 0.0 14.2 1.0 S1 A:F3S107 2.3 16.1 1.0 S3 A:F3S107 2.3 14.1 1.0 SG A:CYS39 2.3 20.0 1.0 S2 A:F3S107 2.3 15.6 1.0 FE4 A:F3S107 2.7 15.7 1.0 FE3 A:F3S107 2.7 13.8 1.0 CB A:CYS39 3.4 19.6 1.0 CA A:CYS39 3.9 19.1 1.0 S4 A:F3S107 4.0 16.0 1.0 N A:ASP41 4.0 20.1 1.0 N A:VAL40 4.1 20.1 1.0 SG A:CYS24 4.2 23.1 1.0 N A:CSS42 4.3 21.9 1.0 C A:CYS39 4.4 19.3 1.0 CA A:ASP41 4.4 20.0 1.0 CG2 A:ILE34 4.6 18.1 1.0 CB A:TYR2 4.7 21.2 1.0 CD2 A:TYR2 4.8 18.5 1.0 SG A:CYS20 4.8 21.5 1.0 N A:GLY43 4.8 21.8 1.0 C A:ASP41 4.8 19.9 1.0 SG A:CYS45 4.9 21.6 1.0 C A:VAL40 4.9 19.9 1.0 N A:TYR2 4.9 21.3 1.0 CG A:TYR2 5.0 19.6 1.0

Iron binding site 2 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:13.8 occ:1.00 FE3 A:F3S107 0.0 13.8 1.0 S1 A:F3S107 2.3 16.1 1.0 S4 A:F3S107 2.3 16.0 1.0 S3 A:F3S107 2.3 14.1 1.0 SG A:CYS45 2.3 21.6 1.0 FE4 A:F3S107 2.7 15.7 1.0 FE1 A:F3S107 2.7 14.2 1.0 CB A:CYS45 3.4 20.6 1.0 S2 A:F3S107 4.0 15.6 1.0 N A:GLY43 4.0 21.8 1.0 N A:CYS45 4.0 21.1 1.0 CA A:CYS45 4.4 21.4 1.0 CA A:GLY43 4.4 21.3 1.0 N A:ALA44 4.5 20.5 1.0 CD1 A:ILE25 4.6 21.1 1.0 CB A:TYR2 4.7 21.2 1.0 C A:GLY43 4.7 20.6 1.0 CD1 A:ILE34 4.7 18.7 1.0 SG A:CYS20 4.7 21.5 1.0 SG A:CYS39 4.8 20.0 1.0 CG A:TYR2 4.8 19.6 1.0 CB A:CYS20 4.9 21.1 1.0

Iron binding site 3 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe107 b:15.7 occ:1.00 FE4 A:F3S107 0.0 15.7 1.0 S2 A:F3S107 2.3 15.6 1.0 S4 A:F3S107 2.3 16.0 1.0 S3 A:F3S107 2.3 14.1 1.0 SG A:CYS20 2.3 21.5 1.0 FE1 A:F3S107 2.7 14.2 1.0 FE3 A:F3S107 2.7 13.8 1.0 CB A:CYS20 3.3 21.1 1.0 CA A:CYS20 3.8 22.0 1.0 S1 A:F3S107 3.9 16.1 1.0 SG A:CYS24 4.0 23.1 1.0 CD A:PRO21 4.2 22.1 1.0 CG2 A:VAL22 4.5 24.4 1.0 CB A:CSS42 4.5 23.1 1.0 C A:CYS20 4.6 22.4 1.0 N A:PRO21 4.7 22.2 1.0 SG A:CYS45 4.8 21.6 1.0 SG A:CYS39 4.8 20.0 1.0 CD1 A:ILE25 4.9 21.1 1.0 CG1 A:ILE25 5.0 21.5 1.0 SG A:CSS42 5.0 27.5 1.0

