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Iron in PDB 1nmo: Structural Genomics, Protein Ybgi, Unknown Function

Protein crystallography data

The structure of Structural Genomics, Protein Ybgi, Unknown Function, PDB code: 1nmo was solved by J.E.Ladner, G.Obmolova, A.Teplyakov, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland, Structure 2 Function Project (S2F), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.60 / 2.20
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 154.660, 154.660, 57.520, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 25.9

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Structural Genomics, Protein Ybgi, Unknown Function (pdb code 1nmo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Structural Genomics, Protein Ybgi, Unknown Function, PDB code: 1nmo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1nmo

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Iron binding site 1 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:30.8
occ:1.00
 NE2 A:HIS64 2.1 15.9 1.0
NE2 A:HIS215 2.3 11.0 1.0
OE1 A:GLU219 2.3 15.0 1.0
CE1 A:HIS64 2.7 14.8 1.0
CE1 A:HIS215 3.0 10.7 1.0
FE A:FE302 3.2 25.4 1.0
O A:HOH448 3.2 14.9 1.0
CD A:GLU219 3.2 13.6 1.0
CD2 A:HIS215 3.4 9.7 1.0
CD2 A:HIS64 3.4 15.0 1.0
OE2 A:GLU219 3.5 13.6 1.0
NE2 A:HIS63 3.7 12.0 1.0
CD2 A:HIS63 3.8 12.8 1.0
ND1 A:HIS64 3.9 12.2 1.0
ND1 A:HIS215 4.2 12.7 1.0
CG A:HIS64 4.3 13.7 1.0
CG A:HIS215 4.4 10.2 1.0
CA A:GLY173 4.5 13.6 1.0
CG A:GLU219 4.5 13.4 1.0
O A:HOH409 4.6 20.3 1.0
NE2 A:HIS97 4.6 18.6 1.0
CE1 A:HIS63 4.9 12.9 1.0
CD2 A:HIS97 4.9 16.7 1.0
CB A:GLU219 5.0 13.3 1.0
N A:GLY174 5.0 14.8 1.0

Iron binding site 2 out of 12 in 1nmo

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Iron binding site 2 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:25.4
occ:1.00
 OE2 A:GLU219 2.3 13.6 1.0
O A:HOH409 2.4 20.3 1.0
OD2 A:ASP101 2.4 16.9 1.0
NE2 A:HIS63 2.5 12.0 1.0
OD1 A:ASP101 2.7 16.0 1.0
CG A:ASP101 2.9 15.0 1.0
CD A:GLU219 3.0 13.6 1.0
OE1 A:GLU219 3.1 15.0 1.0
FE A:FE301 3.2 30.8 1.0
CE1 A:HIS63 3.4 12.9 1.0
CD2 A:HIS63 3.6 12.8 1.0
O A:HOH448 3.7 14.9 1.0
ND2 A:ASN108 4.0 11.4 1.0
OG1 A:THR172 4.2 16.4 1.0
NE2 A:HIS97 4.3 18.6 1.0
CG A:GLU219 4.3 13.4 1.0
CB A:ASP101 4.3 15.0 1.0
O A:THR172 4.4 12.4 1.0
O A:HOH432 4.5 17.4 1.0
CD2 A:HIS97 4.5 16.7 1.0
ND1 A:HIS63 4.6 10.4 1.0
NE2 A:HIS64 4.6 15.9 1.0
CG A:HIS63 4.7 12.1 1.0
CA A:GLY173 4.9 13.6 1.0
C A:THR172 4.9 14.0 1.0
NE2 A:HIS215 5.0 11.0 1.0

Iron binding site 3 out of 12 in 1nmo

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Iron binding site 3 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:27.4
occ:1.00
 NE2 B:HIS64 2.1 12.3 1.0
OE1 B:GLU219 2.2 16.4 1.0
NE2 B:HIS215 2.2 11.6 1.0
CE1 B:HIS64 2.7 17.2 1.0
CE1 B:HIS215 3.2 10.5 1.0
CD2 B:HIS215 3.2 12.8 1.0
CD B:GLU219 3.2 13.0 1.0
CD2 B:HIS64 3.3 14.5 1.0
FE B:FE302 3.4 22.2 1.0
OE2 B:GLU219 3.5 15.1 1.0
NE2 B:HIS63 3.9 8.2 1.0
ND1 B:HIS64 4.0 15.7 1.0
CD2 B:HIS63 4.1 9.5 1.0
CG B:HIS64 4.3 15.9 1.0
ND1 B:HIS215 4.3 12.5 1.0
CG B:HIS215 4.3 11.2 1.0
CG B:GLU219 4.5 13.6 1.0
CA B:GLY173 4.5 12.3 1.0
O B:HOH1002 4.6 23.9 1.0
O B:HOH483 4.6 13.1 1.0
NE2 B:HIS97 4.7 17.0 1.0
CB B:GLU219 4.9 11.9 1.0

