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Iron in PDB 4ooa: Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein

Protein crystallography data

The structure of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein, PDB code: 4ooa was solved by S.Tamir, Y.Eisenberg-Domovich, A.R.Conlan, J.T.Stofleth, C.H.Lipper, M.L.Paddock, R.Mittler, P.A.Jennings, O.Livnah, R.Nechushtai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.51 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.393, 60.985, 135.241, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.6

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein (pdb code 4ooa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein, PDB code: 4ooa:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4ooa

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Iron binding site 1 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:8.5
occ:1.00
 FE1 A:FES200 0.0 8.5 1.0
SG A:CYS101 2.1 12.9 1.0
S1 A:FES200 2.2 9.6 1.0
S2 A:FES200 2.2 8.5 1.0
SG A:CYS99 2.3 10.3 1.0
FE2 A:FES200 2.7 10.0 1.0
N A:CYS101 3.3 9.0 1.0
CB A:CYS99 3.3 12.3 1.0
CB A:CYS101 3.4 11.0 1.0
CA A:CYS99 3.8 8.3 1.0
CA A:CYS101 3.9 9.6 1.0
N A:ARG100 4.0 7.6 1.0
CB A:CYS114 4.1 10.7 1.0
N A:CYS114 4.2 11.0 1.0
C A:CYS99 4.3 7.9 1.0
SG A:CYS114 4.4 10.3 1.0
N A:SER104 4.4 12.6 1.0
N A:TRP102 4.4 8.0 1.0
CB A:SER104 4.5 12.5 1.0
C A:CYS101 4.5 9.1 1.0
CA A:CYS114 4.6 10.5 1.0
N A:ARG103 4.6 10.3 1.0
SG A:CYS110 4.6 11.5 1.0
C A:ARG100 4.6 8.6 1.0
CB A:CYS110 4.7 10.7 1.0
CA A:CYS110 4.7 11.8 1.0
CA A:SER104 4.9 12.1 1.0
CA A:ARG100 4.9 7.2 1.0
N A:CYS99 5.0 8.3 1.0

Iron binding site 2 out of 12 in 4ooa

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Iron binding site 2 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:10.0
occ:1.00
 FE2 A:FES200 0.0 10.0 1.0
S1 A:FES200 2.2 9.6 1.0
S2 A:FES200 2.3 8.5 1.0
SG A:CYS110 2.3 11.5 1.0
SG A:CYS114 2.3 10.3 1.0
FE1 A:FES200 2.7 8.5 1.0
CB A:CYS110 3.2 10.7 1.0
CB A:CYS114 3.3 10.7 1.0
N A:CYS114 3.8 11.0 1.0
CA A:CYS110 3.9 11.8 1.0
N A:GLY112 4.0 11.8 1.0
CA A:CYS114 4.2 10.5 1.0
SG A:CYS101 4.2 12.9 1.0
CA A:GLY112 4.3 13.1 1.0
N A:ASP111 4.4 11.9 1.0
CD A:PRO127 4.4 9.0 1.0
CB A:PRO127 4.4 8.9 1.0
C A:CYS110 4.4 11.5 1.0
N A:SER113 4.5 11.0 1.0
C A:GLY112 4.6 12.4 1.0
CG A:PRO127 4.6 8.8 1.0
SG A:CYS99 4.6 10.3 1.0
N A:PRO127 4.7 8.0 1.0
CA A:CYS99 4.7 8.3 1.0
CB A:CYS99 4.8 12.3 1.0
CA A:PRO127 5.0 8.5 1.0

