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Cadmium in PDB 6w8f: K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+

Protein crystallography data

The structure of K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+, PDB code: 6w8f was solved by M.Lolicato, D.L.Minor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.99 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.671, 119.963, 128.941, 90, 90, 90
R / Rfree (%) 24.7 / 26.7

Other elements in 6w8f:

The structure of K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+ also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Potassium (K) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+ (pdb code 6w8f). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+, PDB code: 6w8f:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 6w8f

Go back to Cadmium Binding Sites List in 6w8f
Cadmium binding site 1 out of 4 in the K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd409

b:184.2
occ:0.50
C20 A:Q6F402 3.4 172.0 1.0
CE1 A:HIS126 3.4 175.9 1.0
ND1 A:HIS126 3.9 175.7 1.0
OD1 A:ASP263 4.0 188.9 1.0
OD2 A:ASP263 4.1 191.2 1.0
NE2 A:HIS126 4.1 175.7 1.0
CG A:ASP263 4.4 190.3 1.0
O A:GLY261 4.7 170.3 1.0
CG A:HIS126 4.8 174.1 1.0
NH2 B:ARG77 4.9 189.1 1.0
CD2 A:HIS126 4.9 174.9 1.0
S03 A:Q6F402 4.9 171.2 1.0

Cadmium binding site 2 out of 4 in 6w8f

Go back to Cadmium Binding Sites List in 6w8f
Cadmium binding site 2 out of 4 in the K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd403

b:254.2
occ:1.00
CE1 B:HIS126 3.4 187.5 1.0
OD2 B:ASP263 3.7 182.6 1.0
OD1 B:ASP263 3.7 182.6 1.0
NE2 B:HIS126 3.8 186.7 1.0
CG B:ASP263 4.0 181.5 1.0
CD1 B:ILE115 4.2 213.9 1.0
ND1 B:HIS126 4.4 186.0 1.0
CD2 B:HIS126 4.9 184.5 1.0
O B:GLY261 5.0 167.4 1.0

Cadmium binding site 3 out of 4 in 6w8f

Go back to Cadmium Binding Sites List in 6w8f
Cadmium binding site 3 out of 4 in the K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd404

b:171.2
occ:1.00
OE1 B:GLU309 2.8 181.4 1.0
CE1 B:HIS313 3.0 189.1 1.0
ND1 B:HIS313 3.2 188.7 1.0
CB B:ALA312 3.3 179.1 1.0
CD B:GLU309 3.4 178.9 1.0
OE2 B:GLU309 3.7 184.2 1.0
O B:GLU309 3.9 161.0 1.0
NE2 B:HIS313 3.9 188.7 1.0
CA B:GLU309 4.0 158.5 1.0
CG B:HIS313 4.2 186.1 1.0
CB B:GLU309 4.3 160.9 1.0
C B:ALA312 4.3 180.3 1.0
N B:HIS313 4.4 181.5 1.0
CA B:ALA312 4.4 178.3 1.0
CG B:GLU309 4.4 166.4 1.0
C B:GLU309 4.4 161.1 1.0
CD2 B:HIS313 4.6 187.1 1.0
O B:ALA312 4.8 180.2 1.0
O B:GLY308 4.9 155.4 1.0

Cadmium binding site 4 out of 4 in 6w8f

Go back to Cadmium Binding Sites List in 6w8f
Cadmium binding site 4 out of 4 in the K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of K2P2.1 (Trek-1):ML335 Complex, 0 Mm K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd405

b:203.6
occ:0.61
OD2 B:ASP128 2.9 168.9 1.0
OD1 B:ASP128 3.6 166.6 1.0
CG B:ASP128 3.6 165.6 1.0
CA B:GLY130 4.0 156.0 1.0
OG B:SER131 4.1 146.1 1.0
N B:SER131 4.2 148.5 1.0
N B:GLY130 4.3 158.8 1.0
C B:GLY130 4.4 151.3 1.0
NZ B:LYS271 4.5 149.5 1.0
C16 B:Q6F409 4.6 153.0 1.0
C31 B:R16411 4.9 139.9 1.0
CB B:ASP128 5.0 158.4 1.0

Reference:

M.Lolicato, A.M.Natale, F.Abderemane-Ali, D.Crottes, S.Capponi, R.Duman, A.Wagner, J.M.Rosenberg, M.Grabe, D.L.Minor Jr.. K 2P Channel C-Type Gating Involves Asymmetric Selectivity Filter Order-Disorder Transitions. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 33127683
DOI: 10.1126/SCIADV.ABC9174
Page generated: Sat Apr 17 14:38:35 2021

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