Iodine in PDB 9krr: Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803

The structure of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803, PDB code: 9krr was solved by B.T.Zhang, S.W.Liu, Y.C.Xu, W.Sheng, Y.Gong, P.Cao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.39 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.899, 74.437, 133.182, 90, 106.11, 90
R / Rfree (%)	16.8 / 21

The structure of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 also contains other interesting chemical elements:

Iron

(Fe)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 (pdb code 9krr). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803, PDB code: 9krr:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:I104 b:42.0 occ:0.56 ND2 A:ASN13 3.3 25.0 1.0 O C:HOH250 3.5 36.0 1.0 CA C:HIS5 3.7 22.7 1.0 CD2 C:HIS5 3.9 30.9 1.0 O C:ALA4 4.0 20.0 1.0 CB C:ALA8 4.1 22.9 1.0 N C:HIS5 4.1 24.8 1.0 CB C:HIS5 4.2 22.0 1.0 O A:HOH275 4.3 43.5 1.0 C C:ALA4 4.3 19.0 1.0 CG A:ASN13 4.4 21.9 1.0 CG C:HIS5 4.4 25.5 1.0 CA A:GLY12 4.5 29.6 1.0 CA A:ILE9 4.5 20.6 1.0 O A:ILE9 4.7 17.1 1.0 O A:HOH244 4.7 40.7 1.0 OD1 A:ASN13 4.7 20.6 1.0 O A:ALA8 4.8 20.1 1.0 C C:HIS5 4.8 24.4 1.0 C A:GLY12 4.9 24.0 1.0 O C:HIS5 4.9 18.2 1.0 CG1 A:ILE9 4.9 26.9 1.0

Iodine binding site 2 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:I105 b:35.8 occ:0.36 N A:ALA57 3.4 23.1 1.0 CGD A:HEC101 3.6 36.4 1.0 O1D A:HEC101 3.7 36.2 1.0 O2D A:HEC101 3.8 36.6 1.0 CB A:ALA57 3.9 23.1 1.0 ND2 A:ASN26 3.9 23.5 1.0 CBD A:HEC101 3.9 19.6 1.0 CA A:GLY56 4.2 28.3 1.0 CMD A:HEC101 4.2 21.9 1.0 CA A:ALA57 4.3 21.9 1.0 C A:GLY56 4.3 22.6 1.0 CAD A:HEC101 4.4 13.6 1.0 O A:HOH273 4.4 42.2 1.0 CB A:ASN26 4.5 22.4 1.0 O A:HOH301 4.6 41.7 1.0 CG A:ASN26 4.7 24.0 1.0 O A:ASN55 4.9 25.8 1.0

Iodine binding site 3 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:I106 b:33.3 occ:0.29 CGD A:HEC101 3.4 36.4 1.0 NE2 A:GLN50 3.4 21.5 1.0 ND2 A:ASN55 3.4 38.5 1.0 CBD A:HEC101 3.5 19.6 1.0 O1D A:HEC101 3.6 36.2 1.0 O2D A:HEC101 3.7 36.6 1.0 O A:HOH255 3.8 36.9 1.0 CAD A:HEC101 3.9 13.6 1.0 CD A:LYS29 4.0 21.8 1.0 OE1 A:GLN50 4.0 26.6 1.0 CHA A:HEC101 4.1 14.8 1.0 CD A:GLN50 4.1 23.8 1.0 CAA A:HEC101 4.1 12.0 1.0 CB A:ASN55 4.2 24.7 1.0 CG A:ASN55 4.3 33.0 1.0 CE A:LYS29 4.5 26.7 1.0 O2A A:HEC101 4.5 18.0 1.0 CG A:LYS29 4.6 21.2 1.0 CE A:LYS41 4.6 26.2 1.0 C3D A:HEC101 4.7 15.3 1.0 C4D A:HEC101 4.8 17.6 1.0 C1A A:HEC101 4.8 11.9 1.0 C2A A:HEC101 4.9 14.0 1.0 CBA A:HEC101 4.9 12.7 1.0 CB A:LYS29 4.9 19.1 1.0