Iron binding site 3 out of 12 in 4ooa

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Iron binding site 3 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:9.2
occ:1.00
 FE1 B:FES200 0.0 9.2 1.0
S1 B:FES200 2.2 10.1 1.0
S2 B:FES200 2.2 8.9 1.0
SG B:CYS101 2.2 9.5 1.0
SG B:CYS99 2.3 8.2 1.0
FE2 B:FES200 2.7 9.9 1.0
CB B:CYS101 3.3 9.5 1.0
CB B:CYS99 3.4 7.7 1.0
N B:CYS101 3.5 8.3 1.0
CA B:CYS99 3.7 7.1 1.0
CA B:CYS101 3.9 9.3 1.0
N B:ARG100 3.9 7.6 1.0
CB B:CYS114 4.1 11.0 1.0
N B:CYS114 4.2 10.2 1.0
C B:CYS99 4.2 7.6 1.0
SG B:CYS114 4.3 11.2 1.0
N B:TRP102 4.3 8.7 1.0
N B:SER104 4.4 11.5 1.0
C B:CYS101 4.4 9.4 1.0
CB B:SER104 4.4 11.2 1.0
CA B:CYS114 4.5 10.1 1.0
N B:ARG103 4.6 11.3 1.0
C B:ARG100 4.6 7.9 1.0
SG B:CYS110 4.6 10.7 1.0
CA B:CYS110 4.8 10.8 1.0
CB B:CYS110 4.8 10.4 1.0
CA B:SER104 4.9 11.4 1.0
CA B:ARG100 4.9 7.1 1.0
N B:CYS99 5.0 7.2 1.0

Iron binding site 4 out of 12 in 4ooa

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Iron binding site 4 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:9.9
occ:1.00
 FE2 B:FES200 0.0 9.9 1.0
S2 B:FES200 2.2 8.9 1.0
S1 B:FES200 2.2 10.1 1.0
SG B:CYS110 2.3 10.7 1.0
SG B:CYS114 2.3 11.2 1.0
FE1 B:FES200 2.7 9.2 1.0
CB B:CYS114 3.3 11.0 1.0
CB B:CYS110 3.3 10.4 1.0
N B:CYS114 3.8 10.2 1.0
CA B:CYS110 3.9 10.8 1.0
N B:GLY112 4.0 12.1 1.0
CA B:CYS114 4.2 10.1 1.0
CD B:PRO127 4.2 9.4 1.0
CA B:GLY112 4.2 12.5 1.0
N B:ASP111 4.3 12.0 1.0
CB B:PRO127 4.4 9.5 1.0
SG B:CYS101 4.4 9.5 1.0
N B:SER113 4.4 10.8 1.0
C B:CYS110 4.5 11.8 1.0
C B:GLY112 4.5 11.7 1.0
CG B:PRO127 4.5 9.6 1.0
SG B:CYS99 4.6 8.2 1.0
N B:PRO127 4.7 9.0 1.0
CA B:CYS99 4.7 7.1 1.0
CB B:CYS99 4.9 7.7 1.0
CA B:PRO127 4.9 8.7 1.0
C B:SER113 5.0 10.2 1.0

Iron binding site 5 out of 12 in 4ooa

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Iron binding site 5 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:15.6
occ:1.00
 FE1 C:FES200 0.0 15.6 1.0
SG C:CYS101 2.1 17.0 1.0
SG C:CYS99 2.2 14.8 1.0
S1 C:FES200 2.2 16.6 1.0
S2 C:FES200 2.2 15.2 1.0
FE2 C:FES200 2.8 17.4 1.0
CB C:CYS99 3.3 15.0 1.0
CB C:CYS101 3.4 15.9 1.0
N C:CYS101 3.6 15.3 1.0
CA C:CYS99 3.6 13.0 1.0
N C:ARG100 3.9 13.0 1.0
CA C:CYS101 4.0 15.1 1.0
C C:CYS99 4.2 13.9 1.0
CB C:CYS114 4.2 21.0 1.0
N C:CYS114 4.2 20.0 1.0
N C:TRP102 4.3 14.0 1.0
SG C:CYS114 4.4 20.4 1.0
N C:SER104 4.4 15.6 1.0
C C:CYS101 4.4 14.8 1.0
CB C:SER104 4.5 17.3 1.0
CA C:CYS114 4.5 20.9 1.0
N C:ARG103 4.5 16.7 1.0
SG C:CYS110 4.6 17.9 1.0
C C:ARG100 4.6 14.2 1.0
CB C:CYS110 4.7 17.6 1.0
CA C:CYS110 4.8 17.2 1.0
CA C:ARG100 4.9 13.4 1.0
CA C:SER104 4.9 16.2 1.0
N C:CYS99 4.9 14.7 1.0

