Iron in PDB 6l7p: Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex

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

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex (pdb code 6l7p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex, PDB code: 6l7p:
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 Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe201 b:67.1 occ:1.00 FE1 I:SF4201 0.0 67.1 1.0 S2 I:SF4201 2.3 67.1 1.0 S4 I:SF4201 2.3 67.1 1.0 S3 I:SF4201 2.3 67.1 1.0 FE3 I:SF4201 2.6 67.1 1.0 FE4 I:SF4201 2.7 67.1 1.0 FE2 I:SF4201 2.7 67.1 1.0 SG I:CYS106 3.2 44.5 1.0 S1 I:SF4201 3.8 67.1 1.0 N I:CYS106 4.4 44.5 1.0 SG I:CYS73 4.4 38.1 1.0 N I:ASN108 4.5 45.2 1.0 N I:ALA107 4.5 46.6 1.0 CB I:CYS106 4.7 44.5 1.0 CB I:ASN108 4.8 45.2 1.0 SG I:CYS109 4.8 44.5 1.0 N I:PHE105 4.8 37.7 1.0 CB I:ILE104 4.9 34.7 1.0 CA I:CYS106 4.9 44.5 1.0 CD I:PRO74 5.0 35.5 1.0

Iron binding site 2 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe201 b:67.1 occ:1.00 FE2 I:SF4201 0.0 67.1 1.0 S4 I:SF4201 2.3 67.1 1.0 S3 I:SF4201 2.3 67.1 1.0 S1 I:SF4201 2.3 67.1 1.0 SG I:CYS103 2.7 34.3 1.0 FE1 I:SF4201 2.7 67.1 1.0 FE3 I:SF4201 2.8 67.1 1.0 FE4 I:SF4201 2.8 67.1 1.0 S2 I:SF4201 4.0 67.1 1.0 CB I:CYS103 4.1 34.3 1.0 N I:PHE105 4.2 37.7 1.0 N I:ILE104 4.2 34.7 1.0 CD1 I:ILE56 4.4 45.6 1.0 CA I:CYS103 4.4 34.3 1.0 CA I:PHE105 4.7 37.7 1.0 C I:CYS103 4.8 34.3 1.0 CD1 I:LEU77 4.8 35.8 1.0 SG I:CYS73 5.0 38.1 1.0

Iron binding site 3 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe201 b:67.1 occ:1.00 FE3 I:SF4201 0.0 67.1 1.0 S2 I:SF4201 2.3 67.1 1.0 S4 I:SF4201 2.3 67.1 1.0 S1 I:SF4201 2.3 67.1 1.0 SG I:CYS109 2.5 44.5 1.0 FE1 I:SF4201 2.6 67.1 1.0 FE2 I:SF4201 2.8 67.1 1.0 FE4 I:SF4201 2.8 67.1 1.0 CB I:CYS109 3.7 44.5 1.0 S3 I:SF4201 3.9 67.1 1.0 N I:CYS109 4.1 44.5 1.0 CA I:CYS109 4.6 44.5 1.0 N I:ASN108 4.7 45.2 1.0 SG I:CYS73 4.7 38.1 1.0 CD1 I:ILE56 4.9 45.6 1.0 CG1 I:ILE56 5.0 45.6 1.0

Iron binding site 4 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe201 b:67.1 occ:1.00 FE4 I:SF4201 0.0 67.1 1.0 SG I:CYS73 2.2 38.1 1.0 S3 I:SF4201 2.3 67.1 1.0 S1 I:SF4201 2.3 67.1 1.0 S2 I:SF4201 2.3 67.1 1.0 FE1 I:SF4201 2.7 67.1 1.0 FE3 I:SF4201 2.8 67.1 1.0 FE2 I:SF4201 2.8 67.1 1.0 CB I:CYS73 3.6 38.1 1.0 S4 I:SF4201 3.9 67.1 1.0 CA I:CYS73 4.4 38.1 1.0 CD1 I:LEU77 4.5 35.8 1.0 SG I:CYS109 4.7 44.5 1.0 CG I:LEU77 4.7 35.8 1.0 CD I:PRO78 4.7 37.7 1.0 CB I:LEU77 4.7 35.8 1.0 CD I:PRO74 4.8 35.5 1.0

Iron binding site 5 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe202 b:0.7 occ:1.00 FE1 I:SF4202 0.0 0.7 1.0 S3 I:SF4202 2.3 0.7 1.0 S2 I:SF4202 2.3 0.7 1.0 S4 I:SF4202 2.3 0.7 1.0 FE4 I:SF4202 2.6 0.7 1.0 FE3 I:SF4202 2.7 0.7 1.0 FE2 I:SF4202 2.7 0.7 1.0 SG I:CYS113 3.1 57.5 1.0 CB I:CYS117 3.4 58.0 1.0 S1 I:SF4202 3.8 0.7 1.0 SG I:CYS117 4.1 58.0 1.0 SG I:CYS69 4.6 49.3 1.0 CA I:CYS117 4.6 58.0 1.0 SG I:CYS66 4.7 61.9 1.0 CB I:CYS113 4.7 57.5 1.0 N I:CYS117 4.8 58.0 1.0 OG1 I:THR115 4.9 59.5 1.0

