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Iron in PDB 4cyb: Dpsc From Streptomyces Coelicolor

Protein crystallography data

The structure of Dpsc From Streptomyces Coelicolor, PDB code: 4cyb was solved by P.D.Townsend, M.D.Hitchings, R.Del Sol, E.Pohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 153.12 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.220, 153.120, 170.280, 90.00, 90.00, 90.00
R / Rfree (%) 15.913 / 19.428

Other elements in 4cyb:

The structure of Dpsc From Streptomyces Coelicolor also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Dpsc From Streptomyces Coelicolor (pdb code 4cyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Dpsc From Streptomyces Coelicolor, PDB code: 4cyb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4cyb

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Iron binding site 1 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1200

b:15.9
occ:0.50
 OE2 A:GLU104 2.3 29.0 1.0
O A:HOH2084 2.3 29.5 1.0
O A:HOH2076 2.3 25.2 1.0
OD2 A:ASP100 2.4 28.2 1.0
O A:HOH2077 2.4 30.8 1.0
NE2 B:HIS73 2.6 22.6 1.0
OD1 A:ASP100 2.6 22.2 1.0
CG A:ASP100 2.9 23.1 1.0
CD A:GLU104 3.3 27.2 1.0
CE1 B:HIS73 3.5 22.6 1.0
CD2 B:HIS73 3.6 21.7 1.0
O A:HOH2078 4.0 43.6 1.0
OE1 A:GLU104 4.0 27.6 1.0
OD2 B:ASP89 4.2 26.7 1.0
O A:HOH2083 4.3 32.0 1.0
NE2 B:HIS85 4.3 21.8 1.0
CE1 B:HIS85 4.3 21.4 1.0
CG A:GLU104 4.4 25.4 1.0
CB A:ASP100 4.4 21.4 1.0
O A:HOH2030 4.4 43.0 1.0
NZ B:LYS70 4.4 22.7 1.0
O A:HOH2080 4.5 45.0 1.0
O A:HOH2079 4.5 32.2 1.0
ND1 B:HIS73 4.7 22.8 1.0
CG B:HIS73 4.7 19.7 1.0
CG B:ASP89 4.7 28.1 1.0
NE1 B:TRP74 4.8 21.4 1.0
OD1 B:ASP89 4.9 29.5 1.0

Iron binding site 2 out of 12 in 4cyb

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Iron binding site 2 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1200

b:17.5
occ:0.50
 O A:HOH2047 2.2 29.8 1.0
OE2 B:GLU104 2.2 29.1 1.0
O A:HOH2044 2.4 23.4 1.0
OD2 B:ASP100 2.5 27.4 1.0
NE2 A:HIS73 2.6 23.2 1.0
O B:HOH2065 2.6 28.2 1.0
OD1 B:ASP100 2.6 24.8 1.0
CG B:ASP100 2.9 25.8 1.0
CD B:GLU104 3.3 27.7 1.0
CE1 A:HIS73 3.4 24.1 1.0
CD2 A:HIS73 3.6 24.4 1.0
OE1 B:GLU104 4.0 28.4 1.0
O B:HOH2068 4.2 36.2 1.0
NZ A:LYS70 4.3 22.7 1.0
CG B:GLU104 4.4 25.9 1.0
OD2 A:ASP89 4.4 32.5 1.0
NE2 A:HIS85 4.4 23.1 1.0
CE1 A:HIS85 4.4 21.5 1.0
CB B:ASP100 4.4 22.6 1.0
ND1 A:HIS73 4.6 22.6 1.0
O B:HOH2066 4.7 31.7 1.0
NE1 A:TRP74 4.7 24.0 1.0
CG A:HIS73 4.7 22.1 1.0
CG A:ASP89 4.8 27.8 1.0
OD1 A:ASP89 4.9 28.1 1.0

