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Iron in PDB 1kgn: R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form

Protein crystallography data

The structure of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form, PDB code: 1kgn was solved by M.Hogbom, Y.Huque, B.M.Sjoberg, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.813, 90.705, 136.810, 90.00, 91.24, 90.00
R / Rfree (%) 15.8 / 21.3

Iron Binding Sites:

The binding sites of Iron atom in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form (pdb code 1kgn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form, PDB code: 1kgn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1kgn

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Iron binding site 1 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:15.6
occ:0.60
 O A:HOH2147 2.0 24.1 1.0
OE1 A:GLU108 2.1 31.2 1.0
ND1 A:HIS111 2.1 11.0 1.0
OD1 A:ASP77 2.1 22.8 1.0
O A:HOH2427 2.3 18.9 1.0
O A:HOH2096 2.7 27.3 1.0
CE1 A:HIS111 2.9 13.5 1.0
CD A:GLU108 3.2 20.8 1.0
CG A:ASP77 3.2 25.2 1.0
CG A:HIS111 3.2 11.0 1.0
OE2 A:GLU202 3.4 45.9 1.0
FE A:FE2001 3.6 16.7 0.9
OE2 A:GLU108 3.6 29.4 1.0
CB A:HIS111 3.7 8.2 1.0
OD2 A:ASP77 3.7 26.3 1.0
CZ A:PHE172 3.8 32.4 1.0
NE2 A:HIS111 4.1 10.1 1.0
CE2 A:PHE172 4.1 31.2 1.0
CD A:GLU202 4.2 46.2 1.0
CD2 A:HIS111 4.3 12.3 1.0
CA A:GLU108 4.3 8.3 1.0
O A:HOH2204 4.3 32.6 1.0
CG2 A:ILE198 4.4 9.9 1.0
CB A:ASP77 4.4 14.9 1.0
CG A:GLU108 4.4 8.9 1.0
OE1 A:GLU202 4.5 41.0 1.0
CE1 A:PHE172 4.5 25.1 1.0
CB A:GLU108 4.6 10.2 1.0
CA A:ASP77 4.9 12.3 1.0
ND1 A:HIS205 5.0 13.9 1.0

Iron binding site 2 out of 8 in 1kgn

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Iron binding site 2 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2001

b:16.7
occ:0.90
 OE2 A:GLU108 1.9 29.4 1.0
O A:HOH2427 2.0 18.9 1.0
OE2 A:GLU168 2.1 21.8 1.0
OE1 A:GLU202 2.2 41.0 1.0
ND1 A:HIS205 2.3 13.9 1.0
O A:HOH2096 2.3 27.3 1.0
CD A:GLU108 2.9 20.8 1.0
CD A:GLU202 3.0 46.2 1.0
CD A:GLU168 3.1 33.5 1.0
CE1 A:HIS205 3.2 9.4 1.0
OE1 A:GLU108 3.2 31.2 1.0
OE2 A:GLU202 3.2 45.9 1.0
CG A:HIS205 3.3 11.1 1.0
FE A:FE1001 3.6 15.6 0.6
CB A:HIS205 3.6 12.0 1.0
CG A:GLU168 3.8 27.0 1.0
OE1 A:GLU168 3.9 43.4 1.0
O A:HOH2147 4.1 24.1 1.0
CG A:GLU108 4.2 8.9 1.0
CA A:GLU202 4.2 17.0 1.0
CG A:GLU202 4.3 35.2 1.0
NE2 A:HIS205 4.3 12.8 1.0
CD2 A:HIS205 4.4 9.5 1.0
CG A:GLN80 4.5 12.2 1.0
CB A:GLU168 4.6 15.6 1.0
CB A:GLU202 4.6 19.6 1.0
CE1 A:HIS111 4.7 13.5 1.0
CG2 A:ILE104 4.7 6.5 1.0
CE2 A:PHE172 4.7 31.2 1.0
ND1 A:HIS111 4.8 11.0 1.0
N A:GLU202 4.8 12.5 1.0

Iron binding site 3 out of 8 in 1kgn

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Iron binding site 3 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:19.4
occ:0.60
 OD1 B:ASP77 2.1 21.0 1.0
O B:HOH2064 2.1 27.0 1.0
OE1 B:GLU108 2.1 28.2 1.0
ND1 B:HIS111 2.2 12.7 1.0
O B:HOH2364 2.5 25.5 1.0
O B:HOH2164 2.8 28.0 1.0
CE1 B:HIS111 3.0 11.2 1.0
CD B:GLU108 3.2 24.9 1.0
OE2 B:GLU202 3.2 49.0 1.0
CG B:ASP77 3.2 25.1 1.0
CG B:HIS111 3.2 9.1 1.0
FE B:FE2002 3.6 15.9 0.8
OE2 B:GLU108 3.6 30.3 1.0
CB B:HIS111 3.6 9.7 1.0
OD2 B:ASP77 3.9 22.0 1.0
CZ B:PHE172 3.9 30.8 1.0
NE2 B:HIS111 4.2 7.8 1.0
CD B:GLU202 4.2 43.4 1.0
CD2 B:HIS111 4.3 7.9 1.0
CE1 B:PHE172 4.3 28.8 1.0
CA B:GLU108 4.3 10.4 1.0
CB B:ASP77 4.4 10.2 1.0
O B:HOH2097 4.4 25.5 1.0
CG2 B:ILE198 4.4 13.1 1.0
CG B:GLU108 4.4 12.2 1.0
CE2 B:PHE172 4.5 38.2 1.0
CB B:GLU108 4.6 10.1 1.0
OE1 B:GLU202 4.7 27.0 1.0
CA B:ASP77 4.8 12.1 1.0
O B:GLU108 5.0 8.8 1.0