Iron binding site 6 out of 12 in 4ooa

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Iron binding site 6 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:17.4
occ:1.00
 FE2 C:FES200 0.0 17.4 1.0
S1 C:FES200 2.2 16.6 1.0
S2 C:FES200 2.3 15.2 1.0
SG C:CYS110 2.3 17.9 1.0
SG C:CYS114 2.3 20.4 1.0
FE1 C:FES200 2.8 15.6 1.0
CB C:CYS110 3.3 17.6 1.0
CB C:CYS114 3.3 21.0 1.0
N C:CYS114 3.8 20.0 1.0
N C:GLY112 3.9 19.9 1.0
CA C:CYS110 3.9 17.2 1.0
CA C:CYS114 4.2 20.9 1.0
CA C:GLY112 4.2 19.3 1.0
CD C:PRO127 4.2 14.8 1.0
SG C:CYS101 4.3 17.0 1.0
CB C:PRO127 4.4 15.5 1.0
N C:SER113 4.4 20.3 1.0
N C:ASP111 4.4 15.4 1.0
C C:GLY112 4.5 19.3 1.0
CG C:PRO127 4.5 15.9 1.0
C C:CYS110 4.5 14.3 1.0
SG C:CYS99 4.6 14.8 1.0
CA C:CYS99 4.6 13.0 1.0
N C:PRO127 4.6 14.2 1.0
CB C:CYS99 4.8 15.0 1.0
CA C:PRO127 4.9 14.6 1.0
C C:SER113 4.9 21.1 1.0

Iron binding site 7 out of 12 in 4ooa

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Iron binding site 7 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:14.7
occ:1.00
 FE1 D:FES200 0.0 14.7 1.0
SG D:CYS101 2.1 15.8 1.0
SG D:CYS99 2.2 13.7 1.0
S1 D:FES200 2.2 16.4 1.0
S2 D:FES200 2.2 15.0 1.0
FE2 D:FES200 2.8 16.1 1.0
CB D:CYS101 3.3 16.1 1.0
CB D:CYS99 3.4 12.8 1.0
N D:CYS101 3.5 14.2 1.0
CA D:CYS99 3.7 12.8 1.0
N D:ARG100 3.9 12.7 1.0
CA D:CYS101 3.9 15.6 1.0
CB D:CYS114 4.1 18.6 1.0
N D:CYS114 4.2 17.3 1.0
C D:CYS99 4.2 13.7 1.0
N D:SER104 4.3 18.2 1.0
SG D:CYS114 4.4 18.9 1.0
N D:TRP102 4.4 14.2 1.0
C D:CYS101 4.4 14.4 1.0
CB D:SER104 4.4 19.4 1.0
CA D:CYS114 4.5 17.1 1.0
N D:ARG103 4.6 16.1 1.0
C D:ARG100 4.6 13.0 1.0
SG D:CYS110 4.7 16.5 1.0
CB D:CYS110 4.8 14.8 1.0
CA D:CYS110 4.8 15.7 1.0
CA D:SER104 4.8 18.8 1.0
CA D:ARG100 4.9 13.2 1.0
N D:CYS99 5.0 12.6 1.0

Iron binding site 8 out of 12 in 4ooa

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Iron binding site 8 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:16.1
occ:1.00
 FE2 D:FES200 0.0 16.1 1.0
S1 D:FES200 2.2 16.4 1.0
S2 D:FES200 2.2 15.0 1.0
SG D:CYS110 2.3 16.5 1.0
SG D:CYS114 2.3 18.9 1.0
FE1 D:FES200 2.8 14.7 1.0
CB D:CYS114 3.3 18.6 1.0
CB D:CYS110 3.3 14.8 1.0
N D:CYS114 3.9 17.3 1.0
CA D:CYS110 4.0 15.7 1.0
N D:GLY112 4.0 19.6 1.0
CA D:CYS114 4.2 17.1 1.0
CA D:GLY112 4.2 20.9 1.0
CD D:PRO127 4.3 14.0 1.0
SG D:CYS101 4.3 15.8 1.0
N D:SER113 4.4 19.9 1.0
N D:ASP111 4.4 17.5 1.0
CB D:PRO127 4.4 14.3 1.0
C D:GLY112 4.5 19.3 1.0
C D:CYS110 4.5 16.6 1.0
SG D:CYS99 4.6 13.7 1.0
CG D:PRO127 4.6 14.7 1.0
N D:PRO127 4.7 13.4 1.0
CA D:CYS99 4.7 12.8 1.0
CB D:CYS99 4.9 12.8 1.0
CA D:PRO127 4.9 13.4 1.0
C D:SER113 5.0 17.1 1.0

