Iron in PDB 1p59: Structure of A Non-Covalent Endonuclease III-Dna Complex
Protein crystallography data
The structure of Structure of A Non-Covalent Endonuclease III-Dna Complex, PDB code: 1p59
was solved by
J.C.Fromme,
G.L.Verdine,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.31 /
2.50
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.321,
105.896,
41.518,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.4 /
26.9
|
Other elements in 1p59:
The structure of Structure of A Non-Covalent Endonuclease III-Dna Complex also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of A Non-Covalent Endonuclease III-Dna Complex
(pdb code 1p59). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of A Non-Covalent Endonuclease III-Dna Complex, PDB code: 1p59:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1p59
Go back to
Iron Binding Sites List in 1p59
Iron binding site 1 out
of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:38.9
occ:1.00
|
FE1
|
A:SF4300
|
0.0
|
38.9
|
1.0
|
S2
|
A:SF4300
|
2.2
|
38.7
|
1.0
|
S4
|
A:SF4300
|
2.2
|
37.5
|
1.0
|
SG
|
A:CYS199
|
2.3
|
36.0
|
1.0
|
S3
|
A:SF4300
|
2.4
|
37.2
|
1.0
|
FE3
|
A:SF4300
|
2.6
|
38.6
|
1.0
|
FE4
|
A:SF4300
|
2.7
|
37.3
|
1.0
|
FE2
|
A:SF4300
|
2.8
|
39.2
|
1.0
|
CB
|
A:CYS199
|
2.9
|
39.0
|
1.0
|
S1
|
A:SF4300
|
3.9
|
37.5
|
1.0
|
CA
|
A:CYS196
|
4.3
|
41.8
|
1.0
|
CZ
|
A:PHE184
|
4.3
|
37.9
|
1.0
|
NE2
|
A:HIS188
|
4.3
|
42.4
|
1.0
|
CA
|
A:CYS199
|
4.3
|
41.1
|
1.0
|
CD2
|
A:HIS188
|
4.5
|
41.4
|
1.0
|
N
|
A:LEU202
|
4.7
|
38.5
|
1.0
|
CB
|
A:LEU201
|
4.8
|
36.4
|
1.0
|
SG
|
A:CYS205
|
4.8
|
32.8
|
1.0
|
CB
|
A:CYS196
|
4.9
|
42.0
|
1.0
|
N
|
A:CYS196
|
4.9
|
40.2
|
1.0
|
CE2
|
A:PHE184
|
4.9
|
37.9
|
1.0
|
SG
|
A:CYS196
|
4.9
|
42.2
|
1.0
|
C
|
A:LEU201
|
4.9
|
38.8
|
1.0
|
C
|
A:CYS199
|
5.0
|
41.4
|
1.0
|
O
|
A:GLN195
|
5.0
|
38.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 1p59
Go back to
Iron Binding Sites List in 1p59
Iron binding site 2 out
of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:39.2
occ:1.00
|
FE2
|
A:SF4300
|
0.0
|
39.2
|
1.0
|
S3
|
A:SF4300
|
2.2
|
37.2
|
1.0
|
S1
|
A:SF4300
|
2.2
|
37.5
|
1.0
|
S4
|
A:SF4300
|
2.3
|
37.5
|
1.0
|
FE4
|
A:SF4300
|
2.5
|
37.3
|
1.0
|
SG
|
A:CYS189
|
2.6
|
36.2
|
1.0
|
FE3
|
A:SF4300
|
2.6
|
38.6
|
1.0
|
FE1
|
A:SF4300
|
2.8
|
38.9
|
1.0
|
CB
|
A:CYS189
|
3.2
|
38.1
|
1.0
|
S2
|
A:SF4300
|
3.6
|
38.7
|
1.0
|
CA
|
A:CYS189
|
3.9
|
38.8
|
1.0
|
CB
|