Iron binding site 3 out of 12 in 4cyb

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Iron binding site 3 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1200

b:18.1
occ:0.50
 OE2 C:GLU104 2.3 28.7 1.0
O C:HOH2093 2.3 36.3 1.0
O C:HOH2087 2.3 29.4 1.0
NE2 D:HIS73 2.4 20.2 1.0
OD2 C:ASP100 2.4 27.5 1.0
O C:HOH2088 2.5 35.1 1.0
OD1 C:ASP100 2.6 25.4 1.0
CG C:ASP100 2.9 23.2 1.0
CD C:GLU104 3.3 29.1 1.0
CE1 D:HIS73 3.4 21.0 1.0
CD2 D:HIS73 3.5 21.1 1.0
OE1 C:GLU104 4.0 29.0 1.0
O C:HOH2092 4.1 39.3 1.0
NE2 D:HIS85 4.3 23.3 1.0
CE1 D:HIS85 4.3 21.9 1.0
CG C:GLU104 4.4 26.8 1.0
CB C:ASP100 4.4 21.9 1.0
OD2 D:ASP89 4.4 28.9 1.0
O C:HOH2089 4.4 36.8 1.0
NZ D:LYS70 4.5 25.4 1.0
ND1 D:HIS73 4.5 21.3 1.0
CG D:HIS73 4.6 21.8 1.0
NE1 D:TRP74 4.7 24.9 1.0
CG D:ASP89 4.8 28.7 1.0
OD1 D:ASP89 5.0 26.6 1.0

Iron binding site 4 out of 12 in 4cyb

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Iron binding site 4 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1200

b:13.6
occ:0.50
 OE2 D:GLU104 2.3 26.5 1.0
O C:HOH2053 2.3 27.1 1.0
OD2 D:ASP100 2.4 23.8 1.0
O D:HOH2074 2.4 28.4 1.0
O C:HOH2046 2.6 26.2 1.0
NE2 C:HIS73 2.6 19.9 1.0
OD1 D:ASP100 2.6 20.6 1.0
CG D:ASP100 2.9 23.9 1.0
CD D:GLU104 3.3 23.3 1.0
CE1 C:HIS73 3.5 20.9 1.0
CD2 C:HIS73 3.6 18.6 1.0
OE1 D:GLU104 3.9 23.5 1.0
O D:HOH2077 4.1 31.4 1.0
OD2 C:ASP89 4.3 27.7 1.0
NE2 C:HIS85 4.3 20.5 1.0
CG D:GLU104 4.3 20.1 1.0
CE1 C:HIS85 4.4 20.7 1.0
CB D:ASP100 4.4 20.7 1.0
NZ C:LYS70 4.4 19.2 1.0
O D:HOH2075 4.5 32.7 1.0
ND1 C:HIS73 4.7 17.6 1.0
O C:HOH2019 4.7 41.1 1.0
CG C:HIS73 4.8 19.1 1.0
CG C:ASP89 4.8 22.9 1.0
NE1 C:TRP74 4.9 22.3 1.0
OD1 C:ASP89 5.0 29.4 1.0

Iron binding site 5 out of 12 in 4cyb

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Iron binding site 5 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1200

b:18.3
occ:0.50
 OE2 E:GLU104 2.3 30.3 1.0
O E:HOH2072 2.3 27.9 1.0
OD2 E:ASP100 2.4 24.9 1.0
O E:HOH2073 2.4 32.6 1.0
O E:HOH2078 2.4 41.0 1.0
NE2 F:HIS73 2.6 26.8 1.0
OD1 E:ASP100 2.6 26.3 1.0
CG E:ASP100 2.8 25.7 1.0
CD E:GLU104 3.3 26.1 1.0
CE1 F:HIS73 3.5 28.3 1.0
CD2 F:HIS73 3.6 24.6 1.0
OE1 E:GLU104 3.9 27.7 1.0
O E:HOH2077 4.1 37.2 1.0
OD2 F:ASP89 4.2 30.6 1.0
NE2 F:HIS85 4.3 25.9 1.0
CG E:GLU104 4.3 26.5 1.0
CB E:ASP100 4.4 21.5 1.0
CE1 F:HIS85 4.4 26.7 1.0
NZ F:LYS70 4.4 24.9 1.0
O E:HOH2074 4.7 33.9 1.0
ND1 F:HIS73 4.7 25.4 1.0
NE1 F:TRP74 4.8 25.3 1.0
CG F:HIS73 4.8 26.4 1.0
CG F:ASP89 4.8 28.3 1.0
OD1 F:ASP89 4.9 30.6 1.0