Iodine binding site 4 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ B:I105 b:27.2 occ:0.44 N B:ALA57 3.8 22.3 1.0 O1D B:HEC101 3.8 24.6 1.0 CMD B:HEC101 3.9 18.6 1.0 CB B:ALA57 3.9 20.6 1.0 CGD B:HEC101 4.0 28.7 1.0 ND2 B:ASN26 4.0 27.0 1.0 CB B:ASN26 4.2 14.8 1.0 CBD B:HEC101 4.3 18.0 1.0 O2D B:HEC101 4.4 27.3 1.0 CA B:ALA57 4.5 17.6 1.0 CAD B:HEC101 4.6 17.3 1.0 CG B:ASN26 4.6 21.7 1.0 CG2 B:ILE25 4.6 16.3 1.0 CA B:GLY56 4.6 24.2 1.0 C B:GLY56 4.7 24.6 1.0 CB A:ALA16 4.8 20.4 1.0

Iodine binding site 5 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ C:I104 b:31.1 occ:0.40 N C:ALA57 3.8 22.4 1.0 CMD C:HEC101 3.8 20.7 1.0 CGD C:HEC101 3.8 32.5 1.0 O1D C:HEC101 3.9 27.1 1.0 CBD C:HEC101 4.1 19.7 1.0 CB C:ALA57 4.2 24.9 1.0 O2D C:HEC101 4.2 34.9 1.0 ND2 C:ASN26 4.3 27.0 1.0 CB C:ASN26 4.3 15.6 1.0 CG2 C:ILE25 4.4 20.1 1.0 CAD C:HEC101 4.4 10.8 1.0 CA C:GLY56 4.5 27.7 1.0 CA C:ALA57 4.6 28.1 1.0 C C:GLY56 4.7 24.3 1.0 CG C:ASN26 4.7 27.0 1.0 C2D C:HEC101 4.9 13.6 1.0

Iodine binding site 6 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ D:I104 b:24.2 occ:0.45 O D:HOH303 3.2 37.5 1.0 N D:ALA57 3.7 24.7 1.0 CGD D:HEC101 3.9 22.7 1.0 CMD D:HEC101 3.9 15.4 1.0 O1D D:HEC101 3.9 27.3 1.0 CB D:ALA57 4.1 16.6 1.0 ND2 D:ASN26 4.1 25.2 1.0 O2D D:HEC101 4.1 24.6 1.0 CBD D:HEC101 4.2 15.1 1.0 CB C:ALA16 4.2 25.9 1.0 CB D:ASN26 4.4 13.5 1.0 CA D:GLY56 4.4 24.9 1.0 CG2 D:ILE25 4.5 18.4 1.0 CAD D:HEC101 4.5 10.2 1.0 CA D:ALA57 4.5 20.1 1.0 O C:HOH291 4.5 43.6 1.0 C D:GLY56 4.6 23.7 1.0 CG D:ASN26 4.7 17.6 1.0 O D:HOH295 4.9 39.2 1.0 C2D D:HEC101 5.0 13.8 1.0

Iodine binding site 7 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ E:I105 b:30.8 occ:0.51 O E:ALA4 3.7 29.9 1.0 CA E:HIS5 3.8 25.4 1.0 C E:ALA4 3.9 25.3 1.0 N E:HIS5 4.0 22.9 1.0 CB E:ALA8 4.2 23.1 1.0 ND1 E:HIS5 4.4 35.8 1.0 CB E:HIS5 4.5 28.5 1.0 CB E:ALA4 4.6 28.9 1.0 CA E:ALA4 4.9 29.2 1.0 CG E:HIS5 4.9 32.5 1.0 C E:HIS5 4.9 25.9 1.0

