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Iron in PDB 6nby: T.Elongatus Ndh (Composite Model)

Enzymatic activity of T.Elongatus Ndh (Composite Model)

All present enzymatic activity of T.Elongatus Ndh (Composite Model):
1.6.5.11;

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the T.Elongatus Ndh (Composite Model) (pdb code 6nby). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the T.Elongatus Ndh (Composite Model), PDB code: 6nby:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6nby

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Iron binding site 1 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:34.4
occ:1.00
 FE1 I:SF4201 0.0 34.4 1.0
S3 I:SF4201 2.3 34.4 1.0
S2 I:SF4201 2.3 34.4 1.0
S4 I:SF4201 2.3 34.4 1.0
FE3 I:SF4201 2.7 34.4 1.0
FE4 I:SF4201 2.7 34.4 1.0
FE2 I:SF4201 2.7 34.4 1.0
O I:ILE104 2.9 32.8 1.0
SG I:CYS106 3.1 35.2 1.0
N I:ALA107 3.5 37.4 1.0
N I:CYS106 3.9 35.2 1.0
S1 I:SF4201 3.9 34.4 1.0
C I:ILE104 4.1 32.8 1.0
CB I:CYS106 4.2 35.2 1.0
CA I:ALA107 4.3 37.4 1.0
CD I:PRO74 4.3 30.1 1.0
C I:CYS106 4.3 35.2 1.0
CA I:CYS106 4.3 35.2 1.0
N I:ASN108 4.4 36.4 1.0
CG1 I:ILE104 4.6 32.8 1.0
SG I:CYS103 4.7 31.9 1.0
C I:PHE105 4.8 33.1 1.0
CA I:PHE105 4.8 33.1 1.0
SG I:CYS73 4.9 31.8 1.0
C I:ALA107 4.9 37.4 1.0
N I:PHE105 5.0 33.1 1.0

Iron binding site 2 out of 12 in 6nby

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Iron binding site 2 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:34.4
occ:1.00
 FE2 I:SF4201 0.0 34.4 1.0
S4 I:SF4201 2.3 34.4 1.0
S1 I:SF4201 2.3 34.4 1.0
S3 I:SF4201 2.3 34.4 1.0
FE4 I:SF4201 2.7 34.4 1.0
FE3 I:SF4201 2.7 34.4 1.0
FE1 I:SF4201 2.7 34.4 1.0
SG I:CYS103 3.1 31.9 1.0
O I:ILE104 3.7 32.8 1.0
CB I:CYS103 3.8 31.9 1.0
S2 I:SF4201 3.9 34.4 1.0
CG2 I:ILE98 4.1 34.5 1.0
CD2 I:LEU77 4.3 31.2 1.0
CA I:CYS103 4.4 31.9 1.0
CG1 I:ILE56 4.6 43.4 1.0
C I:ILE104 4.9 32.8 1.0
CD1 I:ILE56 4.9 43.4 1.0
C I:CYS103 5.0 31.9 1.0

Iron binding site 3 out of 12 in 6nby

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Iron binding site 3 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:34.4
occ:1.00
 FE3 I:SF4201 0.0 34.4 1.0
S4 I:SF4201 2.3 34.4 1.0
S2 I:SF4201 2.3 34.4 1.0
S1 I:SF4201 2.3 34.4 1.0
FE4 I:SF4201 2.7 34.4 1.0
FE1 I:SF4201 2.7 34.4 1.0
FE2 I:SF4201 2.7 34.4 1.0
SG I:CYS109 3.1 40.4 1.0
CB I:CYS109 3.6 40.4 1.0
CA I:ALA107 3.7 37.4 1.0
N I:CYS109 3.7 40.4 1.0
S3 I:SF4201 3.9 34.4 1.0
N I:ALA107 4.0 37.4 1.0
N I:ASN108 4.1 36.4 1.0
CD1 I:ILE56 4.2 43.4 1.0
C I:ALA107 4.3 37.4 1.0
CA I:CYS109 4.3 40.4 1.0
CG1 I:ILE56 4.6 43.4 1.0
C I:ASN108 4.8 36.4 1.0
CB I:ALA107 4.9 37.4 1.0
CA I:ASN108 4.9 36.4 1.0