Iron binding site 6 out of 12 in 4cyb

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Iron binding site 6 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1200

b:17.2
occ:0.50
 OE2 F:GLU104 2.3 30.0 1.0
O E:HOH2042 2.3 26.8 1.0
O E:HOH2045 2.3 34.3 1.0
O F:HOH2052 2.4 31.6 1.0
OD2 F:ASP100 2.4 28.5 1.0
NE2 E:HIS73 2.6 24.0 1.0
OD1 F:ASP100 2.7 25.6 1.0
CG F:ASP100 2.9 25.8 1.0
CD F:GLU104 3.3 28.4 1.0
CE1 E:HIS73 3.5 20.1 1.0
CD2 E:HIS73 3.6 21.9 1.0
OE1 F:GLU104 4.0 29.5 1.0
O F:HOH2055 4.0 29.5 1.0
CB F:ASP100 4.3 24.7 1.0
CG F:GLU104 4.4 28.0 1.0
NZ E:LYS70 4.4 22.6 1.0
OD2 E:ASP89 4.4 30.4 1.0
NE2 E:HIS85 4.4 24.6 1.0
CE1 E:HIS85 4.4 26.8 1.0
O F:HOH2051 4.5 55.0 1.0
O F:HOH2053 4.5 31.9 1.0
ND1 E:HIS73 4.7 19.7 1.0
CG E:HIS73 4.8 24.0 1.0
CG E:ASP89 4.8 28.0 1.0
NE1 E:TRP74 4.9 25.2 1.0
OD1 E:ASP89 4.9 30.2 1.0
O E:HOH2060 5.0 43.5 1.0

Iron binding site 7 out of 12 in 4cyb

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Iron binding site 7 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1200

b:16.1
occ:0.50
 OE2 G:GLU104 2.3 24.0 1.0
O G:HOH2081 2.3 35.9 1.0
O G:HOH2074 2.4 24.6 1.0
O G:HOH2076 2.4 31.3 1.0
OD2 G:ASP100 2.4 28.6 1.0
NE2 H:HIS73 2.6 24.5 1.0
OD1 G:ASP100 2.6 22.8 1.0
CG G:ASP100 2.9 22.3 1.0
CD G:GLU104 3.3 28.6 1.0
CE1 H:HIS73 3.5 20.7 1.0
CD2 H:HIS73 3.6 21.5 1.0
OE1 G:GLU104 3.9 26.8 1.0
O G:HOH2080 4.1 34.7 1.0
OD2 H:ASP89 4.3 34.1 1.0
NE2 H:HIS85 4.3 20.6 1.0
O G:HOH2077 4.3 44.1 1.0
CE1 H:HIS85 4.4 22.3 1.0
CG G:GLU104 4.4 23.1 1.0
CB G:ASP100 4.4 19.9 1.0
NZ H:LYS70 4.5 24.1 1.0
O G:HOH2075 4.7 37.4 1.0
ND1 H:HIS73 4.7 23.1 1.0
NE1 H:TRP74 4.7 24.0 1.0
CG H:HIS73 4.7 23.2 1.0
CG H:ASP89 4.8 27.9 1.0
OD1 H:ASP89 4.9 32.2 1.0

Iron binding site 8 out of 12 in 4cyb

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Iron binding site 8 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe1200

b:15.7
occ:0.50
 OE2 H:GLU104 2.2 27.3 1.0
O H:HOH2062 2.4 33.8 1.0
O G:HOH2042 2.4 27.3 1.0
OD2 H:ASP100 2.4 26.6 1.0
O G:HOH2047 2.5 38.8 1.0
NE2 G:HIS73 2.5 22.1 1.0
OD1 H:ASP100 2.6 20.8 1.0
CG H:ASP100 2.9 21.1 1.0
CD H:GLU104 3.3 28.6 1.0
CE1 G:HIS73 3.4 20.8 1.0
CD2 G:HIS73 3.5 19.6 1.0
OE1 H:GLU104 4.0 26.0 1.0
O H:HOH2066 4.1 30.2 1.0
OD2 G:ASP89 4.2 27.7 1.0
O H:HOH2060 4.3 53.9 1.0
CB H:ASP100 4.4 20.1 1.0
CG H:GLU104 4.4 23.6 1.0
NZ G:LYS70 4.4 22.8 1.0
NE2 G:HIS85 4.4 25.0 1.0
CE1 G:HIS85 4.4 26.1 1.0
ND1 G:HIS73 4.6 22.3 1.0
CG G:HIS73 4.7 21.5 1.0
O H:HOH2061 4.7 29.9 1.0
CG G:ASP89 4.8 29.5 1.0
NE1 G:TRP74 4.8 23.0 1.0
OD1 G:ASP89 4.9 29.9 1.0

