Iron in PDB 6qkr: 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex)
Protein crystallography data
The structure of 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex), PDB code: 6qkr
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)
|
30.24 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.670,
86.050,
96.900,
90.00,
90.67,
90.00
|
R / Rfree (%)
|
17.8 /
21.8
|
Iron Binding Sites:
The binding sites of Iron atom in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex)
(pdb code 6qkr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex), PDB code: 6qkr:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6qkr
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Iron Binding Sites List in 6qkr
Iron binding site 1 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked 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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:60.4
occ:1.00
|
FE1
|
A:SF4801
|
0.0
|
60.4
|
1.0
|
SG
|
A:CYS374
|
2.3
|
62.1
|
1.0
|
S2
|
A:SF4801
|
2.3
|
62.0
|
1.0
|
S4
|
A:SF4801
|
2.3
|
56.8
|
1.0
|
S3
|
A:SF4801
|
2.3
|
61.8
|
1.0
|
FE3
|
A:SF4801
|
2.8
|
57.0
|
1.0
|
FE2
|
A:SF4801
|
2.8
|
59.1
|
1.0
|
FE4
|
A:SF4801
|
2.8
|
83.1
|
1.0
|
CB
|
A:CYS374
|
3.3
|
58.8
|
1.0
|
N
|
A:CYS374
|
3.9
|
60.0
|
1.0
|
S1
|
A:SF4801
|
4.0
|
65.4
|
1.0
|
CG
|
A:ARG344
|
4.1
|
48.1
|
1.0
|
CA
|
A:CYS374
|
4.2
|
59.3
|
1.0
|
CD
|
A:ARG344
|
4.4
|
48.8
|
1.0
|
N
|
A:ASN371
|
4.4
|
63.1
|
1.0
|
CA
|
A:ASN371
|
4.5
|
63.0
|
1.0
|
CB
|
A:ARG344
|
4.6
|
47.2
|
1.0
|
N
|
A:GLN372
|
4.8
|
67.1
|
1.0
|
SG
|
A:CYS367
|
4.8
|
55.0
|
1.0
|
SG
|
A:CYS386
|
4.8
|
55.0
|
1.0
|
SG
|
A:CYS370
|
4.8
|
65.4
|
1.0
|
C
|
A:ASN371
|
4.9
|
69.6
|
1.0
|
N
|
A:GLY373
|
4.9
|
62.8
|
1.0
|
CG2
|
A:ILE347
|
5.0
|
46.9
|
1.0
|
C
|
A:GLY373
|
5.0
|
63.8
|
1.0
|
|
Iron binding site 2 out
of 8 in 6qkr
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Iron Binding Sites List in 6qkr
Iron binding site 2 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked 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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:59.1
occ:1.00
|
FE2
|
A:SF4801
|
0.0
|
59.1
|
1.0
|
SG
|
A:CYS386
|
2.3
|
55.0
|
1.0
|
S4
|
A:SF4801
|
2.3
|
56.8
|
1.0
|
S3
|
A:SF4801
|
2.3
|
61.8
|
1.0
|
S1
|
A:SF4801
|
2.4
|
65.4
|
1.0
|
FE3
|
A:SF4801
|
2.8
|
57.0
|
1.0
|
FE1
|
A:SF4801
|
2.8
|
60.4
|
1.0
|
FE4
|
A:SF4801
|
2.8
|
83.1
|
1.0
|
CB
|
A:CYS386
|
3.4
|
49.8
|