Iron binding site 4 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:15.7 occ:1.00 FE1 A:F3S108 0.0 15.7 1.0 S3 A:F3S108 2.2 16.9 1.0 S1 A:F3S108 2.3 17.8 1.0 S2 A:F3S108 2.3 16.9 1.0 SG A:CYS16 2.4 21.7 1.0 FE3 A:F3S108 2.6 15.9 1.0 FE4 A:F3S108 2.7 16.4 1.0 CB A:CYS16 3.4 22.6 1.0 S4 A:F3S108 3.9 19.6 1.0 N A:LYS14 4.0 23.1 1.0 N A:CYS16 4.1 22.5 1.0 CA A:LYS14 4.2 23.4 1.0 CA A:CYS16 4.4 22.4 1.0 N A:ALA15 4.5 23.1 1.0 CD1 A:ILE54 4.6 21.3 1.0 C A:LYS14 4.6 23.5 1.0 SG A:CYS49 4.8 20.4 1.0 CD2 A:LEU32 4.8 23.9 1.0 SG A:CYS8 4.8 20.4 1.0 CD1 A:ILE4 4.9 18.3 0.7 N A:ASP13 4.9 23.3 1.0

Iron binding site 5 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:15.9 occ:1.00 FE3 A:F3S108 0.0 15.9 1.0 S1 A:F3S108 2.1 17.8 1.0 S3 A:F3S108 2.1 16.9 1.0 S4 A:F3S108 2.1 19.6 1.0 SG A:CYS8 2.4 20.4 1.0 FE1 A:F3S108 2.6 15.7 1.0 FE4 A:F3S108 2.6 16.4 1.0 CB A:CYS8 3.3 21.0 1.0 S2 A:F3S108 3.9 16.9 1.0 CA A:CYS8 4.0 21.0 1.0 CD1 A:ILE4 4.1 19.1 0.3 CA A:LYS12 4.1 23.1 1.0 N A:ASP13 4.2 23.3 1.0 N A:LYS12 4.4 22.9 1.0 C A:LYS12 4.5 23.1 1.0 CG2 A:ILE4 4.6 19.2 0.7 CG1 A:ILE4 4.7 19.7 0.3 O A:CYS8 4.7 21.1 1.0 SG A:CYS49 4.7 20.4 1.0 CB A:ALA53 4.7 21.5 1.0 N A:LYS14 4.8 23.1 1.0 CB A:LEU32 4.8 20.6 1.0 SG A:CYS16 4.8 21.7 1.0 C A:CYS8 4.9 21.3 1.0

Iron binding site 6 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:16.4 occ:1.00 FE4 A:F3S108 0.0 16.4 1.0 S2 A:F3S108 2.2 16.9 1.0 S3 A:F3S108 2.2 16.9 1.0 S4 A:F3S108 2.3 19.6 1.0 SG A:CYS49 2.4 20.4 1.0 FE3 A:F3S108 2.6 15.9 1.0 FE1 A:F3S108 2.7 15.7 1.0 CB A:CYS49 3.3 22.4 1.0 S1 A:F3S108 3.8 17.8 1.0 CA A:CYS49 3.9 21.8 1.0 CD A:PRO50 4.3 21.7 1.0 CB A:ALA53 4.3 21.5 1.0 CG2 A:VAL51 4.5 20.5 1.0 CB A:ASP13 4.6 22.8 1.0 C A:CYS49 4.7 22.0 1.0 N A:PRO50 4.8 21.9 1.0 N A:ASP13 4.8 23.3 1.0 CD1 A:ILE4 4.8 19.1 0.3 SG A:CYS16 4.9 21.7 1.0 SG A:CYS8 4.9 20.4 1.0 N A:LYS14 5.0 23.1 1.0

Iron binding site 7 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe107 b:12.3 occ:1.00 FE1 B:F3S107 0.0 12.3 1.0 SG B:CYS39 2.2 16.6 1.0 S2 B:F3S107 2.3 13.5 1.0 S3 B:F3S107 2.3 12.4 1.0 S1 B:F3S107 2.3 14.2 1.0 FE3 B:F3S107 2.7 14.6 1.0 FE4 B:F3S107 2.8 12.7 1.0 CB B:CYS39 3.3 17.5 1.0 CA B:CYS39 3.8 17.4 1.0 S4 B:F3S107 4.0 14.7 1.0 N B:ASP41 4.0 18.0 1.0 N B:VAL40 4.1 18.1 1.0 SG B:CYS24 4.2 20.3 1.0 N B:CSS42 4.2 18.4 1.0 C B:CYS39 4.3 17.9 1.0 CA B:ASP41 4.4 17.5 1.0 CG2 B:ILE34 4.5 17.6 1.0 C B:ASP41 4.8 17.2 1.0 CD1 B:TYR2 4.8 16.3 1.0 CB B:TYR2 4.8 14.9 1.0 SG B:CYS20 4.9 18.2 1.0 SG B:CYS45 4.9 18.6 1.0 N B:GLY43 4.9 17.6 1.0 C B:VAL40 5.0 17.9 1.0 N B:TYR2 5.0 17.1 1.0

