Iron in PDB 2a3p: Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate
Protein crystallography data
The structure of Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate, PDB code: 2a3p
was solved by
M.V.Pattarkine,
Y.-H.Lee,
J.J.Tanner,
J.D.Wall,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.13 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.160,
43.700,
57.887,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
24.8
|
Other elements in 2a3p:
The structure of Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate
(pdb code 2a3p). 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 Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate, PDB code: 2a3p:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2a3p
Go back to
Iron Binding Sites List in 2a3p
Iron binding site 1 out
of 4 in the Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:34.6
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
34.6
|
1.0
|
NE2
|
A:HIS33
|
1.9
|
32.7
|
1.0
|
NE2
|
A:HIS21
|
1.9
|
33.3
|
1.0
|
NA
|
A:HEM501
|
2.0
|
33.2
|
1.0
|
NB
|
A:HEM501
|
2.1
|
32.4
|
1.0
|
ND
|
A:HEM501
|
2.1
|
33.2
|
1.0
|
NC
|
A:HEM501
|
2.1
|
34.0
|
1.0
|
CE1
|
A:HIS33
|
2.8
|
33.7
|
1.0
|
CE1
|
A:HIS21
|
2.8
|
33.9
|
1.0
|
CD2
|
A:HIS33
|
3.0
|
33.6
|
1.0
|
C4A
|
A:HEM501
|
3.0
|
33.6
|
1.0
|
CD2
|
A:HIS21
|
3.0
|
31.6
|
1.0
|
C1A
|
A:HEM501
|
3.0
|
31.2
|
1.0
|
C1B
|
A:HEM501
|
3.0
|
30.2
|
1.0
|
C4D
|
A:HEM501
|
3.1
|
32.0
|
1.0
|
C1D
|
A:HEM501
|
3.1
|
32.2
|
1.0
|
C4C
|
A:HEM501
|
3.1
|
35.9
|
1.0
|
C4B
|
A:HEM501
|
3.1
|
32.3
|
1.0
|
C1C
|
A:HEM501
|
3.2
|
33.8
|
1.0
|
CHB
|
A:HEM501
|
3.4
|
32.5
|
1.0
|
CHA
|
A:HEM501
|
3.4
|
33.2
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
34.6
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
32.5
|
1.0
|
ND1
|
A:HIS33
|
4.0
|
34.0
|
1.0
|
ND1
|
A:HIS21
|
4.0
|
33.7
|
1.0
|
CG
|
A:HIS33
|
4.1
|
34.3
|
1.0
|
CG
|
A:HIS21
|
4.1
|
29.7
|
1.0
|
C3A
|
A:HEM501
|
4.2
|
33.8
|
1.0
|
C2A
|
A:HEM501
|
4.2
|
33.5
|
1.0
|
C2B
|
A:HEM501
|
4.3
|
28.9
|
1.0
|
C3B
|
A:HEM501
|
4.3
|
31.8
|
1.0
|
C3D
|
A:HEM501
|
4.3
|
33.1
|
1.0
|
C2D
|
A:HEM501
|
4.3
|
32.2
|
1.0
|
C3C
|
A:HEM501
|
4.4
|
33.0
|
1.0
|
C2C
|
A:HEM501
|
4.4
|
32.9
|
1.0
|
CE2
|
A:PHE19
|
4.7
|
34.2
|
1.0
|
CD
|
A:PRO4
|
4.7
|
33.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 2a3p
Go back to
Iron Binding Sites List in 2a3p
