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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:

Chlorine (Cl) 2 atoms

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 Dec 13 19:40:05 2020

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