1.0
|
N
|
A:MET387
|
3.7
|
50.1
|
1.0
|
CA
|
A:CYS386
|
3.8
|
49.1
|
1.0
|
S2
|
A:SF4801
|
4.0
|
62.0
|
1.0
|
C
|
A:CYS386
|
4.2
|
54.8
|
1.0
|
CG2
|
A:VAL388
|
4.3
|
55.4
|
1.0
|
N
|
A:VAL388
|
4.4
|
49.5
|
1.0
|
CG2
|
A:ILE347
|
4.6
|
46.9
|
1.0
|
CB
|
A:ALA348
|
4.6
|
50.9
|
1.0
|
CB
|
A:MET387
|
4.7
|
54.7
|
1.0
|
CA
|
A:MET387
|
4.7
|
51.7
|
1.0
|
CA
|
A:ALA348
|
4.7
|
49.8
|
1.0
|
N
|
A:ALA348
|
4.8
|
48.5
|
1.0
|
SG
|
A:CYS370
|
4.8
|
65.4
|
1.0
|
|
Iron binding site 3 out
of 8 in 6qkr
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Iron Binding Sites List in 6qkr
Iron binding site 3 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked 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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:57.0
occ:1.00
|
FE3
|
A:SF4801
|
0.0
|
57.0
|
1.0
|
S2
|
A:SF4801
|
2.3
|
62.0
|
1.0
|
S4
|
A:SF4801
|
2.3
|
56.8
|
1.0
|
S1
|
A:SF4801
|
2.4
|
65.4
|
1.0
|
SG
|
A:CYS367
|
2.4
|
55.0
|
1.0
|
FE1
|
A:SF4801
|
2.8
|
60.4
|
1.0
|
FE4
|
A:SF4801
|
2.8
|
83.1
|
1.0
|
FE2
|
A:SF4801
|
2.8
|
59.1
|
1.0
|
CB
|
A:CYS367
|
3.3
|
52.0
|
1.0
|
CA
|
A:CYS367
|
3.8
|
53.6
|
1.0
|
S3
|
A:SF4801
|
4.0
|
61.8
|
1.0
|
CB
|
A:ARG344
|
4.0
|
47.2
|
1.0
|
N
|
A:THR368
|
4.1
|
57.8
|
1.0
|
N
|
A:ALA369
|
4.1
|
63.9
|
1.0
|
C
|
A:CYS367
|
4.3
|
59.9
|
1.0
|
CG
|
A:ARG344
|
4.5
|
48.1
|
1.0
|
CA
|
A:ALA369
|
4.5
|
63.1
|
1.0
|
O
|
A:ARG344
|
4.6
|
53.6
|
1.0
|
CB
|
A:ALA348
|
4.6
|
50.9
|
1.0
|
N
|
A:CYS370
|
4.6
|
62.6
|
1.0
|
CD
|
A:ARG344
|
4.7
|
48.8
|
1.0
|
SG
|
A:CYS374
|
4.8
|
62.1
|
1.0
|
C
|
A:ARG344
|
4.8
|
51.7
|
1.0
|
SG
|
A:CYS386
|
4.8
|
55.0
|
1.0
|
CA
|
A:ARG344
|
4.8
|
46.2
|
1.0
|
|
Iron binding site 4 out
of 8 in 6qkr
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Iron Binding Sites List in 6qkr
Iron binding site 4 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked 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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:83.1
occ:1.00
|
FE4
|
A:SF4801
|
0.0
|
83.1
|
1.0
|
S1
|
A:SF4801
|
2.3
|
65.4
|
1.0
|
S3
|
A:SF4801
|
2.4
|
61.8
|
1.0
|
S2
|
A:SF4801
|
2.4
|
62.0
|
1.0
|
SG
|
A:CYS370
|
2.4
|
65.4
|
1.0
|
FE3
|
A:SF4801
|
2.8
|
57.0
|
1.0
|
FE1
|
A:SF4801
|
2.8
|
60.4
|
1.0
|
FE2
|
A:SF4801
|
2.8
|
59.1
|
1.0
|
N
|
A:CYS370
|
3.5
|
62.6
|
1.0
|
CB
|
A:CYS370
|
3.5
|
61.4
|
1.0
|
N
|
A:ASN371
|
3.7
|
63.1
|
1.0
|
CA
|
A:CYS370
|
3.8
|
62.0
|
1.0
|
S4
|
A:SF4801
|
4.0
|
56.8
|
1.0
