Iodine in PDB 5lbd: Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
Enzymatic activity of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
All present enzymatic activity of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase:
3.6.3.54;
Protein crystallography data
The structure of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase, PDB code: 5lbd
was solved by
H.Mayerhofer,
S.Ravaud,
E.Pebay-Peyroula,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.96 /
1.50
|
Space group
|
P 2 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.800,
65.191,
85.590,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
20.7
|
Other elements in 5lbd:
The structure of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
(pdb code 5lbd). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the
Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase, PDB code: 5lbd:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
Iodine binding site 1 out
of 5 in 5lbd
Go back to
Iodine Binding Sites List in 5lbd
Iodine binding site 1 out
of 5 in the Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I801
b:39.8
occ:0.52
|
N
|
A:NH4805
|
2.9
|
25.0
|
1.0
|
HD22
|
A:ASN683
|
2.9
|
60.9
|
1.0
|
HZ1
|
A:LYS685
|
3.0
|
59.5
|
1.0
|
HE2
|
A:MSE663
|
3.1
|
82.8
|
0.8
|
HZ3
|
A:TRP627
|
3.6
|
56.1
|
1.0
|
HZ2
|
A:LYS685
|
3.6
|
59.5
|
1.0
|
NZ
|
A:LYS685
|
3.6
|
49.6
|
1.0
|
HE3
|
A:LYS685
|
3.7
|
51.6
|
1.0
|
ND2
|
A:ASN683
|
3.8
|
50.8
|
1.0
|
CE
|
A:MSE663
|
3.9
|
69.0
|
0.8
|
HB2
|
A:ASN683
|
4.0
|
37.8
|
1.0
|
HE1
|
A:MSE663
|
4.0
|
82.8
|
0.8
|
SE
|
A:MSE663
|
4.1
|
64.2
|
0.2
|
HB3
|
A:ASN683
|
4.2
|
37.8
|
1.0
|
CE
|
A:LYS685
|
4.2
|
43.0
|
1.0
|
HD21
|
A:ASN683
|
4.2
|
60.9
|
1.0
|
HH2
|
A:TRP627
|
4.3
|
60.5
|
1.0
|
HD21
|
A:LEU635
|
4.3
|
23.9
|
1.0
|
CZ3
|
A:TRP627
|
4.4
|
46.8
|
1.0
|
HZ3
|
A:LYS685
|
4.4
|
59.5
|
1.0
|
CB
|
A:ASN683
|
4.4
|
31.5
|
1.0
|
HG2
|
A:MSE663
|
4.5
|
78.3
|
0.8
|
HE2
|
A:LYS685
|
4.6
|
51.6
|
1.0
|
SE
|
A:MSE663
|
4.6
|
75.9
|
0.8
|
CG
|
A:ASN683
|
4.6
|
51.6
|
1.0
|
HE3
|
A:MSE663
|
4.7
|
82.8
|
0.8
|
CH2
|
A:TRP627
|
4.7
|
50.4
|
1.0
|
HE1
|
A:MSE663
|
4.9
|
79.8
|
0.2
|
|
Iodine binding site 2 out
of 5 in 5lbd
Go back to
Iodine Binding Sites List in 5lbd
Iodine binding site 2 out
of 5 in the Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I802
b:34.5
occ:0.40
|
HD21
|
A:ASN703
|
3.2
|
76.9
|
1.0
|
HD12
|
A:LEU705
|
3.8
|
67.2
|
1.0
|
O
|
A:PRO616
|
4.0
|
47.2
|
1.0
|
HA
|
A:PRO616
|
4.0
|
41.5
|
1.0
|
ND2
|
A:ASN703
|
4.1
|
64.1
|
1.0
|
HB2
|
A:PRO616
|
4.2
|
64.6
|
1.0
|
HB3
|
A:PRO616
|
4.4
|
64.6
|
1.0
|
HB2
|
A:LEU705
|
4.4
|