Iodine binding site 8 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ F:I105 b:30.4 occ:0.41 N F:ALA57 3.7 23.8 1.0 CMD F:HEC101 3.8 17.9 1.0 CGD F:HEC101 3.9 30.7 1.0 CB F:ALA57 4.0 23.0 1.0 O1D F:HEC101 4.0 23.6 1.0 ND2 F:ASN26 4.1 30.3 1.0 O2D F:HEC101 4.1 33.0 1.0 CB F:ASN26 4.3 22.1 1.0 CBD F:HEC101 4.3 18.2 1.0 CG2 F:ILE25 4.4 25.3 1.0 CA F:ALA57 4.5 28.6 1.0 CA F:GLY56 4.5 26.4 1.0 CAD F:HEC101 4.5 12.6 1.0 C F:GLY56 4.6 25.1 1.0 CG F:ASN26 4.6 22.6 1.0 C2D F:HEC101 5.0 16.4 1.0

Iodine binding site 9 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ F:I106 b:53.7 occ:0.33 O F:HOH212 3.4 15.6 1.0 N F:TRP85 3.5 18.3 1.0 O F:HOH265 3.5 31.7 1.0 CA F:GLY84 3.6 28.0 1.0 CG F:LYS32 3.9 17.6 1.0 CD1 F:TRP85 4.0 16.9 1.0 C F:GLY84 4.0 29.8 1.0 O F:HOH240 4.2 37.6 1.0 CB F:TRP85 4.3 19.3 1.0 CA F:TRP85 4.5 18.8 1.0 CG F:TRP85 4.6 13.5 1.0 CD F:LYS32 4.6 24.3 1.0 CB F:LYS32 4.6 13.3 1.0 CE F:LYS32 4.7 32.4 1.0 N F:GLY84 4.8 25.4 1.0 NZ F:LYS32 4.8 37.0 1.0 CA F:LYS32 4.9 13.0 1.0

Iodine binding site 10 out of 16 in the Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Reduced Cytochrome C6 From Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ G:I104 b:31.7 occ:0.42 O2D G:HEC102 3.0 33.0 1.0 O G:HOH290 3.3 35.6 1.0 CGD G:HEC102 3.7 29.0 1.0 N G:ALA57 3.8 21.4 1.0 CBD G:HEC102 4.0 19.4 1.0 ND2 G:ASN26 4.2 24.9 1.0 CMD G:HEC102 4.2 14.0 1.0 CB G:ALA57 4.3 24.9 1.0 CAD G:HEC102 4.3 12.9 1.0 OG F:SER0 4.3 30.2 1.0 O G:HOH296 4.3 39.6 1.0 CA G:GLY56 4.4 28.1 1.0 O G:HOH310 4.4 27.5 1.0 CB G:ASN26 4.5 18.9 1.0 CB F:SER0 4.5 26.5 1.0 O F:SER0 4.5 21.8 1.0 C F:SER0 4.6 22.1 1.0 C G:GLY56 4.6 23.0 1.0 CA G:ALA57 4.7 21.9 1.0 CA F:ALA1 4.7 27.2 1.0 N F:ALA1 4.7 20.9 1.0 O1D G:HEC102 4.7 30.6 1.0 CG G:ASN26 4.8 24.4 1.0 O G:ASN55 4.9 22.7 1.0 O F:HOH234 4.9 24.4 1.0 O G:HOH287 4.9 40.5 1.0 CG2 G:ILE25 5.0 22.1 1.0 CB F:ALA4 5.0 20.2 1.0

B.Zhang, Y.Xu, S.Liu, S.Chen, W.Zhao, Z.Li, J.Wang, W.Zhao, H.Zhang, Y.Dong, Y.Gong, W.Sheng, P.Cao. A High-Resolution Crystallographic Study of Cytochrome C6: Structural Basis For Electron Transfer in Cyanobacterial Photosynthesis Int J Mol Sci V. 26 2025.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS26020824