|
C
|
A:CYS370
|
4.1
|
65.3
|
1.0
|
OG1
|
A:THR368
|
4.3
|
69.9
|
1.0
|
CB
|
A:MET387
|
4.3
|
54.7
|
1.0
|
N
|
A:GLN372
|
4.4
|
67.1
|
1.0
|
C
|
A:ALA369
|
4.6
|
68.2
|
1.0
|
CA
|
A:ASN371
|
4.6
|
63.0
|
1.0
|
N
|
A:ALA369
|
4.7
|
63.9
|
1.0
|
N
|
A:MET387
|
4.7
|
50.1
|
1.0
|
CE
|
A:MET387
|
4.7
|
61.8
|
1.0
|
SG
|
A:CYS374
|
4.7
|
62.1
|
1.0
|
SG
|
A:CYS367
|
4.8
|
55.0
|
1.0
|
CA
|
A:ALA369
|
4.9
|
63.1
|
1.0
|
SG
|
A:CYS386
|
4.9
|
55.0
|
1.0
|
C
|
A:ASN371
|
5.0
|
69.6
|
1.0
|
N
|
A:THR368
|
5.0
|
57.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 6qkr
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Iron Binding Sites List in 6qkr
Iron binding site 5 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe801
b:54.2
occ:1.00
|
FE1
|
B:SF4801
|
0.0
|
54.2
|
1.0
|
S2
|
B:SF4801
|
2.3
|
61.8
|
1.0
|
S4
|
B:SF4801
|
2.3
|
53.6
|
1.0
|
S3
|
B:SF4801
|
2.3
|
57.7
|
1.0
|
SG
|
B:CYS374
|
2.3
|
54.5
|
1.0
|
FE3
|
B:SF4801
|
2.8
|
54.0
|
1.0
|
FE4
|
B:SF4801
|
2.8
|
80.2
|
1.0
|
FE2
|
B:SF4801
|
2.8
|
55.2
|
1.0
|
CB
|
B:CYS374
|
3.3
|
51.8
|
1.0
|
N
|
B:CYS374
|
4.0
|
55.1
|
1.0
|
S1
|
B:SF4801
|
4.0
|
61.3
|
1.0
|
CG
|
B:ARG344
|
4.1
|
49.6
|
1.0
|
CA
|
B:CYS374
|
4.2
|
52.8
|
1.0
|
CD
|
B:ARG344
|
4.3
|
45.9
|
1.0
|
N
|
B:ASN371
|
4.4
|
54.2
|
1.0
|
CA
|
B:ASN371
|
4.4
|
54.1
|
1.0
|
CB
|
B:ARG344
|
4.6
|
42.7
|
1.0
|
SG
|
B:CYS367
|
4.7
|
50.8
|
1.0
|
SG
|
B:CYS370
|
4.7
|
58.5
|
1.0
|
N
|
B:GLN372
|
4.8
|
57.1
|
1.0
|
SG
|
B:CYS386
|
4.8
|
50.5
|
1.0
|
C
|
B:ASN371
|
4.8
|
59.2
|
1.0
|
N
|
B:GLY373
|
4.9
|
58.0
|
1.0
|
CG2
|
B:ILE347
|
5.0
|
47.4
|
1.0
|
|
Iron binding site 6 out
of 8 in 6qkr
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Iron Binding Sites List in 6qkr
Iron binding site 6 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe801
b:55.2
occ:1.00
|
FE2
|
B:SF4801
|
0.0
|
55.2
|
1.0
|
SG
|
B:CYS386
|
2.2
|
50.5
|
1.0
|
S4
|
B:SF4801
|
2.4
|
53.6
|
1.0
|
S1
|
B:SF4801
|
2.4
|
61.3
|
1.0
|
S3
|
B:SF4801
|
2.4
|
57.7
|
1.0
|
FE1
|
B:SF4801
|
2.8
|
54.2
|
1.0
|
FE3
|
B:SF4801
|
2.8
|
54.0
|
1.0
|
FE4
|
B:SF4801
|
2.8
|
80.2
|
1.0
|
CB
|
B:CYS386
|
3.4
|
47.0
|
1.0
|
N
|
B:MET387
|
3.7
|
50.5
|
1.0
|
CA
|
B:CYS386
|
3.8
|
47.8
|
1.0
|
S2
|
B:SF4801
|
4.0
|
61.8
|
1.0
|
C
|
B:CYS386
|
4.2
|
52.5
|
1.0
|
CG2
|
B:VAL388
|
4.3
|
52.0
|
1.0
|
N
|
B:VAL388
|
4.4
|
48.8
|
1.0
|
CG2
|
B:ILE347
|
4.6
|
47.4
|
1.0
|
CB
|
B:ALA348
|
4.6
|
47.1
|
1.0
|
CA
|
B:MET387
|
4.6
|
52.5
