Iron in PDB 6rpd: Structure of Ferrous Kpdyp in Complex with Cyanide
Protein crystallography data
The structure of Structure of Ferrous Kpdyp in Complex with Cyanide, PDB code: 6rpd
was solved by
V.Pfanzagl,
J.Beale,
S.Hofbauer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.62 /
1.52
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.570,
75.740,
75.710,
90.00,
107.85,
90.00
|
R / Rfree (%)
|
17.1 /
18.9
|
Other elements in 6rpd:
The structure of Structure of Ferrous Kpdyp in Complex with Cyanide also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Ferrous Kpdyp in Complex with Cyanide
(pdb code 6rpd). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Structure of Ferrous Kpdyp in Complex with Cyanide, PDB code: 6rpd:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 6rpd
Go back to
Iron Binding Sites List in 6rpd
Iron binding site 1 out
of 2 in the Structure of Ferrous Kpdyp in Complex with Cyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Ferrous Kpdyp in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:15.2
occ:1.00
|
FE
|
A:HEM401
|
0.0
|
15.2
|
1.0
|
NA
|
A:HEM401
|
2.0
|
15.3
|
1.0
|
NB
|
A:HEM401
|
2.0
|
14.6
|
1.0
|
ND
|
A:HEM401
|
2.0
|
15.2
|
1.0
|
NC
|
A:HEM401
|
2.0
|
14.8
|
1.0
|
NE2
|
A:HIS215
|
2.1
|
15.4
|
1.0
|
C
|
A:CYN407
|
2.2
|
19.9
|
1.0
|
C4B
|
A:HEM401
|
3.0
|
14.8
|
1.0
|
C1B
|
A:HEM401
|
3.0
|
15.0
|
1.0
|
C4D
|
A:HEM401
|
3.0
|
15.5
|
1.0
|
C4A
|
A:HEM401
|
3.0
|
15.2
|
1.0
|
C1D
|
A:HEM401
|
3.0
|
15.4
|
1.0
|
C1A
|
A:HEM401
|
3.0
|
15.5
|
1.0
|
C4C
|
A:HEM401
|
3.0
|
14.9
|
1.0
|
C1C
|
A:HEM401
|
3.0
|
14.5
|
1.0
|
CE1
|
A:HIS215
|
3.1
|
14.5
|
1.0
|
CD2
|
A:HIS215
|
3.1
|
16.0
|
1.0
|
N
|
A:CYN407
|
3.3
|
22.4
|
1.0
|
HE1
|
A:HIS215
|
3.3
|
14.4
|
1.0
|
HD2
|
A:HIS215
|
3.4
|
15.9
|
1.0
|
CHB
|
A:HEM401
|
3.4
|
15.5
|
1.0
|
CHA
|
A:HEM401
|
3.4
|
15.9
|
1.0
|
CHC
|
A:HEM401
|
3.4
|
15.1
|
1.0
|
CHD
|
A:HEM401
|
3.4
|
15.6
|
1.0
|
HE1
|
A:PHE248
|
3.7
|
13.6
|
1.0
|
HG21
|
A:VAL219
|
3.8
|
15.2
|
1.0
|
HE1
|
A:MET276
|
3.9
|
17.7
|
1.0
|
HH11
|
A:ARG232
|
4.0
|
15.8
|
1.0
|
CG
|
A:HIS215
|
4.2
|
15.2
|
1.0
|
ND1
|
A:HIS215
|
4.2
|
15.3
|
1.0
|
C3A
|
A:HEM401
|
4.2
|
15.8
|
1.0
|
C3B
|
A:HEM401
|
4.2
|
15.2
|
1.0
|
C2B
|
A:HEM401
|
4.2
|
15.1
|
1.0
|
C2A
|
A:HEM401
|
4.2
|
15.9
|
1.0
|
C2C
|
A:HEM401
|
4.3
|
14.9
|
1.0
|
C3D
|
A:HEM401
|
4.3
|
15.9
|
1.0
|
C3C
|
A:HEM401
|
4.3
|
15.2
|
1.0
|
C2D
|
A:HEM401
|
4.3
|
15.8
|
1.0
|
HD3
|
A:ARG232
|
4.3
|
16.1
|
1.0
|
HHA
|
A:HEM401
|
4.3
|
15.9
|
1.0
|
NH1
|
A:ARG232
|
4.4
|
15.8
|
1.0
|
HHC
|
A:HEM401
|
4.4
|
14.9
|
1.0
|
HHD
|
A:HEM401
|
4.4
|
15.5
|
1.0
|
HHB
|
A:HEM401
|
4.5
|
15.3
|
1.0
|
HD2
|
A:ARG232
|
4.6
|
16.0
|
1.0
|
CE1
|
A:PHE248
|
4.6
|
13.6
|
1.0
|
HH12
|
A:ARG232
|
4.7
|
15.9
|
1.0
|
HG11
|
A:VAL219
|
4.7