41.0
|
1.0
|
HD22
|
A:ASN703
|
4.6
|
76.9
|
1.0
|
CB
|
A:PRO616
|
4.6
|
53.8
|
1.0
|
HD13
|
A:LEU705
|
4.6
|
67.2
|
1.0
|
CD1
|
A:LEU705
|
4.6
|
56.0
|
1.0
|
CA
|
A:PRO616
|
4.6
|
34.6
|
1.0
|
C
|
A:PRO616
|
4.8
|
38.9
|
1.0
|
OD1
|
A:ASN703
|
4.8
|
49.8
|
1.0
|
CG
|
A:ASN703
|
4.9
|
62.1
|
1.0
|
HB3
|
A:LEU705
|
5.0
|
41.0
|
1.0
|
|
Iodine binding site 3 out
of 5 in 5lbd
Go back to
Iodine Binding Sites List in 5lbd
Iodine binding site 3 out
of 5 in the Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I803
b:43.3
occ:0.42
|
HZ1
|
A:LYS696
|
2.6
|
68.7
|
1.0
|
H
|
A:ASN703
|
2.9
|
57.8
|
1.0
|
HD21
|
A:LEU692
|
2.9
|
38.5
|
1.0
|
HA3
|
A:GLY702
|
3.1
|
53.5
|
1.0
|
HE3
|
A:LYS696
|
3.1
|
60.3
|
1.0
|
NZ
|
A:LYS696
|
3.3
|
57.3
|
1.0
|
HE2
|
A:LYS696
|
3.4
|
60.3
|
1.0
|
N
|
A:ASN703
|
3.5
|
48.1
|
1.0
|
CE
|
A:LYS696
|
3.5
|
50.3
|
1.0
|
HA
|
A:SER704
|
3.7
|
44.7
|
1.0
|
HZ2
|
A:LYS696
|
3.7
|
68.7
|
1.0
|
CA
|
A:GLY702
|
3.8
|
44.6
|
1.0
|
HA2
|
A:GLY702
|
3.8
|
53.5
|
1.0
|
CD2
|
A:LEU692
|
3.9
|
32.1
|
1.0
|
HZ3
|
A:LYS696
|
4.0
|
68.7
|
1.0
|
N
|
A:SER704
|
4.0
|
56.0
|
1.0
|
HD11
|
A:LEU692
|
4.0
|
31.7
|
1.0
|
C
|
A:ASN703
|
4.0
|
43.1
|
1.0
|
C
|
A:GLY702
|
4.0
|
44.0
|
1.0
|
H
|
A:SER704
|
4.2
|
67.2
|
1.0
|
CA
|
A:SER704
|
4.3
|
37.2
|
1.0
|
HD22
|
A:LEU692
|
4.3
|
38.5
|
1.0
|
HD23
|
A:LEU692
|
4.3
|
38.5
|
1.0
|
HB3
|
A:SER704
|
4.3
|
61.4
|
1.0
|
CA
|
A:ASN703
|
4.4
|
52.5
|
1.0
|
O
|
A:ASN703
|
4.4
|
51.7
|
1.0
|
HG
|
A:LEU692
|
4.7
|
28.0
|
1.0
|
CG
|
A:LEU692
|
4.7
|
23.3
|
1.0
|
HA
|
A:ASN703
|
4.8
|
63.1
|
1.0
|
CD1
|
A:LEU692
|
4.8
|
26.4
|
1.0
|
CB
|
A:SER704
|
4.9
|
51.1
|
1.0
|
CD
|
A:LYS696
|
5.0
|
35.8
|
1.0
|
|
Iodine binding site 4 out
of 5 in 5lbd
Go back to
Iodine Binding Sites List in 5lbd
Iodine binding site 4 out
of 5 in the Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I804
b:21.0
occ:0.73
|
HH11
|
A:ARG697
|
3.1
|
27.5
|
1.0
|
HD3
|
A:ARG697
|
3.2
|
27.9
|
1.0
|
HA
|
A:TRP694
|
3.3
|
17.3
|
1.0
|
HE3
|
A:TRP694
|
3.4
|
20.5
|
1.0
|
O
|
A:HOH919
|
3.5
|
24.6
|
1.0
|
HB3
|
A:SER676
|
3.5
|
27.9
|
1.0
|
HE3
|
B:LYS664
|
3.6
|
60.8
|
1.0
|
HB2
|
A:GLU693
|
3.6
|
27.7
|
1.0
|
NH1
|
A:ARG697
|
3.7
|
22.9
|
1.0
|
HG
|
A:SER676
|
3.8
|
29.1
|
1.0
|
HB3
|
A:GLU693
|
3.8
|
27.7
|
1.0
|
HZ2
|
B:LYS664
|
3.8
|
67.0
|
1.0
|
HB2
|
A:TRP694
|
3.9
|
19.5
|
1.0
|
N
|
A:TRP694
|
4.0
|
16.3
|
1.0
|
CA
|
A:TRP694
|
4.0
|
14.4
|
1.0
|
HH12
|
A:ARG697
|
4.0
|
27.5
|
1.0
|
CD
|
A:ARG697
|
4.1
|
23.2
|
1.0
|
C
|
A:GLU693
|
4.1
|
16.3
|
1.0
|
OG
|
A:SER676
|
4.2
|
24.2
|
1.0
|
CB
|
A:GLU693
|
4.2
|
23.1
|
1.0
|
HB2
|
A:ARG697
|
4.2
|
24.0
|
1.0
|
H