Iron binding site 4 out of 8 in 1kgn

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Iron binding site 4 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe2002

b:15.9
occ:0.80
 OE2 B:GLU108 1.9 30.3 1.0
O B:HOH2364 2.0 25.5 1.0
OE1 B:GLU202 2.1 27.0 1.0
ND1 B:HIS205 2.2 9.8 1.0
OE2 B:GLU168 2.3 29.1 1.0
O B:HOH2164 2.3 28.0 1.0
CD B:GLU202 2.8 43.4 1.0
CD B:GLU108 2.9 24.9 1.0
OE2 B:GLU202 2.9 49.0 1.0
CE1 B:HIS205 3.0 11.7 1.0
OE1 B:GLU108 3.2 28.2 1.0
CG B:HIS205 3.3 11.3 1.0
CD B:GLU168 3.4 37.6 1.0
FE B:FE1002 3.6 19.4 0.6
CB B:HIS205 3.7 9.8 1.0
CG B:GLU168 4.0 30.7 1.0
CG B:GLU202 4.1 32.1 1.0
CA B:GLU202 4.2 12.0 1.0
CG B:GLU108 4.2 12.2 1.0
NE2 B:HIS205 4.2 10.6 1.0
O B:HOH2064 4.3 27.0 1.0
CD2 B:HIS205 4.3 9.4 1.0
OE1 B:GLU168 4.3 45.9 1.0
CB B:GLU202 4.5 18.8 1.0
CE1 B:HIS111 4.6 11.2 1.0
CB B:GLU168 4.6 18.3 1.0
CG B:GLN80 4.6 12.9 1.0
ND1 B:HIS111 4.7 12.7 1.0
N B:GLU202 4.8 13.1 1.0
CG2 B:ILE104 4.8 12.4 1.0

Iron binding site 5 out of 8 in 1kgn

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Iron binding site 5 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3001

b:16.8
occ:0.60
 OE1 C:GLU108 2.0 29.5 1.0
O C:HOH3403 2.1 22.9 1.0
OD1 C:ASP77 2.1 24.1 1.0
ND1 C:HIS111 2.1 10.8 1.0
O C:HOH3060 2.3 24.6 1.0
O C:HOH3051 2.7 24.1 1.0
CE1 C:HIS111 2.9 11.1 1.0
CD C:GLU108 3.2 21.1 1.0
CG C:HIS111 3.2 12.6 1.0
CG C:ASP77 3.3 25.1 1.0
FE C:FE3002 3.5 16.6 0.8
OE2 C:GLU202 3.7 37.7 1.0
CB C:HIS111 3.7 10.0 1.0
OE2 C:GLU108 3.7 25.4 1.0
OD2 C:ASP77 3.9 22.9 1.0
O C:HOH3066 4.0 29.0 1.0
CE2 C:PHE172 4.1 44.2 1.0
CZ C:PHE172 4.1 47.2 1.0
NE2 C:HIS111 4.1 9.9 1.0
CD2 C:HIS111 4.3 11.0 1.0
CA C:GLU108 4.3 9.5 1.0
CD C:GLU202 4.3 35.0 1.0
CG C:GLU108 4.4 11.3 1.0
CB C:ASP77 4.4 17.2 1.0
CG2 C:ILE198 4.5 15.1 1.0
CB C:GLU108 4.5 9.3 1.0
CD2 C:PHE172 4.6 39.5 1.0
OE1 C:GLU202 4.6 24.6 1.0
CE1 C:PHE172 4.6 34.1 1.0
ND1 C:HIS205 4.9 11.3 1.0
CA C:ASP77 5.0 12.7 1.0
CE1 C:HIS205 5.0 14.6 1.0