Iron binding site 4 out of 12 in 1nmo

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Iron binding site 4 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:22.2
occ:1.00
 OE2 B:GLU219 2.3 15.1 1.0
O B:HOH483 2.3 13.1 1.0
NE2 B:HIS63 2.4 8.2 1.0
OD2 B:ASP101 2.4 14.6 1.0
OD1 B:ASP101 2.6 14.1 1.0
CG B:ASP101 2.9 13.9 1.0
CD B:GLU219 2.9 13.0 1.0
OE1 B:GLU219 2.9 16.4 1.0
CE1 B:HIS63 3.2 10.8 1.0
FE B:FE301 3.4 27.4 1.0
CD2 B:HIS63 3.6 9.5 1.0
O B:HOH941 3.9 35.6 1.0
ND2 B:ASN108 4.0 8.9 1.0
NE2 B:HIS97 4.2 17.0 1.0
CG B:GLU219 4.3 13.6 1.0
CB B:ASP101 4.4 13.5 1.0
OG1 B:THR172 4.4 14.0 1.0
CD2 B:HIS97 4.4 16.7 1.0
ND1 B:HIS63 4.5 10.6 1.0
CG B:HIS63 4.6 9.4 1.0
NE2 B:HIS64 4.7 12.3 1.0
O B:THR172 4.8 11.9 1.0

Iron binding site 5 out of 12 in 1nmo

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Iron binding site 5 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:27.9
occ:1.00
 NE2 C:HIS215 2.1 11.7 1.0
OE1 C:GLU219 2.2 10.3 1.0
NE2 C:HIS64 2.2 16.4 1.0
CE1 C:HIS64 2.7 13.6 1.0
CD C:GLU219 3.0 10.5 1.0
CE1 C:HIS215 3.0 10.7 1.0
CD2 C:HIS215 3.1 11.7 1.0
O C:HOH562 3.2 17.1 1.0
OE2 C:GLU219 3.3 12.1 1.0
FE C:FE302 3.3 27.0 1.0
CD2 C:HIS64 3.5 13.7 1.0
NE2 C:HIS63 3.9 8.3 1.0
CD2 C:HIS63 3.9 7.4 1.0
ND1 C:HIS64 4.0 14.6 1.0
ND1 C:HIS215 4.2 11.5 1.0
CG C:HIS215 4.2 10.4 1.0
CG C:GLU219 4.3 7.3 1.0
CA C:GLY173 4.4 12.9 1.0
CG C:HIS64 4.4 12.8 1.0
O D:HOH891 4.7 38.6 1.0
NE2 C:HIS97 4.8 19.1 1.0
O C:HOH644 4.9 24.2 1.0
N C:GLY174 4.9 11.5 1.0
CB C:GLU219 5.0 10.3 1.0

Iron binding site 6 out of 12 in 1nmo

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Iron binding site 6 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:27.0
occ:1.00
 OE2 C:GLU219 2.3 12.1 1.0
OD2 C:ASP101 2.4 17.7 1.0
O C:HOH644 2.5 24.2 1.0
NE2 C:HIS63 2.5 8.3 1.0
OD1 C:ASP101 2.7 15.9 1.0
CG C:ASP101 2.9 16.9 1.0
CD C:GLU219 3.2 10.5 1.0
FE C:FE301 3.3 27.9 1.0
CE1 C:HIS63 3.4 8.2 1.0
OE1 C:GLU219 3.4 10.3 1.0
CD2 C:HIS63 3.6 7.4 1.0
O C:HOH562 3.7 17.1 1.0
O C:HOH1008 3.8 23.5 1.0
ND2 C:ASN108 4.1 10.9 1.0
NE2 C:HIS97 4.2 19.1 1.0
OG1 C:THR172 4.2 13.6 1.0
CD2 C:HIS97 4.4 18.9 1.0
CB C:ASP101 4.4 16.2 1.0
CG C:GLU219 4.5 7.3 1.0
ND1 C:HIS63 4.6 7.7 1.0
NE2 C:HIS64 4.7 16.4 1.0
O C:THR172 4.7 12.8 1.0
CG C:HIS63 4.8 7.8 1.0
CA C:GLY173 4.9 12.9 1.0

Iron binding site 7 out of 12 in 1nmo

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Iron binding site 7 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:27.1
occ:1.00
 NE2 D:HIS215 2.1 13.6 1.0
NE2 D:HIS64 2.1 11.4 1.0
OE1 D:GLU219 2.2 11.7 1.0
CE1 D:HIS64 2.7 10.0 1.0
CE1 D:HIS215 2.9 12.6 1.0
CD2 D:HIS215 3.2 14.7 1.0
O D:HOH628 3.2 20.7 1.0
CD D:GLU219 3.3 10.1 1.0
CD2 D:HIS64 3.3 12.1 1.0
FE D:FE302 3.4 18.2 1.0
OE2 D:GLU219 3.6 9.4 1.0
ND1 D:HIS64 4.0 11.9 1.0
ND1 D:HIS215 4.1 16.0 1.0
CD2 D:HIS63 4.1 10.1 1.0
NE2 D:HIS63 4.1 7.5 1.0
CG D:HIS215 4.2 14.1 1.0
CG D:HIS64 4.3 11.1 1.0
CA D:GLY173 4.5 13.3 1.0
NE2 D:HIS97 4.5 18.6 1.0
CG D:GLU219 4.6 8.0 1.0
O D:HOH865 4.6 20.0 1.0
N D:GLY174 4.8 12.2 1.0