Iron binding site 9 out of 12 in 4ooa

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Iron binding site 9 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:11.4
occ:1.00
 FE1 E:FES200 0.0 11.4 1.0
SG E:CYS101 2.1 17.5 1.0
SG E:CYS99 2.2 13.4 1.0
S1 E:FES200 2.2 12.7 1.0
S2 E:FES200 2.2 11.1 1.0
FE2 E:FES200 2.7 12.2 1.0
CB E:CYS99 3.1 14.7 1.0
N E:CYS101 3.4 11.0 1.0
CB E:CYS101 3.5 14.6 1.0
CA E:CYS99 3.7 10.2 1.0
N E:ARG100 3.9 9.4 1.0
CA E:CYS101 4.0 11.3 1.0
CB E:CYS114 4.1 14.2 1.0
N E:CYS114 4.2 14.3 1.0
C E:CYS99 4.4 9.5 1.0
SG E:CYS114 4.4 13.8 1.0
CB E:SER104 4.4 13.9 1.0
N E:SER104 4.4 12.7 1.0
N E:TRP102 4.4 10.9 1.0
CA E:CYS114 4.5 13.5 1.0
SG E:CYS110 4.6 13.2 1.0
N E:ARG103 4.6 12.8 1.0
C E:CYS101 4.6 10.6 1.0
C E:ARG100 4.6 9.9 1.0
CB E:CYS110 4.8 11.4 1.0
CA E:CYS110 4.8 11.2 1.0
CA E:SER104 4.9 13.4 1.0
CA E:ARG100 4.9 9.2 1.0
N E:CYS99 5.0 10.1 1.0

Iron binding site 10 out of 12 in 4ooa

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Iron binding site 10 out of 12 in the Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of NAF1 (MINER1): H114C the Redox-Active 2FE-2S Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:12.2
occ:1.00
 FE2 E:FES200 0.0 12.2 1.0
S1 E:FES200 2.2 12.7 1.0
S2 E:FES200 2.3 11.1 1.0
SG E:CYS110 2.3 13.2 1.0
SG E:CYS114 2.3 13.8 1.0
FE1 E:FES200 2.7 11.4 1.0
CB E:CYS114 3.2 14.2 1.0
CB E:CYS110 3.3 11.4 1.0
N E:CYS114 3.8 14.3 1.0
CA E:CYS110 3.9 11.2 1.0
N E:GLY112 4.0 14.2 1.0
CA E:CYS114 4.1 13.5 1.0
SG E:CYS101 4.2 17.5 1.0
CA E:GLY112 4.3 15.3 1.0
N E:ASP111 4.3 13.8 1.0
CD E:PRO127 4.3 10.7 1.0
N E:SER113 4.4 13.5 1.0
C E:CYS110 4.5 12.8 1.0
CB E:PRO127 4.5 10.0 1.0
C E:GLY112 4.6 14.4 1.0
CG E:PRO127 4.6 10.4 1.0
SG E:CYS99 4.6 13.4 1.0
CB E:CYS99 4.7 14.7 1.0
N E:PRO127 4.7 10.1 1.0
CA E:CYS99 4.8 10.2 1.0
C E:SER113 4.9 13.1 1.0

Reference:

S.Tamir, Y.Eisenberg-Domovich, A.R.Conlan, J.T.Stofleth, C.H.Lipper, M.L.Paddock, R.Mittler, P.A.Jennings, O.Livnah, R.Nechushtai. A Point Mutation in the [2FE-2S] Cluster Binding Region of the Naf-1 Protein (H114C) Dramatically Hinders the Cluster Donor Properties. Acta Crystallogr.,Sect.D V. 70 1572 2014.
ISSN: ISSN 0907-4449
PubMed: 24914968
DOI: 10.1107/S1399004714005458
Page generated: Mon Aug 5 08:11:24 2024

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