A:PRO194
|
4.4
|
43.3
|
1.0
|
CE2
|
A:PHE184
|
4.5
|
37.9
|
1.0
|
CD
|
A:ARG148
|
4.7
|
33.5
|
1.0
|
SG
|
A:CYS196
|
4.7
|
42.2
|
1.0
|
NH1
|
A:ARG148
|
4.7
|
29.3
|
1.0
|
CZ
|
A:PHE184
|
4.8
|
37.9
|
1.0
|
SG
|
A:CYS205
|
4.8
|
32.8
|
1.0
|
C
|
A:CYS189
|
4.9
|
38.4
|
1.0
|
SG
|
A:CYS199
|
4.9
|
36.0
|
1.0
|
N
|
A:CYS189
|
5.0
|
38.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 1p59
Go back to
Iron Binding Sites List in 1p59
Iron binding site 3 out
of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:38.6
occ:1.00
|
FE3
|
A:SF4300
|
0.0
|
38.6
|
1.0
|
S4
|
A:SF4300
|
2.1
|
37.5
|
1.0
|
S2
|
A:SF4300
|
2.1
|
38.7
|
1.0
|
S1
|
A:SF4300
|
2.3
|
37.5
|
1.0
|
SG
|
A:CYS196
|
2.5
|
42.2
|
1.0
|
FE1
|
A:SF4300
|
2.6
|
38.9
|
1.0
|
FE2
|
A:SF4300
|
2.6
|
39.2
|
1.0
|
FE4
|
A:SF4300
|
2.7
|
37.3
|
1.0
|
CB
|
A:CYS196
|
3.1
|
42.0
|
1.0
|
CA
|
A:CYS196
|
3.3
|
41.8
|
1.0
|
N
|
A:CYS196
|
3.8
|
40.2
|
1.0
|
S3
|
A:SF4300
|
3.8
|
37.2
|
1.0
|
CA
|
A:GLY208
|
4.0
|
44.5
|
1.0
|
CB
|
A:PRO194
|
4.1
|
43.3
|
1.0
|
CB
|
A:CYS199
|
4.5
|
39.0
|
1.0
|
N
|
A:GLY208
|
4.5
|
42.1
|
1.0
|
C
|
A:CYS196
|
4.6
|
43.0
|
1.0
|
C
|
A:GLN195
|
4.6
|
39.8
|
1.0
|
CG
|
A:PRO194
|
4.7
|
41.7
|
1.0
|
SG
|
A:CYS199
|
4.8
|
36.0
|
1.0
|
SG
|
A:CYS205
|
4.8
|
32.8
|
1.0
|
O
|
A:CYS196
|
5.0
|
44.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 1p59
Go back to
Iron Binding Sites List in 1p59
Iron binding site 4 out
of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:37.3
occ:1.00
|
FE4
|
A:SF4300
|
0.0
|
37.3
|
1.0
|
S2
|
A:SF4300
|
2.1
|
38.7
|
1.0
|
S3
|
A:SF4300
|
2.3
|
37.2
|
1.0
|
S1
|
A:SF4300
|
2.3
|
37.5
|
1.0
|
SG
|
A:CYS205
|
2.4
|
32.8
|
1.0
|
FE2
|
A:SF4300
|
2.5
|
39.2
|
1.0
|
FE3
|
A:SF4300
|
2.7
|
38.6
|
1.0
|
FE1
|
A:SF4300
|
2.7
|
38.9
|
1.0
|
CB
|
A:CYS205
|
3.5
|
37.8
|
1.0
|
S4
|
A:SF4300
|
3.8
|
37.5
|
1.0
|
N
|
A:GLY208
|
3.8
|
42.1
|
1.0
|
CD1
|
A:LEU149
|
4.0
|
30.2
|
1.0
|
CA
|
A:GLY208
|
4.0
|
44.5
|
1.0
|
CB
|
A:GLU207
|
4.5
|
38.3
|
1.0
|
C
|
A:GLU207
|
4.6
|
39.7
|
1.0
|
SG
|
A:CYS199
|
4.8
|
36.0
|
1.0
|
SG
|
A:CYS189
|
4.9
|
36.2
|
1.0
|
CA
|
A:CYS205
|
4.9
|
38.1
|
1.0
|
CB
|
A:ARG148
|
4.9
|
33.7
|
1.0
|
SG
|
A:CYS196
|
4.9
|
42.2
|
1.0
|
|
Reference:
J.C.Fromme,
G.L.Verdine.
Structure of A Trapped Endonuclease III-Dna Covalent Intermediate Embo J. V. 22 3461 2003.
ISSN: ISSN 0261-4189
PubMed: 12840008
DOI: 10.1093/EMBOJ/CDG311
Page generated: Sat Aug 3 12:57:33 2024
|