Iron binding site 6 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe202 b:0.7 occ:1.00 FE2 I:SF4202 0.0 0.7 1.0 S4 I:SF4202 2.3 0.7 1.0 S3 I:SF4202 2.3 0.7 1.0 S1 I:SF4202 2.3 0.7 1.0 FE1 I:SF4202 2.7 0.7 1.0 SG I:CYS69 2.7 49.3 1.0 FE3 I:SF4202 2.8 0.7 1.0 FE4 I:SF4202 2.8 0.7 1.0 S2 I:SF4202 4.0 0.7 1.0 CB I:CYS69 4.1 49.3 1.0 OH I:TYR96 4.6 46.5 1.0 N I:CYS69 4.7 49.3 1.0

Iron binding site 7 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe202 b:0.7 occ:1.00 FE3 I:SF4202 0.0 0.7 1.0 S4 I:SF4202 2.3 0.7 1.0 S2 I:SF4202 2.3 0.7 1.0 S1 I:SF4202 2.3 0.7 1.0 FE1 I:SF4202 2.7 0.7 1.0 FE4 I:SF4202 2.8 0.7 1.0 SG I:CYS63 2.8 64.4 1.0 FE2 I:SF4202 2.8 0.7 1.0 SG I:CYS117 3.4 58.0 1.0 S3 I:SF4202 3.9 0.7 1.0 CB I:CYS117 3.9 58.0 1.0 CB I:CYS63 4.1 64.4 1.0 CE2 I:PHE58 4.3 50.9 1.0 CA I:CYS63 4.4 64.4 1.0 N I:ALA65 4.5 63.1 1.0 N I:ILE64 4.5 66.5 1.0 CA I:ALA65 4.9 63.1 1.0 CZ I:PHE58 5.0 50.9 1.0 SG I:CYS66 5.0 61.9 1.0

Iron binding site 8 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe202 b:0.7 occ:1.00 FE4 I:SF4202 0.0 0.7 1.0 S3 I:SF4202 2.3 0.7 1.0 S2 I:SF4202 2.3 0.7 1.0 S1 I:SF4202 2.3 0.7 1.0 SG I:CYS66 2.4 61.9 1.0 FE1 I:SF4202 2.6 0.7 1.0 FE3 I:SF4202 2.8 0.7 1.0 FE2 I:SF4202 2.8 0.7 1.0 N I:CYS66 3.8 61.9 1.0 S4 I:SF4202 3.9 0.7 1.0 CB I:CYS66 4.0 61.9 1.0 N I:GLU67 4.2 57.3 1.0 CA I:CYS66 4.3 61.9 1.0 N I:VAL68 4.5 54.6 1.0 C I:CYS66 4.6 61.9 1.0 N I:ALA65 4.7 63.1 1.0 C I:ALA65 4.8 63.1 1.0 CA I:ALA65 4.9 63.1 1.0 CG1 I:ILE64 4.9 66.5 1.0 SG I:CYS69 4.9 49.3 1.0 CB I:VAL68 5.0 54.6 1.0

Iron binding site 9 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ K:Fe301 b:57.9 occ:1.00 FE1 K:SF4301 0.0 57.9 1.0 S3 K:SF4301 2.3 57.9 1.0 S4 K:SF4301 2.3 57.9 1.0 S2 K:SF4301 2.3 57.9 1.0 SG K:CYS117 2.4 26.7 1.0 FE4 K:SF4301 2.6 57.9 1.0 FE2 K:SF4301 2.7 57.9 1.0 FE3 K:SF4301 2.8 57.9 1.0 CB K:CYS117 3.7 26.7 1.0 S1 K:SF4301 3.9 57.9 1.0 OG1 K:THR89 4.0 27.9 1.0 N K:CYS117 4.3 26.7 1.0 SG K:CYS148 4.5 31.6 1.0 CA K:CYS117 4.7 26.7 1.0 N K:THR89 4.9 27.9 1.0 SG K:CYS53 5.0 31.6 1.0

Iron binding site 10 out of 12 in the Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Cyanobacteria Ndh-1LDELV Complex within 5.0Å range: probe atom residue distance (Å) B Occ K:Fe301 b:57.9 occ:1.00 FE2 K:SF4301 0.0 57.9 1.0 S1 K:SF4301 2.3 57.9 1.0 S4 K:SF4301 2.3 57.9 1.0 S3 K:SF4301 2.3 57.9 1.0 SG K:CYS53 2.5 31.6 1.0 FE1 K:SF4301 2.7 57.9 1.0 FE3 K:SF4301 2.7 57.9 1.0 FE4 K:SF4301 2.7 57.9 1.0 S2 K:SF4301 3.9 57.9 1.0 SG K:CYS117 4.1 26.7 1.0 CB K:CYS53 4.2 31.6 1.0 SG K:CYS52 4.5 34.5 1.0 CA K:GLY115 4.6 24.4 1.0 N K:CYS53 4.7 31.6 1.0 CB K:PRO149 4.8 32.3 1.0 CA K:PRO149 4.8 32.3 1.0 CA K:CYS53 4.9 31.6 1.0 N K:ALA116 5.0 24.7 1.0

W.Ma, M.Lei, J.Wu, J.Shuai, C.Zhang, Z.Ran, J.Zhao, Z.Wu, R.Liao. Structural Insights Into Ndh-1 Mediated Cyclic Electron Transfer Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-14732-Z