Iron binding site 9 out of 12 in 4cyb

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Iron binding site 9 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe1200

b:14.7
occ:0.50
 OE2 I:GLU104 2.3 24.6 1.0
O I:HOH2098 2.3 32.8 1.0
O I:HOH2091 2.4 23.4 1.0
OD2 I:ASP100 2.4 23.8 1.0
O I:HOH2092 2.4 32.5 1.0
NE2 J:HIS73 2.5 18.3 1.0
OD1 I:ASP100 2.6 22.4 1.0
CG I:ASP100 2.8 21.5 1.0
CD I:GLU104 3.3 28.3 1.0
CE1 J:HIS73 3.4 19.1 1.0
CD2 J:HIS73 3.5 19.7 1.0
OE1 I:GLU104 3.9 26.1 1.0
O I:HOH2097 4.1 31.1 1.0
O I:HOH2090 4.3 52.5 1.0
CB I:ASP100 4.3 19.6 1.0
CG I:GLU104 4.3 25.4 1.0
NE2 J:HIS85 4.4 19.2 1.0
OD2 J:ASP89 4.4 28.3 1.0
CE1 J:HIS85 4.4 23.0 1.0
NZ J:LYS70 4.4 20.3 1.0
O I:HOH2093 4.6 34.4 1.0
ND1 J:HIS73 4.6 18.9 1.0
CG J:HIS73 4.7 18.8 1.0
NE1 J:TRP74 4.8 21.3 1.0
CG J:ASP89 4.8 28.0 1.0
OD1 J:ASP89 5.0 28.9 1.0

Iron binding site 10 out of 12 in 4cyb

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Iron binding site 10 out of 12 in the Dpsc From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Dpsc From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe1201

b:14.8
occ:0.50
 OE2 J:GLU104 2.3 27.0 1.0
O I:HOH2065 2.3 33.1 1.0
O I:HOH2060 2.4 23.4 1.0
O J:HOH2059 2.4 29.9 1.0
OD2 J:ASP100 2.5 24.6 1.0
NE2 I:HIS73 2.5 19.7 1.0
OD1 J:ASP100 2.6 22.3 1.0
CG J:ASP100 2.9 23.5 1.0
CD J:GLU104 3.3 24.9 1.0
CE1 I:HIS73 3.4 19.9 1.0
CD2 I:HIS73 3.5 18.8 1.0
O J:HOH2057 3.8 33.7 1.0
OE1 J:GLU104 4.0 26.9 1.0
O J:HOH2064 4.1 30.2 1.0
O J:HOH2060 4.3 50.0 1.0
NZ I:LYS70 4.3 20.5 1.0
OD2 I:ASP89 4.3 27.8 1.0
NE2 I:HIS85 4.4 22.2 1.0
CB J:ASP100 4.4 21.2 1.0
CG J:GLU104 4.4 22.3 1.0
CE1 I:HIS85 4.4 22.3 1.0
O J:HOH2058 4.5 29.4 1.0
ND1 I:HIS73 4.6 21.3 1.0
CG I:HIS73 4.7 19.3 1.0
CG I:ASP89 4.8 26.1 1.0
NE1 I:TRP74 4.8 20.3 1.0
OD1 I:ASP89 5.0 27.4 1.0

Reference:

M.D.Hitchings, P.D.Townsend, E.Pohl, P.D.Facey, D.H.Jones, P.J.Dyson, R.Del Sol. A Tale of Tails: Deciphering the Contribution of Terminal Tails to the Biochemical Properties of Two Dps Proteins From Streptomyces Coelicolor Cell.Mol.Life Sci. 2014.
ISSN: ESSN 1420-9071
PubMed: 24915944
DOI: 10.1007/S00018-014-1658-4
Page generated: Sun Dec 13 15:30:58 2020

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