Iron binding site 4 out of 12 in 6nby

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Iron binding site 4 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:34.4
occ:1.00
 FE4 I:SF4201 0.0 34.4 1.0
S1 I:SF4201 2.3 34.4 1.0
S2 I:SF4201 2.3 34.4 1.0
S3 I:SF4201 2.3 34.4 1.0
FE3 I:SF4201 2.7 34.4 1.0
FE2 I:SF4201 2.7 34.4 1.0
FE1 I:SF4201 2.7 34.4 1.0
SG I:CYS73 3.0 31.8 1.0
CB I:CYS73 3.3 31.8 1.0
S4 I:SF4201 3.9 34.4 1.0
CA I:CYS73 4.0 31.8 1.0
CD I:PRO78 4.1 32.4 1.0
CD I:PRO74 4.5 30.1 1.0
CB I:LEU77 4.5 31.2 1.0
CB I:CYS109 4.8 40.4 1.0
O I:CYS69 4.8 37.5 1.0
CG I:PRO78 4.8 32.4 1.0
C I:CYS73 5.0 31.8 1.0

Iron binding site 5 out of 12 in 6nby

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Iron binding site 5 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe202

b:49.3
occ:1.00
 FE1 I:SF4202 0.0 49.3 1.0
S2 I:SF4202 2.3 49.3 1.0
S4 I:SF4202 2.3 49.3 1.0
S3 I:SF4202 2.3 49.3 1.0
FE3 I:SF4202 2.7 49.3 1.0
FE4 I:SF4202 2.7 49.3 1.0
FE2 I:SF4202 2.7 49.3 1.0
CB I:CYS113 3.2 49.2 1.0
S1 I:SF4202 3.9 49.3 1.0
CA I:CYS113 4.0 49.2 1.0
CG2 I:THR115 4.2 52.9 1.0
CD1 I:LEU118 4.3 45.9 1.0
CB I:CYS117 4.3 52.1 1.0
CD I:PRO114 4.4 50.7 1.0
SG I:CYS113 4.7 49.2 1.0
CG I:LEU118 4.7 45.9 1.0
C I:CYS113 4.7 49.2 1.0
N I:LEU118 4.8 45.9 1.0
N I:PRO114 4.8 50.7 1.0
N I:CYS117 4.8 52.1 1.0

Iron binding site 6 out of 12 in 6nby

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Iron binding site 6 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe202

b:49.3
occ:1.00
 FE2 I:SF4202 0.0 49.3 1.0
S1 I:SF4202 2.3 49.3 1.0
S4 I:SF4202 2.3 49.3 1.0
S3 I:SF4202 2.3 49.3 1.0
FE4 I:SF4202 2.7 49.3 1.0
FE3 I:SF4202 2.7 49.3 1.0
FE1 I:SF4202 2.7 49.3 1.0
SG I:CYS69 3.1 37.5 1.0
CB I:CYS69 3.4 37.5 1.0
CD1 I:LEU118 3.5 45.9 1.0
S2 I:SF4202 3.9 49.3 1.0
N I:CYS69 4.1 37.5 1.0
OH I:TYR96 4.2 42.0 1.0
SG I:CYS63 4.3 50.4 1.0
CA I:CYS69 4.4 37.5 1.0
CG I:LEU118 4.4 45.9 1.0
CE1 I:TYR96 4.6 42.0 1.0
CZ I:TYR96 4.8 42.0 1.0

Iron binding site 7 out of 12 in 6nby

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Iron binding site 7 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe202

b:49.3
occ:1.00
 FE3 I:SF4202 0.0 49.3 1.0
S4 I:SF4202 2.3 49.3 1.0
S2 I:SF4202 2.3 49.3 1.0
S1 I:SF4202 2.3 49.3 1.0
FE1 I:SF4202 2.7 49.3 1.0
FE2 I:SF4202 2.7 49.3 1.0
FE4 I:SF4202 2.7 49.3 1.0
SG I:CYS63 3.1 50.4 1.0
CA I:CYS63 3.6 50.4 1.0
CB I:CYS63 3.8 50.4 1.0
S3 I:SF4202 3.9 49.3 1.0
N I:ILE64 3.9 48.7 1.0
C I:CYS63 4.1 50.4 1.0
SG I:CYS66 4.3 42.2 1.0
C I:ILE64 4.4 48.7 1.0
O I:ILE64 4.4 48.7 1.0
N I:ALA65 4.5 48.3 1.0
CG2 I:THR115 4.6 52.9 1.0
N I:CYS63 4.8 50.4 1.0
N I:CYS66 4.8 42.2 1.0
CA I:ILE64 4.9 48.7 1.0

