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Iron in PDB 7p0p: Naf-1 Bound to M1 Molecule

Protein crystallography data

The structure of Naf-1 Bound to M1 Molecule, PDB code: 7p0p was solved by O.Livnah, Y.Eisenberg-Domovich, H.B.Marjault, R.Nechushtai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.21 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.573, 47.589, 125.948, 90, 90, 90
R / Rfree (%) 20.4 / 25.4

Iron Binding Sites:

The binding sites of Iron atom in the Naf-1 Bound to M1 Molecule (pdb code 7p0p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Naf-1 Bound to M1 Molecule, PDB code: 7p0p:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7p0p

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Iron binding site 1 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:22.8
occ:1.00
FE1 A:FES200 0.0 22.8 1.0
S2 A:FES200 2.2 22.4 1.0
S1 A:FES200 2.2 25.1 1.0
SG A:CYS101 2.3 25.2 1.0
SG A:CYS99 2.4 23.2 1.0
FE2 A:FES200 2.7 23.5 1.0
CB A:CYS101 3.3 27.8 1.0
CB A:CYS99 3.4 23.6 1.0
N A:CYS101 3.6 25.4 1.0
CA A:CYS99 3.7 21.9 1.0
N A:ARG100 3.9 20.1 1.0
CA A:CYS101 3.9 26.1 1.0
CB A:HIS114 4.0 24.0 1.0
N A:HIS114 4.1 22.4 1.0
C A:CYS99 4.2 19.8 1.0
N A:SER104 4.3 25.8 1.0
ND1 A:HIS114 4.4 24.1 1.0
N A:TRP102 4.4 25.8 1.0
CA A:HIS114 4.4 24.0 1.0
C A:CYS101 4.4 26.2 1.0
CB A:SER104 4.5 26.5 1.0
N A:ARG103 4.6 25.1 1.0
C A:ARG100 4.6 23.1 1.0
SG A:CYS110 4.7 24.7 1.0
CG A:HIS114 4.7 22.0 1.0
CA A:CYS110 4.8 25.6 1.0
CA A:SER104 4.8 27.5 1.0
CB A:CYS110 4.9 23.4 1.0
CA A:ARG100 5.0 20.8 1.0

Iron binding site 2 out of 8 in 7p0p

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Iron binding site 2 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:23.5
occ:1.00
FE2 A:FES200 0.0 23.5 1.0
S1 A:FES200 2.2 25.1 1.0
ND1 A:HIS114 2.2 24.1 1.0
SG A:CYS110 2.3 24.7 1.0
S2 A:FES200 2.3 22.4 1.0
FE1 A:FES200 2.7 22.8 1.0
CE1 A:HIS114 3.2 22.5 1.0
CG A:HIS114 3.2 22.0 1.0
CB A:CYS110 3.3 23.4 1.0
CB A:HIS114 3.5 24.0 1.0
CA A:CYS110 3.8 25.6 1.0
N A:HIS114 3.9 22.4 1.0
N A:GLY112 4.0 26.9 1.0
CB A:PRO127 4.2 22.6 1.0
CD A:PRO127 4.3 23.1 1.0
NE2 A:HIS114 4.3 23.2 1.0
CA A:GLY112 4.3 25.2 1.0
N A:ASP111 4.3 26.9 1.0
CD2 A:HIS114 4.3 21.6 1.0
CA A:HIS114 4.3 24.0 1.0
N A:SER113 4.4 24.5 1.0
CG A:PRO127 4.4 22.6 1.0
C A:CYS110 4.4 26.0 1.0
C A:GLY112 4.5 24.1 1.0
SG A:CYS101 4.5 25.2 1.0
CA A:CYS99 4.6 21.9 1.0
SG A:CYS99 4.6 23.2 1.0
N A:PRO127 4.6 22.4 1.0
CB A:CYS99 4.7 23.6 1.0
CA A:PRO127 4.8 23.4 1.0
C A:SER113 5.0 22.2 1.0

Iron binding site 3 out of 8 in 7p0p

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Iron binding site 3 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:23.9
occ:1.00
FE1 B:FES200 0.0 23.9 1.0
S1 B:FES200 2.2 24.7 1.0
S2 B:FES200 2.2 23.2 1.0
SG B:CYS101 2.3 24.8 1.0
SG B:CYS99 2.4 22.7 1.0
FE2 B:FES200 2.7 23.6 1.0
CB B:CYS99 3.3 25.6 1.0
CB B:CYS101 3.3 23.6 1.0
N B:CYS101 3.6 21.6 1.0
CA B:CYS99 3.6 24.8 1.0
N B:ARG100 3.9 22.0 1.0
CA B:CYS101 3.9 23.6 1.0
CB B:HIS114 4.1 22.6 1.0
C B:CYS99 4.2 23.0 1.0
ND1 B:HIS114 4.2 22.0 1.0
N B:HIS114 4.3 23.9 1.0
N B:TRP102 4.4 25.0 1.0
C B:CYS101 4.4 23.7 1.0
CB B:SER104 4.5 26.3 1.0
N B:SER104 4.5 26.8 1.0
CA B:HIS114 4.6 23.9 1.0
SG B:CYS110 4.6 25.3 1.0
N B:ARG103 4.6 26.3 1.0
CG B:HIS114 4.7 23.4 1.0
C B:ARG100 4.7 22.9 1.0
CA B:CYS110 4.8 25.6 1.0
CB B:CYS110 4.8 27.5 1.0
CA B:SER104 4.9 27.5 1.0
CA B:ARG100 5.0 22.2 1.0
N B:CYS99 5.0 24.2 1.0