Iron binding site 6 out of 8 in 1kgn

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Iron binding site 6 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:16.6
occ:0.80
 OE2 C:GLU108 2.0 25.4 1.0
OE2 C:GLU168 2.0 25.8 1.0
O C:HOH3403 2.1 22.9 1.0
ND1 C:HIS205 2.2 11.3 1.0
OE1 C:GLU202 2.3 24.6 1.0
O C:HOH3051 2.3 24.1 1.0
CD C:GLU108 2.9 21.1 1.0
CD C:GLU202 3.1 35.0 1.0
OE1 C:GLU108 3.1 29.5 1.0
CD C:GLU168 3.1 33.9 1.0
CE1 C:HIS205 3.1 14.6 1.0
CG C:HIS205 3.3 10.4 1.0
OE2 C:GLU202 3.3 37.7 1.0
FE C:FE3001 3.5 16.8 0.6
CB C:HIS205 3.6 12.3 1.0
CG C:GLU168 3.7 29.9 1.0
OE1 C:GLU168 4.0 35.7 1.0
NE2 C:HIS205 4.3 11.3 1.0
CG C:GLU108 4.3 11.3 1.0
CA C:GLU202 4.3 12.8 1.0
CG C:GLU202 4.4 29.6 1.0
O C:HOH3060 4.4 24.6 1.0
CD2 C:HIS205 4.4 12.5 1.0
CG C:GLN80 4.6 16.3 1.0
CB C:GLU202 4.6 17.9 1.0
CE1 C:HIS111 4.6 11.1 1.0
CB C:GLU168 4.7 17.7 1.0
CG2 C:ILE104 4.7 7.0 1.0
ND1 C:HIS111 4.8 10.8 1.0
N C:GLU202 4.9 13.1 1.0
CE2 C:PHE172 5.0 44.2 1.0

Iron binding site 7 out of 8 in 1kgn

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Iron binding site 7 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1003

b:20.2
occ:0.60
 OE2 D:GLU202 2.1 39.6 1.0
OD1 D:ASP77 2.1 22.9 1.0
OE1 D:GLU108 2.1 25.2 1.0
ND1 D:HIS111 2.1 12.0 1.0
OE1 D:GLU202 2.5 27.9 1.0
CD D:GLU202 2.5 34.7 1.0
CE1 D:HIS111 3.0 12.7 1.0
CD D:GLU108 3.1 19.8 1.0
CG D:ASP77 3.2 18.2 1.0
CG D:HIS111 3.2 11.5 1.0
OE2 D:GLU108 3.4 26.9 1.0
CB D:HIS111 3.6 12.5 1.0
FE D:FE1004 3.7 17.0 0.8
CZ D:PHE172 3.7 30.4 1.0
OD2 D:ASP77 3.7 19.9 1.0
CG D:GLU202 4.0 23.2 1.0
CE2 D:PHE172 4.1 32.8 1.0
NE2 D:HIS111 4.2 8.9 1.0
O D:HOH1122 4.2 31.2 1.0
CG2 D:ILE198 4.3 10.5 1.0
CD2 D:HIS111 4.3 8.3 1.0
CA D:GLU108 4.3 6.4 1.0
CB D:ASP77 4.3 14.6 1.0
CG D:GLU108 4.4 13.8 1.0
CE1 D:PHE172 4.5 26.8 1.0
CB D:GLU108 4.6 6.3 1.0
CA D:ASP77 4.8 9.8 1.0
OE1 D:GLU168 4.9 30.2 1.0

Iron binding site 8 out of 8 in 1kgn

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Iron binding site 8 out of 8 in the R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of R2F From Corynebacterium Ammoniagenes in Its Oxidised, Fe Containing, Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1004

b:17.0
occ:0.80
 OE2 D:GLU108 1.9 26.9 1.0
OE1 D:GLU168 2.0 30.2 1.0
OE1 D:GLU202 2.1 27.9 1.0
ND1 D:HIS205 2.1 11.8 1.0
OE2 D:GLU168 2.3 19.4 1.0
CD D:GLU168 2.4 24.6 1.0
CD D:GLU108 3.0 19.8 1.0
CE1 D:HIS205 3.1 12.6 1.0
CG D:HIS205 3.2 9.9 1.0
CD D:GLU202 3.2 34.7 1.0
OE1 D:GLU108 3.4 25.2 1.0
CB D:HIS205 3.6 12.0 1.0
FE D:FE1003 3.7 20.2 0.6
OE2 D:GLU202 3.9 39.6 1.0
CG D:GLU168 3.9 24.2 1.0
CA D:GLU202 4.1 14.4 1.0
NE2 D:HIS205 4.2 11.6 1.0
CG D:GLU108 4.3 13.8 1.0
CG D:GLU202 4.3 23.2 1.0
CD2 D:HIS205 4.3 12.7 1.0
CB D:GLU202 4.3 16.4 1.0
CG D:GLN80 4.4 17.9 1.0
CE2 D:PHE172 4.5 32.8 1.0
CG2 D:ILE104 4.7 8.1 1.0
CB D:GLU168 4.7 11.0 1.0
CE1 D:HIS111 4.7 12.7 1.0
N D:GLU202 4.7 16.2 1.0
NE2 D:GLN80 4.8 22.9 1.0
ND1 D:HIS111 4.9 12.0 1.0

Reference:

M.Hogbom, Y.Huque, B.M.Sjoberg, P.Nordlund. Crystal Structure of the Di-Iron/Radical Protein of Ribonucleotide Reductase From Corynebacterium Ammoniagenes. Biochemistry V. 41 1381 2002.
ISSN: ISSN 0006-2960
PubMed: 11802741
DOI: 10.1021/BI011429L
Page generated: Sat Aug 3 09:13:15 2024

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