Iron binding site 8 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe107 b:14.6 occ:1.00 FE3 B:F3S107 0.0 14.6 1.0 S4 B:F3S107 2.3 14.7 1.0 S1 B:F3S107 2.3 14.2 1.0 S3 B:F3S107 2.3 12.4 1.0 SG B:CYS20 2.4 18.2 1.0 FE4 B:F3S107 2.7 12.7 1.0 FE1 B:F3S107 2.7 12.3 1.0 CB B:CYS20 3.3 18.9 1.0 CA B:CYS20 3.8 18.4 1.0 S2 B:F3S107 3.8 13.5 1.0 SG B:CYS24 4.0 20.3 1.0 CD B:PRO21 4.2 19.7 1.0 CG2 B:VAL22 4.4 19.4 1.0 CB B:CSS42 4.5 20.2 1.0 C B:CYS20 4.5 18.9 1.0 N B:PRO21 4.6 18.7 1.0 SG B:CYS45 4.8 18.6 1.0 SG B:CYS39 4.9 16.6 1.0 N B:CSS42 4.9 18.4 1.0 CD1 B:ILE25 4.9 16.3 1.0 SG B:CSS42 5.0 24.9 1.0

Iron binding site 9 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe107 b:12.7 occ:1.00 FE4 B:F3S107 0.0 12.7 1.0 S2 B:F3S107 2.3 13.5 1.0 S4 B:F3S107 2.3 14.7 1.0 S3 B:F3S107 2.3 12.4 1.0 SG B:CYS45 2.3 18.6 1.0 FE3 B:F3S107 2.7 14.6 1.0 FE1 B:F3S107 2.8 12.3 1.0 CB B:CYS45 3.4 18.6 1.0 S1 B:F3S107 4.0 14.2 1.0 N B:CYS45 4.0 18.6 1.0 N B:GLY43 4.2 17.6 1.0 CA B:CYS45 4.3 19.2 1.0 CA B:GLY43 4.4 16.9 1.0 N B:ALA44 4.5 18.4 1.0 C B:GLY43 4.7 17.8 1.0 SG B:CYS39 4.7 16.6 1.0 CD1 B:ILE25 4.7 16.3 1.0 SG B:CYS20 4.8 18.2 1.0 CD1 B:ILE34 4.8 15.8 1.0 CG B:TYR2 4.9 16.5 1.0 CB B:TYR2 4.9 14.9 1.0

Iron binding site 10 out of 12 in the The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe108 b:15.2 occ:1.00 FE1 B:F3S108 0.0 15.2 1.0 S3 B:F3S108 2.3 14.4 1.0 S1 B:F3S108 2.3 16.5 1.0 S2 B:F3S108 2.3 14.4 1.0 SG B:CYS16 2.4 18.7 1.0 FE3 B:F3S108 2.6 15.6 1.0 FE4 B:F3S108 2.6 15.7 1.0 CB B:CYS16 3.4 19.1 1.0 S4 B:F3S108 3.9 17.6 1.0 N B:LYS14 4.0 19.4 1.0 N B:CYS16 4.1 19.8 1.0 CA B:LYS14 4.3 20.4 1.0 CA B:CYS16 4.4 19.4 1.0 CD1 B:ILE54 4.6 19.7 1.0 N B:ALA15 4.6 20.0 1.0 C B:LYS14 4.7 20.1 1.0 CD2 B:LEU32 4.8 18.9 1.0 SG B:CYS8 4.8 17.1 1.0 SG B:CYS49 4.8 17.7 1.0 CD1 B:ILE4 4.8 18.1 1.0 N B:ASP13 4.9 19.1 1.0 CB B:CYS49 4.9 18.6 1.0

S.Ricagno, M.De Rosa, A.Aliverti, G.Zanetti, M.Bolognesi. The Crystal Structure of Fdxa, A 7FE Ferredoxin From Mycobacterium Smegmatis. Biochem.Biophys.Res.Commun. V. 360 97 2007.
ISSN: ISSN 0006-291X
PubMed: 17577575
DOI: 10.1016/J.BBRC.2007.06.013