Iron in PDB 6qkx: 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex)
Protein crystallography data
The structure of 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex), PDB code: 6qkx
was solved by
K.Kayastha,
U.Ermler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.42 /
2.40
|
Space group
|
I 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
176.860,
176.860,
49.220,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.9 /
27.4
|
Iron Binding Sites:
The binding sites of Iron atom in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex)
(pdb code 6qkx). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex), PDB code: 6qkx:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6qkx
Go back to
Iron Binding Sites List in 6qkx
Iron binding site 1 out
of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:77.5
occ:1.00
|
FE1
|
A:SF4801
|
0.0
|
77.5
|
1.0
|
S3
|
A:SF4801
|
2.3
|
67.4
|
1.0
|
S4
|
A:SF4801
|
2.3
|
78.0
|
1.0
|
S2
|
A:SF4801
|
2.3
|
65.1
|
0.8
|
SG
|
A:CYS374
|
2.6
|
70.3
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
76.2
|
0.8
|
FE2
|
A:SF4801
|
2.7
|
76.5
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
65.3
|
0.8
|
CB
|
A:CYS374
|
3.2
|
70.1
|
1.0
|
N
|
A:CYS374
|
3.7
|
70.6
|
1.0
|
S1
|
A:SF4801
|
3.9
|
67.8
|
0.8
|
CA
|
A:CYS374
|
4.1
|
65.3
|
1.0
|
CG
|
A:ARG344
|
4.4
|
75.1
|
1.0
|
N
|
A:ASN371
|
4.5
|
79.5
|
1.0
|
CD
|
A:ARG344
|
4.5
|
73.4
|
1.0
|
CA
|
A:ASN371
|
4.6
|
79.8
|
1.0
|
C
|
A:GLY373
|
4.7
|
71.9
|
1.0
|
N
|
A:GLY373
|
4.7
|
86.7
|
1.0
|
CB
|
A:ARG344
|
4.7
|
75.9
|
1.0
|
SG
|
A:CYS370
|
4.8
|
81.6
|
1.0
|
N
|
A:GLN372
|
4.9
|
88.7
|
1.0
|
CA
|
A:GLY373
|
5.0
|
82.3
|
1.0
|
SG
|
A:CYS367
|
5.0
|
84.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 6qkx
Go back to
Iron Binding Sites List in 6qkx
Iron binding site 2 out
of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:76.5
occ:1.00
|
FE2
|
A:SF4801
|
0.0
|
76.5
|
1.0
|
S4
|
A:SF4801
|
2.3
|
78.0
|
1.0
|
S1
|
A:SF4801
|
2.3
|
67.8
|
0.8
|
S3
|
A:SF4801
|
2.3
|
67.4
|
1.0
|
SG
|
A:CYS386
|
2.6
|
77.4
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
77.5
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
65.3
|
0.8
|
FE4
|
A:SF4801
|
2.7
|
76.2
|
0.8
|
N
|
A:MET387
|
3.6
|
85.0
|
1.0
|
CB
|
A:CYS386
|
3.7
|
78.4
|
1.0
|
CA
|
A:CYS386
|
3.9
|
83.7
|
1.0
|
S2
|
A:SF4801
|
3.9
|
65.1
|
0.8
|
C
|
A:CYS386
|
4.2
|
83.7
|
1.0
|
CG2
|
A:VAL388
|
4.4
|
78.2
|
1.0
|
N
|
A:VAL388
|
4.5
|
83.4
|
1.0
|
CB
|
A:ALA348
|
4.6
|
89.5
|
1.0
|
CB
|
A:MET387
|
4.6
|
88.8
|
1.0
|
CA
|
A:MET387
|
4.6
|
85.8
|
1.0
|
CG2
|
A:ILE347
|
4.7
|
69.8
|
1.0
|
CA
|
A:ALA348
|
4.8
|
86.6
|
1.0
|
SG
|
A:CYS370
|
4.9