Iron binding site 4 out of 8 in 7p0p

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Iron binding site 4 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:23.6
occ:1.00
FE2 B:FES200 0.0 23.6 1.0
ND1 B:HIS114 2.2 22.0 1.0
S1 B:FES200 2.2 24.7 1.0
S2 B:FES200 2.2 23.2 1.0
SG B:CYS110 2.3 25.3 1.0
FE1 B:FES200 2.7 23.9 1.0
CE1 B:HIS114 3.0 21.0 1.0
CB B:CYS110 3.3 27.5 1.0
CG B:HIS114 3.3 23.4 1.0
CB B:HIS114 3.7 22.6 1.0
CA B:CYS110 3.8 25.6 1.0
N B:GLY112 4.0 25.9 1.0
N B:HIS114 4.0 23.9 1.0
NE2 B:HIS114 4.2 22.4 1.0
CA B:GLY112 4.2 25.1 1.0
CD B:PRO127 4.3 23.5 1.0
CB B:PRO127 4.3 21.6 1.0
CD2 B:HIS114 4.3 24.2 1.0
N B:ASP111 4.4 27.8 1.0
C B:CYS110 4.4 26.2 1.0
SG B:CYS101 4.5 24.8 1.0
CA B:HIS114 4.5 23.9 1.0
N B:SER113 4.5 22.1 1.0
CG B:PRO127 4.6 22.3 1.0
CA B:CYS99 4.6 24.8 1.0
C B:GLY112 4.6 24.3 1.0
N B:PRO127 4.6 22.5 1.0
SG B:CYS99 4.7 22.7 1.0
CB B:CYS99 4.7 25.6 1.0
CA B:PRO127 4.8 20.9 1.0

Iron binding site 5 out of 8 in 7p0p

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Iron binding site 5 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:23.4
occ:1.00
FE1 C:FES200 0.0 23.4 1.0
S2 C:FES200 2.2 23.0 1.0
S1 C:FES200 2.2 25.5 1.0
SG C:CYS101 2.3 23.8 1.0
SG C:CYS99 2.4 23.5 1.0
FE2 C:FES200 2.7 23.2 1.0
CB C:CYS101 3.4 22.8 1.0
CB C:CYS99 3.4 22.4 1.0
N C:CYS101 3.6 22.2 1.0
CA C:CYS99 3.7 22.2 1.0
N C:ARG100 3.9 20.1 1.0
CA C:CYS101 4.0 22.4 1.0
CB C:HIS114 4.0 23.9 1.0
C C:CYS99 4.2 21.0 1.0
N C:HIS114 4.3 22.2 1.0
ND1 C:HIS114 4.3 26.0 1.0
N C:TRP102 4.3 24.4 1.0
N C:SER104 4.4 26.4 1.0
C C:CYS101 4.5 23.1 1.0
CB C:SER104 4.5 25.2 1.0
CA C:HIS114 4.6 25.2 1.0
N C:ARG103 4.6 25.8 1.0
C C:ARG100 4.6 22.1 1.0
SG C:CYS110 4.6 26.4 1.0
CG C:HIS114 4.7 26.0 1.0
CA C:SER104 4.9 26.9 1.0
CA C:CYS110 4.9 25.7 1.0
CA C:ARG100 4.9 22.7 1.0
CB C:CYS110 5.0 26.4 1.0
N C:CYS99 5.0 21.7 1.0

Iron binding site 6 out of 8 in 7p0p

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Iron binding site 6 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:23.2
occ:1.00
FE2 C:FES200 0.0 23.2 1.0
ND1 C:HIS114 2.2 26.0 1.0
S1 C:FES200 2.2 25.5 1.0
S2 C:FES200 2.3 23.0 1.0
SG C:CYS110 2.3 26.4 1.0
FE1 C:FES200 2.7 23.4 1.0
CE1 C:HIS114 3.1 26.4 1.0
CG C:HIS114 3.2 26.0 1.0
CB C:CYS110 3.4 26.4 1.0
CB C:HIS114 3.6 23.9 1.0
CA C:CYS110 3.9 25.7 1.0
N C:GLY112 4.0 25.9 1.0
N C:HIS114 4.0 22.2 1.0
CD C:PRO127 4.1 23.5 1.0
NE2 C:HIS114 4.2 24.5 1.0
CA C:GLY112 4.3 26.1 1.0
CD2 C:HIS114 4.3 24.1 1.0
N C:ASP111 4.4 26.2 1.0
CB C:PRO127 4.4 21.0 1.0
SG C:CYS101 4.4 23.8 1.0
CA C:HIS114 4.4 25.2 1.0
CG C:PRO127 4.5 23.0 1.0
C C:CYS110 4.5 26.2 1.0
N C:SER113 4.5 24.0 1.0
C C:GLY112 4.6 26.1 1.0
CA C:CYS99 4.6 22.2 1.0
N C:PRO127 4.6 24.7 1.0
SG C:CYS99 4.7 23.5 1.0
CB C:CYS99 4.8 22.4 1.0
CA C:PRO127 4.9 21.7 1.0