Iron binding site 8 out of 12 in 6nby

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Iron binding site 8 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe202

b:49.3
occ:1.00
 FE4 I:SF4202 0.0 49.3 1.0
S3 I:SF4202 2.3 49.3 1.0
S2 I:SF4202 2.3 49.3 1.0
S1 I:SF4202 2.3 49.3 1.0
FE2 I:SF4202 2.7 49.3 1.0
FE3 I:SF4202 2.7 49.3 1.0
FE1 I:SF4202 2.7 49.3 1.0
SG I:CYS66 3.1 42.2 1.0
CB I:VAL68 3.7 38.7 1.0
N I:VAL68 3.8 38.7 1.0
CG2 I:VAL68 3.9 38.7 1.0
S4 I:SF4202 3.9 49.3 1.0
N I:CYS69 4.2 37.5 1.0
CA I:VAL68 4.2 38.7 1.0
N I:GLU67 4.3 41.0 1.0
CD I:PRO114 4.5 50.7 1.0
CB I:CYS66 4.6 42.2 1.0
C I:VAL68 4.6 38.7 1.0
C I:CYS66 4.7 42.2 1.0
N I:CYS66 4.8 42.2 1.0
C I:GLU67 4.8 41.0 1.0
SG I:CYS69 4.9 37.5 1.0
CG1 I:VAL68 4.9 38.7 1.0
CA I:CYS66 5.0 42.2 1.0
CA I:GLU67 5.0 41.0 1.0
O I:TYR112 5.0 42.2 1.0

Iron binding site 9 out of 12 in 6nby

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Iron binding site 9 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe301

b:32.8
occ:1.00
 FE1 K:SF4301 0.0 32.8 1.0
S4 K:SF4301 2.3 32.8 1.0
S2 K:SF4301 2.3 32.8 1.0
S3 K:SF4301 2.3 32.8 1.0
FE3 K:SF4301 2.7 32.8 1.0
FE4 K:SF4301 2.7 32.8 1.0
FE2 K:SF4301 2.7 32.8 1.0
OG1 K:THR89 2.9 32.6 1.0
SG K:CYS117 3.1 31.2 1.0
CB K:CYS117 3.1 31.2 1.0
S1 K:SF4301 3.9 32.8 1.0
N K:CYS117 4.2 31.2 1.0
CE K:MET123 4.2 29.3 1.0
CB K:THR89 4.2 32.6 1.0
CA K:CYS117 4.3 31.2 1.0
N K:THR89 4.5 32.6 1.0
CE2 K:PHE124 4.5 29.8 1.0
CA K:THR89 4.8 32.6 1.0
CG2 K:THR89 4.9 32.6 1.0

Iron binding site 10 out of 12 in 6nby

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Iron binding site 10 out of 12 in the T.Elongatus Ndh (Composite Model)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of T.Elongatus Ndh (Composite Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe301

b:32.8
occ:1.00
 FE2 K:SF4301 0.0 32.8 1.0
S3 K:SF4301 2.3 32.8 1.0
S1 K:SF4301 2.3 32.8 1.0
S4 K:SF4301 2.3 32.8 1.0
FE4 K:SF4301 2.7 32.8 1.0
FE1 K:SF4301 2.7 32.8 1.0
FE3 K:SF4301 2.7 32.8 1.0
SG K:CYS53 3.0 35.7 1.0
S2 K:SF4301 3.9 32.8 1.0
CA K:GLY115 3.9 30.6 1.0
N K:ALA116 4.1 30.4 1.0
O K:GLY147 4.3 31.2 1.0
CA K:CYS148 4.4 32.5 1.0
CB K:CYS53 4.4 35.7 1.0
C K:GLY115 4.4 30.6 1.0
N K:CYS117 4.5 31.2 1.0
SG K:CYS148 4.6 32.5 1.0
CB K:CYS148 4.6 32.5 1.0
CA K:PRO149 4.7 32.4 1.0
CB K:CYS117 4.9 31.2 1.0
N K:CYS53 4.9 35.7 1.0

Reference:

T.G.Laughlin, A.N.Bayne, J.F.Trempe, D.F.Savage, K.M.Davies. Structure of the Complex I-Like Molecule Ndh of Oxygenic Photosynthesis. Nature V. 566 411 2019.
ISSN: ESSN 1476-4687
PubMed: 30742075
DOI: 10.1038/S41586-019-0921-0
Page generated: Wed Aug 7 02:58:44 2024

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