Iron binding site 2 out
of 4 in the Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:37.0
occ:1.00
|
FE
|
A:HEM502
|
0.0
|
37.0
|
1.0
|
NE2
|
A:HIS34
|
1.9
|
33.9
|
1.0
|
NE2
|
A:HIS51
|
1.9
|
41.6
|
1.0
|
NA
|
A:HEM502
|
2.0
|
35.3
|
1.0
|
NB
|
A:HEM502
|
2.1
|
35.7
|
1.0
|
NC
|
A:HEM502
|
2.1
|
34.6
|
1.0
|
ND
|
A:HEM502
|
2.1
|
35.9
|
1.0
|
CE1
|
A:HIS34
|
2.7
|
31.2
|
1.0
|
CE1
|
A:HIS51
|
2.8
|
40.2
|
1.0
|
CD2
|
A:HIS51
|
3.0
|
40.6
|
1.0
|
C1A
|
A:HEM502
|
3.0
|
34.9
|
1.0
|
CD2
|
A:HIS34
|
3.0
|
32.5
|
1.0
|
C4A
|
A:HEM502
|
3.0
|
34.8
|
1.0
|
C1B
|
A:HEM502
|
3.1
|
34.6
|
1.0
|
C4D
|
A:HEM502
|
3.1
|
36.2
|
1.0
|
C1C
|
A:HEM502
|
3.1
|
38.2
|
1.0
|
C4C
|
A:HEM502
|
3.1
|
36.1
|
1.0
|
C1D
|
A:HEM502
|
3.1
|
36.2
|
1.0
|
C4B
|
A:HEM502
|
3.1
|
33.4
|
1.0
|
CHA
|
A:HEM502
|
3.4
|
34.0
|
1.0
|
CHB
|
A:HEM502
|
3.4
|
34.6
|
1.0
|
CHD
|
A:HEM502
|
3.5
|
36.4
|
1.0
|
CHC
|
A:HEM502
|
3.5
|
35.3
|
1.0
|
ND1
|
A:HIS34
|
3.8
|
27.8
|
1.0
|
ND1
|
A:HIS51
|
3.9
|
38.0
|
1.0
|
CG
|
A:HIS34
|
4.1
|
32.9
|
1.0
|
CG
|
A:HIS51
|
4.1
|
40.4
|
1.0
|
C3A
|
A:HEM502
|
4.2
|
33.9
|
1.0
|
C2A
|
A:HEM502
|
4.2
|
37.5
|
1.0
|
C2B
|
A:HEM502
|
4.3
|
35.5
|
1.0
|
C2C
|
A:HEM502
|
4.3
|
35.4
|
1.0
|
C3B
|
A:HEM502
|
4.3
|
29.2
|
1.0
|
C3D
|
A:HEM502
|
4.4
|
39.5
|
1.0
|
C2D
|
A:HEM502
|
4.4
|
39.6
|
1.0
|
C3C
|
A:HEM502
|
4.4
|
31.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 2a3p
Go back to
Iron Binding Sites List in 2a3p
Iron binding site 3 out
of 4 in the Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:34.9
occ:1.00
|
FE
|
A:HEM503
|
0.0
|
34.9
|
1.0
|
NE2
|
A:HIS24
|
1.9
|
33.6
|
1.0
|
NE2
|
A:HIS83
|
1.9
|
42.8
|
1.0
|
NC
|
A:HEM503
|
2.0
|
29.3
|
1.0
|
ND
|
A:HEM503
|
2.1
|
30.8
|
1.0
|
NB
|
A:HEM503
|
2.1
|
31.2
|
1.0
|
NA
|
A:HEM503
|
2.1
|
30.7
|
1.0
|
CE1
|
A:HIS83
|
2.8
|
42.4
|
1.0
|
CE1
|
A:HIS24
|
2.9
|
31.8
|
1.0
|
CD2
|
A:HIS24
|
2.9
|
32.3
|
1.0
|
CD2
|
A:HIS83
|
3.0
|
38.0
|
1.0
|
C4C
|
A:HEM503
|
3.0
|
27.6
|
1.0
|
C1C
|
A:HEM503
|
3.0
|
31.1
|
1.0
|
C1D
|
A:HEM503
|
3.1
|
32.2
|
1.0
|
C4D
|
A:HEM503
|
3.1
|
32.5
|
1.0
|
C4B
|
A:HEM503
|
3.1
|
33.5
|
1.0
|
C1B
|
A:HEM503
|
3.1
|
31.6
|
1.0
|
C1A
|
A:HEM503
|
3.1
|
32.8
|
1.0
|
C4A
|
A:HEM503
|
3.1
|
32.9
|
1.0
|
CHD
|
A:HEM503
|
3.4
|
29.9
|
1.0
|
CHC
|
A:HEM503
|
3.4
|
33.4
|
1.0
|
CHA
|
A:HEM503
|
3.5
|
30.9
|
1.0
|
CHB
|
A:HEM503