Iron binding site 8 out of 12 in 1nmo

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Iron binding site 8 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:18.2
occ:1.00
 OE2 D:GLU219 2.3 9.4 1.0
O D:HOH865 2.3 20.0 1.0
OD2 D:ASP101 2.3 12.4 1.0
NE2 D:HIS63 2.4 7.5 1.0
OD1 D:ASP101 2.5 10.7 1.0
CG D:ASP101 2.8 12.4 1.0
CD D:GLU219 3.1 10.1 1.0
OE1 D:GLU219 3.2 11.7 1.0
CE1 D:HIS63 3.3 8.2 1.0
FE D:FE301 3.4 27.1 1.0
CD2 D:HIS63 3.5 10.1 1.0
NE2 D:HIS97 4.0 18.6 1.0
O D:HOH628 4.0 20.7 1.0
ND2 D:ASN108 4.3 7.8 1.0
CB D:ASP101 4.3 12.0 1.0
CD2 D:HIS97 4.3 18.5 1.0
OG1 D:THR172 4.4 12.9 1.0
ND1 D:HIS63 4.5 10.9 1.0
CG D:GLU219 4.5 8.0 1.0
NE2 D:HIS64 4.6 11.4 1.0
CG D:HIS63 4.6 11.1 1.0
O D:THR172 4.7 12.6 1.0
CE1 D:HIS97 5.0 18.8 1.0

Iron binding site 9 out of 12 in 1nmo

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Iron binding site 9 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:22.5
occ:1.00
 OE1 E:GLU219 2.1 16.2 1.0
NE2 E:HIS64 2.2 15.4 1.0
NE2 E:HIS215 2.2 11.4 1.0
CE1 E:HIS64 3.1 15.4 1.0
CE1 E:HIS215 3.1 9.4 1.0
CD E:GLU219 3.2 13.3 1.0
CD2 E:HIS64 3.2 14.6 1.0
CD2 E:HIS215 3.3 8.5 1.0
FE E:FE302 3.4 17.9 1.0
OE2 E:GLU219 3.6 12.9 1.0
NE2 E:HIS63 4.0 10.9 1.0
CD2 E:HIS63 4.1 5.8 1.0
ND1 E:HIS64 4.2 16.9 1.0
ND1 E:HIS215 4.2 12.3 1.0
NE2 E:HIS97 4.3 15.0 1.0
CG E:HIS64 4.3 17.1 1.0
CA E:GLY173 4.3 12.6 1.0
O F:HOH898 4.4 16.3 1.0
CG E:HIS215 4.4 10.9 1.0
CG E:GLU219 4.5 11.7 1.0
O E:HOH694 4.6 14.3 1.0
CD2 E:HIS97 4.9 14.3 1.0
CB E:GLU219 4.9 9.5 1.0

Iron binding site 10 out of 12 in 1nmo

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Iron binding site 10 out of 12 in the Structural Genomics, Protein Ybgi, Unknown Function


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structural Genomics, Protein Ybgi, Unknown Function within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe302

b:17.9
occ:1.00
 OE2 E:GLU219 2.3 12.9 1.0
O E:HOH694 2.3 14.3 1.0
OD1 E:ASP101 2.3 18.5 1.0
OD2 E:ASP101 2.3 19.0 1.0
NE2 E:HIS63 2.5 10.9 1.0
CG E:ASP101 2.7 16.7 1.0
CD E:GLU219 2.9 13.3 1.0
OE1 E:GLU219 3.0 16.2 1.0
CE1 E:HIS63 3.4 8.5 1.0
FE E:FE301 3.4 22.5 1.0
CD2 E:HIS63 3.6 5.8 1.0
NE2 E:HIS97 4.1 15.0 1.0
OG1 E:THR172 4.1 14.8 1.0
ND2 E:ASN108 4.2 9.8 1.0
CB E:ASP101 4.2 12.3 1.0
CG E:GLU219 4.3 11.7 1.0
O E:HOH738 4.4 30.3 1.0
O E:THR172 4.4 15.3 1.0
CD2 E:HIS97 4.4 14.3 1.0
ND1 E:HIS63 4.6 6.0 1.0
CG E:HIS63 4.7 7.8 1.0
CA E:GLY173 4.8 12.6 1.0
C E:THR172 4.8 13.5 1.0
NE2 E:HIS64 4.9 15.4 1.0
CE1 E:HIS97 4.9 13.3 1.0

Reference:

J.E.Ladner, G.Obmolova, A.Teplyakov, A.J.Howard, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland. Crystal Structure of Escherichia Coli Protein Ybgi, A Toroidal Structure with A Dinuclear Metal Site Bmc Struct.Biol. V. 3 7 2003.
ISSN: ESSN 1472-6807
PubMed: 14519207
DOI: 10.1186/1472-6807-3-7
Page generated: Sat Aug 3 11:57:18 2024

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