|
81.6
|
1.0
|
N
|
A:ALA348
|
4.9
|
76.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 6qkx
Go back to
Iron Binding Sites List in 6qkx
Iron binding site 3 out
of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:65.3
occ:0.80
|
FE3
|
A:SF4801
|
0.0
|
65.3
|
0.8
|
S4
|
A:SF4801
|
2.3
|
78.0
|
1.0
|
S2
|
A:SF4801
|
2.3
|
65.1
|
0.8
|
S1
|
A:SF4801
|
2.3
|
67.8
|
0.8
|
SG
|
A:CYS367
|
2.5
|
84.7
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
77.5
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
76.2
|
0.8
|
FE2
|
A:SF4801
|
2.7
|
76.5
|
1.0
|
CB
|
A:CYS367
|
3.5
|
85.0
|
1.0
|
S3
|
A:SF4801
|
3.9
|
67.4
|
1.0
|
CB
|
A:ARG344
|
3.9
|
75.9
|
1.0
|
CA
|
A:CYS367
|
3.9
|
86.0
|
1.0
|
N
|
A:ALA369
|
4.1
|
81.8
|
1.0
|
N
|
A:THR368
|
4.2
|
89.4
|
1.0
|
CG
|
A:ARG344
|
4.4
|
75.1
|
1.0
|
C
|
A:CYS367
|
4.4
|
87.5
|
1.0
|
CD
|
A:ARG344
|
4.5
|
73.4
|
1.0
|
CA
|
A:ALA369
|
4.5
|
80.3
|
1.0
|
O
|
A:ARG344
|
4.5
|
72.3
|
1.0
|
CA
|
A:ARG344
|
4.7
|
75.3
|
1.0
|
N
|
A:CYS370
|
4.7
|
81.5
|
1.0
|
C
|
A:ARG344
|
4.8
|
70.1
|
1.0
|
SG
|
A:CYS374
|
4.8
|
70.3
|
1.0
|
CB
|
A:ALA348
|
4.8
|
89.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 6qkx
Go back to
Iron Binding Sites List in 6qkx
Iron binding site 4 out
of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:76.2
occ:0.80
|
FE4
|
A:SF4801
|
0.0
|
76.2
|
0.8
|
S2
|
A:SF4801
|
2.3
|
65.1
|
0.8
|
S3
|
A:SF4801
|
2.3
|
67.4
|
1.0
|
S1
|
A:SF4801
|
2.3
|
67.8
|
0.8
|
SG
|
A:CYS370
|
2.6
|
81.6
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
77.5
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
65.3
|
0.8
|
FE2
|
A:SF4801
|
2.7
|
76.5
|
1.0
|
N
|
A:CYS370
|
3.4
|
81.5
|
1.0
|
CB
|
A:CYS370
|
3.7
|
83.2
|
1.0
|
N
|
A:ASN371
|
3.7
|
79.5
|
1.0
|
S4
|
A:SF4801
|
3.9
|
78.0
|
1.0
|
CA
|
A:CYS370
|
3.9
|
81.6
|
1.0
|
C
|
A:CYS370
|
4.2
|
79.4
|
1.0
|
CB
|
A:MET387
|
4.2
|
88.8
|
1.0
|
OG1
|
A:THR368
|
4.3
|
88.8
|
1.0
|
N
|
A:ALA369
|
4.4
|
81.8
|
1.0
|
C
|
A:ALA369
|
4.4
|
79.5
|
1.0
|
N
|
A:GLN372
|
4.5
|
88.7
|
1.0
|
N
|
A:MET387
|
4.6
|
85.0
|
1.0
|
CA
|
A:ASN371
|
4.6
|
79.8
|
1.0
|
CA
|
A:ALA369
|
4.7
|
80.3
|
1.0
|
CE
|
A:MET387
|
4.7
|
92.9
|
1.0
|
SG
|
A:CYS374
|
4.8
|
70.3
|
1.0
|
SG
|
A:CYS367
|
4.9
|
84.7
|
1.0
|
N
|
A:GLY373
|
4.9
|
86.7
|
1.0
|
|
Reference:
M.Willistein,
D.F.Bechtel,
C.S.Muller,
U.Demmer,
L.Heimann,
K.Kayastha,
V.Schunemann,
A.J.Pierik,
G.M.Ullmann,
U.Ermler,
M.Boll.
Low Potential Enzymatic Hydride Transfer Via Highly Cooperative and Inversely Functionalized Flavin Cofactors. Nat Commun V. 10 2074 2019.
ISSN: ESSN 2041-1723
PubMed: 31061390
DOI: 10.1038/S41467-019-10078-3
Page generated: Wed Aug 7 08:03:53 2024
|