|
15.7
|
1.0
|
HD1
|
A:PHE248
|
4.8
|
14.0
|
1.0
|
CG2
|
A:VAL219
|
4.8
|
15.3
|
1.0
|
OD1
|
A:ASP143
|
4.9
|
38.2
|
0.5
|
CD
|
A:ARG232
|
4.9
|
16.1
|
1.0
|
CE
|
A:MET276
|
5.0
|
17.8
|
1.0
|
|
Iron binding site 2 out
of 2 in 6rpd
Go back to
Iron Binding Sites List in 6rpd
Iron binding site 2 out
of 2 in the Structure of Ferrous Kpdyp in Complex with Cyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Ferrous Kpdyp in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:17.2
occ:1.00
|
FE
|
B:HEM401
|
0.0
|
17.2
|
1.0
|
NB
|
B:HEM401
|
2.0
|
16.8
|
1.0
|
NA
|
B:HEM401
|
2.0
|
17.4
|
1.0
|
NC
|
B:HEM401
|
2.0
|
17.0
|
1.0
|
ND
|
B:HEM401
|
2.0
|
17.2
|
1.0
|
NE2
|
B:HIS215
|
2.1
|
17.8
|
1.0
|
C
|
B:CYN406
|
2.5
|
22.2
|
1.0
|
C4B
|
B:HEM401
|
3.0
|
16.9
|
1.0
|
C1B
|
B:HEM401
|
3.0
|
17.1
|
1.0
|
C4A
|
B:HEM401
|
3.0
|
17.3
|
1.0
|
C4D
|
B:HEM401
|
3.0
|
17.5
|
1.0
|
C1D
|
B:HEM401
|
3.0
|
17.5
|
1.0
|
C4C
|
B:HEM401
|
3.0
|
17.1
|
1.0
|
C1C
|
B:HEM401
|
3.0
|
16.8
|
1.0
|
C1A
|
B:HEM401
|
3.0
|
17.5
|
1.0
|
CE1
|
B:HIS215
|
3.0
|
17.3
|
1.0
|
CD2
|
B:HIS215
|
3.1
|
18.3
|
1.0
|
HE1
|
B:HIS215
|
3.3
|
17.3
|
1.0
|
HD2
|
B:HIS215
|
3.3
|
18.3
|
1.0
|
CHB
|
B:HEM401
|
3.4
|
17.6
|
1.0
|
CHC
|
B:HEM401
|
3.4
|
17.4
|
1.0
|
CHA
|
B:HEM401
|
3.4
|
17.9
|
1.0
|
CHD
|
B:HEM401
|
3.4
|
17.8
|
1.0
|
N
|
B:CYN406
|
3.6
|
27.9
|
1.0
|
HE1
|
B:PHE248
|
3.8
|
16.0
|
1.0
|
HG21
|
B:VAL219
|
3.8
|
20.1
|
1.0
|
HE1
|
B:MET276
|
3.9
|
19.3
|
1.0
|
HH11
|
B:ARG232
|
4.0
|
16.8
|
1.0
|
CG
|
B:HIS215
|
4.2
|
17.7
|
1.0
|
ND1
|
B:HIS215
|
4.2
|
18.2
|
1.0
|
C3B
|
B:HEM401
|
4.2
|
17.4
|
1.0
|
C2B
|
B:HEM401
|
4.2
|
17.2
|
1.0
|
C3A
|
B:HEM401
|
4.2
|
17.9
|
1.0
|
C2C
|
B:HEM401
|
4.3
|
17.2
|
1.0
|
C2A
|
B:HEM401
|
4.3
|
17.9
|
1.0
|
C3C
|
B:HEM401
|
4.3
|
17.4
|
1.0
|
C3D
|
B:HEM401
|
4.3
|
18.0
|
1.0
|
C2D
|
B:HEM401
|
4.3
|
17.9
|
1.0
|
HD3
|
B:ARG232
|
4.3
|
18.0
|
1.0
|
HHA
|
B:HEM401
|
4.3
|
17.9
|
1.0
|
HHC
|
B:HEM401
|
4.4
|
17.1
|
1.0
|
NH1
|
B:ARG232
|
4.4
|
16.9
|
1.0
|
HHD
|
B:HEM401
|
4.4
|
17.7
|
1.0
|
HHB
|
B:HEM401
|
4.5
|
17.4
|
1.0
|
HD2
|
B:ARG232
|
4.6
|
17.9
|
1.0
|
CE1
|
B:PHE248
|
4.6
|
16.1
|
1.0
|
HG11
|
B:VAL219
|
4.7
|
19.0
|
1.0
|
HH12
|
B:ARG232
|
4.7
|
16.9
|
1.0
|
OD1
|
B:ASP143
|
4.7
|
42.5
|
1.0
|
HD1
|
B:PHE248
|
4.8
|
16.0
|
1.0
|
CG2
|
B:VAL219
|
4.8
|
20.2
|
1.0
|
CD
|
B:ARG232
|
4.9
|
18.0
|
1.0
|
CE
|
B:MET276
|
5.0
|
19.5
|
1.0
|
|
Reference:
V.Pfanzagl,
J.H.Beale,
H.Michlits,
D.Schmidt,
T.Gabler,
C.Obinger,
K.Djinovic-Carugo,
S.Hofbauer.
X-Ray-Induced Photoreduction of Heme Metal Centers Rapidly Induces Active-Site Perturbations in A Protein-Independent Manner. J.Biol.Chem. V. 295 13488 2020.
ISSN: ESSN 1083-351X
PubMed: 32723869
DOI: 10.1074/JBC.RA120.014087
Page generated: Wed Aug 7 08:54:09 2024
|