Iron binding site 7 out of 8 in 7p0p

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Iron binding site 7 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:22.3
occ:1.00
FE1 D:FES201 0.0 22.3 1.0
S1 D:FES201 2.2 23.1 1.0
S2 D:FES201 2.2 23.1 1.0
SG D:CYS101 2.4 23.4 1.0
SG D:CYS99 2.4 22.6 1.0
FE2 D:FES201 2.7 23.4 1.0
CB D:CYS99 3.4 20.6 1.0
CB D:CYS101 3.5 24.0 1.0
N D:CYS101 3.6 20.7 1.0
CA D:CYS99 3.7 21.4 1.0
N D:ARG100 4.0 19.6 1.0
CA D:CYS101 4.0 22.4 1.0
CB D:HIS114 4.0 25.4 1.0
N D:HIS114 4.0 25.0 1.0
C D:CYS99 4.3 19.7 1.0
N D:SER104 4.4 20.3 1.0
ND1 D:HIS114 4.4 23.3 1.0
CB D:SER104 4.4 21.4 1.0
N D:TRP102 4.4 21.8 1.0
CA D:HIS114 4.4 25.1 1.0
C D:CYS101 4.5 24.4 1.0
N D:ARG103 4.6 22.6 1.0
SG D:CYS110 4.6 24.4 1.0
C D:ARG100 4.7 21.5 1.0
CG D:HIS114 4.7 23.9 1.0
CB D:CYS110 4.7 22.6 1.0
CA D:SER104 4.8 21.8 1.0
CA D:CYS110 4.8 24.5 1.0
C D:SER113 4.9 23.2 1.0
CA D:ARG100 5.0 20.8 1.0

Iron binding site 8 out of 8 in 7p0p

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Iron binding site 8 out of 8 in the Naf-1 Bound to M1 Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:23.4
occ:1.00
FE2 D:FES201 0.0 23.4 1.0
S2 D:FES201 2.2 23.1 1.0
S1 D:FES201 2.2 23.1 1.0
SG D:CYS110 2.2 24.4 1.0
ND1 D:HIS114 2.2 23.3 1.0
FE1 D:FES201 2.7 22.3 1.0
CE1 D:HIS114 3.2 23.2 1.0
CG D:HIS114 3.2 23.9 1.0
CB D:CYS110 3.2 22.6 1.0
CB D:HIS114 3.5 25.4 1.0
CA D:CYS110 3.9 24.5 1.0
N D:HIS114 3.9 25.0 1.0
N D:GLY112 4.0 23.4 1.0
CB D:PRO127 4.2 22.7 1.0
NE2 D:HIS114 4.3 22.3 1.0
CD D:PRO127 4.3 22.2 1.0
CA D:GLY112 4.3 22.0 1.0
CD2 D:HIS114 4.3 24.9 1.0
N D:ASP111 4.3 22.9 1.0
CA D:HIS114 4.3 25.1 1.0
N D:SER113 4.4 22.3 1.0
C D:CYS110 4.4 23.9 1.0
C D:GLY112 4.5 21.6 1.0
SG D:CYS101 4.5 23.4 1.0
CG D:PRO127 4.5 22.2 1.0
N D:PRO127 4.6 22.7 1.0
CA D:CYS99 4.6 21.4 1.0
SG D:CYS99 4.7 22.6 1.0
CA D:PRO127 4.8 23.5 1.0
CB D:CYS99 4.9 20.6 1.0
C D:SER113 5.0 23.2 1.0

Reference:

H.B.Marjault, O.Karmi, K.Zuo, D.Michaeli, Y.Eisenberg-Domovich, G.Rossetti, B.De Chassey, J.Vonderscher, I.Cabantchik, P.Carloni, R.Mittler, O.Livnah, E.Meldrum, R.Nechushtai. An Anti-Diabetic Drug Targets Neet (Cisd) Proteins Through Destabilization of Their [2FE-2S] Clusters. Commun Biol V. 5 437 2022.
ISSN: ESSN 2399-3642
PubMed: 35538231
DOI: 10.1038/S42003-022-03393-X
Page generated: Thu Aug 8 14:51:49 2024

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