|
1.0
|
CB
|
B:MET387
|
4.6
|
55.9
|
1.0
|
CA
|
B:ALA348
|
4.8
|
46.5
|
1.0
|
SG
|
B:CYS370
|
4.8
|
58.5
|
1.0
|
N
|
B:ALA348
|
4.8
|
46.6
|
1.0
|
|
Iron binding site 7 out
of 8 in 6qkr
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Iron Binding Sites List in 6qkr
Iron binding site 7 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe801
b:54.0
occ:1.00
|
FE3
|
B:SF4801
|
0.0
|
54.0
|
1.0
|
SG
|
B:CYS367
|
2.3
|
50.8
|
1.0
|
S2
|
B:SF4801
|
2.3
|
61.8
|
1.0
|
S4
|
B:SF4801
|
2.3
|
53.6
|
1.0
|
S1
|
B:SF4801
|
2.4
|
61.3
|
1.0
|
FE1
|
B:SF4801
|
2.8
|
54.2
|
1.0
|
FE4
|
B:SF4801
|
2.8
|
80.2
|
1.0
|
FE2
|
B:SF4801
|
2.8
|
55.2
|
1.0
|
CB
|
B:CYS367
|
3.3
|
48.7
|
1.0
|
CA
|
B:CYS367
|
3.8
|
49.6
|
1.0
|
CB
|
B:ARG344
|
4.0
|
42.7
|
1.0
|
S3
|
B:SF4801
|
4.0
|
57.7
|
1.0
|
N
|
B:THR368
|
4.0
|
47.7
|
1.0
|
N
|
B:ALA369
|
4.1
|
57.7
|
1.0
|
C
|
B:CYS367
|
4.3
|
53.7
|
1.0
|
CG
|
B:ARG344
|
4.5
|
49.6
|
1.0
|
CA
|
B:ALA369
|
4.6
|
57.7
|
1.0
|
O
|
B:ARG344
|
4.6
|
46.2
|
1.0
|
CB
|
B:ALA348
|
4.7
|
47.1
|
1.0
|
N
|
B:CYS370
|
4.7
|
54.7
|
1.0
|
CD
|
B:ARG344
|
4.7
|
45.9
|
1.0
|
C
|
B:ARG344
|
4.8
|
46.3
|
1.0
|
SG
|
B:CYS374
|
4.8
|
54.5
|
1.0
|
CA
|
B:ARG344
|
4.8
|
43.8
|
1.0
|
SG
|
B:CYS386
|
4.8
|
50.5
|
1.0
|
|
Iron binding site 8 out
of 8 in 6qkr
Go back to
Iron Binding Sites List in 6qkr
Iron binding site 8 out
of 8 in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe801
b:80.2
occ:1.00
|
FE4
|
B:SF4801
|
0.0
|
80.2
|
1.0
|
S1
|
B:SF4801
|
2.3
|
61.3
|
1.0
|
S3
|
B:SF4801
|
2.4
|
57.7
|
1.0
|
SG
|
B:CYS370
|
2.4
|
58.5
|
1.0
|
S2
|
B:SF4801
|
2.4
|
61.8
|
1.0
|
FE1
|
B:SF4801
|
2.8
|
54.2
|
1.0
|
FE3
|
B:SF4801
|
2.8
|
54.0
|
1.0
|
FE2
|
B:SF4801
|
2.8
|
55.2
|
1.0
|
N
|
B:CYS370
|
3.5
|
54.7
|
1.0
|
CB
|
B:CYS370
|
3.5
|
54.7
|
1.0
|
N
|
B:ASN371
|
3.6
|
54.2
|
1.0
|
CA
|
B:CYS370
|
3.9
|
54.2
|
1.0
|
S4
|
B:SF4801
|
4.0
|
53.6
|
1.0
|
C
|
B:CYS370
|
4.1
|
57.5
|
1.0
|
OG1
|
B:THR368
|
4.2
|
54.8
|
1.0
|
CB
|
B:MET387
|
4.3
|
55.9
|
1.0
|
N
|
B:GLN372
|
4.4
|
57.1
|
1.0
|
CA
|
B:ASN371
|
4.5
|
54.1
|
1.0
|
C
|
B:ALA369
|
4.6
|
61.7
|
1.0
|
N
|
B:MET387
|
4.7
|
50.5
|
1.0
|
N
|
B:ALA369
|
4.7
|
57.7
|
1.0
|
SG
|
B:CYS374
|
4.7
|
54.5
|
1.0
|
SG
|
B:CYS367
|
4.8
|
50.8
|
1.0
|
CA
|
B:ALA369
|
4.9
|
57.7
|
1.0
|
SG
|
B:CYS386
|
4.9
|
50.5
|
1.0
|
C
|
B:ASN371
|
4.9
|
59.2
|
1.0
|
N
|
B:THR368
|
5.0
|
47.7
|
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 08:03:14 2024
|