|
A:TRP694
|
4.3
|
19.5
|
1.0
|
CB
|
A:SER676
|
4.3
|
23.2
|
1.0
|
O
|
A:GLU693
|
4.3
|
19.6
|
1.0
|
HZ1
|
B:LYS664
|
4.3
|
67.0
|
1.0
|
NZ
|
B:LYS664
|
4.3
|
55.8
|
1.0
|
CE
|
B:LYS664
|
4.3
|
50.7
|
1.0
|
HG1
|
A:THR691
|
4.4
|
21.7
|
1.0
|
CE3
|
A:TRP694
|
4.4
|
17.1
|
1.0
|
HD2
|
A:ARG697
|
4.4
|
27.9
|
1.0
|
O
|
A:HOH922
|
4.4
|
34.3
|
1.0
|
CB
|
A:TRP694
|
4.5
|
16.3
|
1.0
|
HD3
|
B:LYS664
|
4.5
|
62.1
|
1.0
|
CZ
|
A:ARG697
|
4.6
|
27.0
|
1.0
|
HB3
|
A:ARG697
|
4.7
|
24.0
|
1.0
|
NE
|
A:ARG697
|
4.7
|
22.1
|
1.0
|
O
|
A:HOH932
|
4.7
|
33.6
|
1.0
|
HB2
|
A:SER676
|
4.8
|
27.9
|
1.0
|
CB
|
A:ARG697
|
4.8
|
20.0
|
1.0
|
OG1
|
A:THR691
|
4.8
|
18.1
|
1.0
|
CA
|
A:GLU693
|
4.8
|
20.0
|
1.0
|
CD
|
B:LYS664
|
5.0
|
51.8
|
1.0
|
|
Iodine binding site 5 out
of 5 in 5lbd
Go back to
Iodine Binding Sites List in 5lbd
Iodine binding site 5 out
of 5 in the Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Crystal Structure of the N-Domain of HMA6, A Copper-Transporting P- Type Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I801
b:36.8
occ:0.49
|
HZ3
|
B:TRP627
|
2.6
|
61.9
|
1.0
|
O
|
B:HOH955
|
2.8
|
36.4
|
1.0
|
O
|
B:HOH952
|
3.2
|
32.3
|
1.0
|
CZ3
|
B:TRP627
|
3.4
|
51.6
|
1.0
|
HG2
|
B:GLU631
|
3.4
|
23.9
|
1.0
|
HD11
|
B:LEU635
|
3.7
|
21.3
|
1.0
|
HB3
|
B:GLU631
|
3.7
|
20.1
|
1.0
|
HE3
|
B:TRP627
|
3.7
|
32.9
|
1.0
|
HD21
|
B:LEU635
|
3.8
|
23.6
|
1.0
|
HE3
|
B:LYS685
|
3.8
|
32.5
|
1.0
|
CE3
|
B:TRP627
|
3.9
|
27.4
|
1.0
|
HE1
|
B:MSE663
|
3.9
|
59.7
|
0.4
|
HG
|
B:LEU635
|
4.1
|
21.8
|
1.0
|
CG
|
B:GLU631
|
4.2
|
19.9
|
1.0
|
CH2
|
B:TRP627
|
4.3
|
44.2
|
1.0
|
HH2
|
B:TRP627
|
4.4
|
53.0
|
1.0
|
HE3
|
B:MSE663
|
4.4
|
59.7
|
0.4
|
CB
|
B:GLU631
|
4.4
|
16.7
|
1.0
|
CD1
|
B:LEU635
|
4.5
|
17.7
|
1.0
|
CD
|
B:GLU631
|
4.5
|
20.3
|
1.0
|
CG
|
B:LEU635
|
4.6
|
18.1
|
1.0
|
CE
|
B:MSE663
|
4.6
|
49.7
|
0.4
|
CD2
|
B:LEU635
|
4.6
|
19.6
|
1.0
|
OE2
|
B:GLU631
|
4.7
|
24.9
|
1.0
|
HZ1
|
B:LYS685
|
4.7
|
39.8
|
1.0
|
HA
|
B:GLU631
|
4.7
|
20.4
|
1.0
|
CE
|
B:LYS685
|
4.8
|
27.1
|
1.0
|
HZ2
|
B:LYS685
|
4.8
|
39.8
|
1.0
|
HD12
|
B:LEU635
|
4.8
|
21.3
|
1.0
|
HE1
|
B:MSE663
|
4.9
|
35.5
|
0.6
|
NZ
|
B:LYS685
|
5.0
|
33.2
|
1.0
|
HD23
|
B:LEU635
|
5.0
|
23.6
|
1.0
|
HG3
|
B:GLU631
|
5.0
|
23.9
|
1.0
|
|
Reference:
H.Mayerhofer,
E.Sautron,
N.Rolland,
P.Catty,
D.Seigneurin-Berny,
E.Pebay-Peyroula,
S.Ravaud.
Structural Insights Into the Nucleotide-Binding Domains of the P1B-Type Atpases HMA6 and HMA8 From Arabidopsis Thaliana. Plos One V. 11 65666 2016.
ISSN: ESSN 1932-6203
PubMed: 27802305
DOI: 10.1371/JOURNAL.PONE.0165666
Page generated: Sun Aug 11 21:22:38 2024
|