|
3.5
|
33.7
|
1.0
|
ND1
|
A:HIS83
|
3.9
|
37.5
|
1.0
|
ND1
|
A:HIS24
|
4.0
|
30.6
|
1.0
|
CG
|
A:HIS24
|
4.0
|
32.6
|
1.0
|
CG
|
A:HIS83
|
4.1
|
38.6
|
1.0
|
C3C
|
A:HEM503
|
4.2
|
29.9
|
1.0
|
C2C
|
A:HEM503
|
4.2
|
30.5
|
1.0
|
C2D
|
A:HEM503
|
4.3
|
30.6
|
1.0
|
C3D
|
A:HEM503
|
4.3
|
31.1
|
1.0
|
C2B
|
A:HEM503
|
4.3
|
34.3
|
1.0
|
C3B
|
A:HEM503
|
4.3
|
37.1
|
1.0
|
C3A
|
A:HEM503
|
4.3
|
32.4
|
1.0
|
C2A
|
A:HEM503
|
4.3
|
34.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 2a3p
Go back to
Iron Binding Sites List in 2a3p
Iron binding site 4 out
of 4 in the Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome with Bound Molybdate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe504
b:38.2
occ:1.00
|
FE
|
A:HEM504
|
0.0
|
38.2
|
1.0
|
NE2
|
A:HIS106
|
1.9
|
35.0
|
1.0
|
NE2
|
A:HIS69
|
1.9
|
34.4
|
1.0
|
NC
|
A:HEM504
|
2.0
|
35.8
|
1.0
|
NB
|
A:HEM504
|
2.1
|
34.3
|
1.0
|
NA
|
A:HEM504
|
2.1
|
38.2
|
1.0
|
ND
|
A:HEM504
|
2.2
|
37.0
|
1.0
|
CD2
|
A:HIS69
|
2.9
|
35.9
|
1.0
|
CE1
|
A:HIS106
|
2.9
|
36.1
|
1.0
|
CE1
|
A:HIS69
|
2.9
|
32.0
|
1.0
|
CD2
|
A:HIS106
|
2.9
|
32.3
|
1.0
|
C1C
|
A:HEM504
|
3.0
|
35.4
|
1.0
|
C4C
|
A:HEM504
|
3.0
|
36.7
|
1.0
|
C1B
|
A:HEM504
|
3.1
|
33.5
|
1.0
|
C4A
|
A:HEM504
|
3.1
|
36.8
|
1.0
|
C4B
|
A:HEM504
|
3.1
|
38.3
|
1.0
|
C1D
|
A:HEM504
|
3.1
|
34.1
|
1.0
|
C1A
|
A:HEM504
|
3.2
|
37.0
|
1.0
|
C4D
|
A:HEM504
|
3.2
|
36.5
|
1.0
|
CHC
|
A:HEM504
|
3.4
|
35.4
|
1.0
|
CHB
|
A:HEM504
|
3.4
|
37.6
|
1.0
|
CHD
|
A:HEM504
|
3.4
|
34.5
|
1.0
|
CHA
|
A:HEM504
|
3.5
|
34.3
|
1.0
|
ND1
|
A:HIS69
|
4.0
|
30.4
|
1.0
|
ND1
|
A:HIS106
|
4.0
|
33.8
|
1.0
|
CG
|
A:HIS69
|
4.0
|
33.6
|
1.0
|
CG
|
A:HIS106
|
4.0
|
33.1
|
1.0
|
C2C
|
A:HEM504
|
4.2
|
34.1
|
1.0
|
C3C
|
A:HEM504
|
4.2
|
35.5
|
1.0
|
C2B
|
A:HEM504
|
4.3
|
34.9
|
1.0
|
C3A
|
A:HEM504
|
4.3
|
36.1
|
1.0
|
C3B
|
A:HEM504
|
4.3
|
35.4
|
1.0
|
C2A
|
A:HEM504
|
4.4
|
34.6
|
1.0
|
C2D
|
A:HEM504
|
4.4
|
33.8
|
1.0
|
C3D
|
A:HEM504
|
4.4
|
32.3
|
1.0
|
CG2
|
A:ILE68
|
4.9
|
33.3
|
1.0
|
|
Reference:
M.V.Pattarkine,
J.J.Tanner,
C.A.Bottoms,
Y.-H.Lee,
J.D.Wall.
Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome Structure at 1.5A and Cytochrome Interaction with Metal Complexes J.Mol.Biol. V. 358 1314 2006.
ISSN: ISSN 0022-2836
PubMed: 16580681
DOI: 10.1016/J.JMB.2006.03.010
Page generated: Sat Aug 3 18:51:08 2024
|