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Cadmium in PDB 1wvr: Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom

Protein crystallography data

The structure of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom, PDB code: 1wvr was solved by Y.Shikamoto, K.Suto, Y.Yamazaki, T.Morita, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.11 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.374, 83.374, 85.680, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 28.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom (pdb code 1wvr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom, PDB code: 1wvr:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 1wvr

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Cadmium binding site 1 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:61.7
occ:1.00
NE2 A:HIS60 2.1 38.7 1.0
NE2 A:HIS115 2.1 43.4 1.0
O A:HOH526 2.7 60.6 1.0
O A:HOH423 2.7 45.4 1.0
CE1 A:HIS115 2.8 43.1 1.0
CD2 A:HIS60 3.1 40.9 1.0
CE1 A:HIS60 3.1 39.0 1.0
O A:HOH469 3.1 58.0 1.0
CD2 A:HIS115 3.2 48.4 1.0
O A:HOH452 3.4 72.1 1.0
ND1 A:HIS115 4.0 50.9 1.0
CG A:HIS115 4.1 49.7 1.0
ND1 A:HIS60 4.2 40.8 1.0
CG A:HIS60 4.2 41.9 1.0
O A:HOH425 4.8 54.6 1.0

Cadmium binding site 2 out of 9 in 1wvr

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Cadmium binding site 2 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:44.9
occ:0.50
O A:HOH465 2.1 56.4 1.0
OE2 A:GLU40 2.4 56.8 1.0
OE1 A:GLU40 2.6 55.4 1.0
CD A:GLU40 2.8 51.3 1.0
CG A:GLU40 4.3 48.6 1.0
O A:HOH510 4.6 74.7 1.0
O A:HOH458 4.6 53.9 1.0
NH1 A:ARG126 5.0 56.3 1.0

Cadmium binding site 3 out of 9 in 1wvr

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Cadmium binding site 3 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:86.0
occ:1.00
O A:HOH524 2.0 31.6 1.0
OD2 A:ASP175 2.5 43.3 1.0
OD1 A:ASP175 2.7 46.6 1.0
CG A:ASP175 3.0 43.2 1.0
NZ A:LYS38 3.8 35.6 1.0
OD1 A:ASN176 3.9 46.6 1.0
O A:HOH436 4.1 67.9 1.0
CB A:ASP175 4.5 41.3 1.0

Cadmium binding site 4 out of 9 in 1wvr

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Cadmium binding site 4 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:84.3
occ:1.00
OE2 A:GLU13 2.6 61.1 1.0
OE1 A:GLU13 3.3 61.8 1.0
CD A:GLU13 3.3 60.7 1.0
OD1 A:ASN16 3.9 48.5 1.0
CG A:GLU13 4.8 56.6 1.0
CG A:ASN16 5.0 45.0 1.0

Cadmium binding site 5 out of 9 in 1wvr

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Cadmium binding site 5 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:83.0
occ:1.00
OE2 A:GLU17 2.2 61.6 1.0
OE2 A:GLU7 2.5 65.7 1.0
CD A:GLU7 2.8 62.0 1.0
OE1 A:GLU7 2.9 64.9 1.0
O A:HOH455 2.9 51.0 1.0
CD A:GLU17 3.2 59.4 1.0
OE1 A:GLU17 3.4 59.2 1.0
CG A:GLU7 3.8 60.9 1.0
CD1 A:ILE14 4.0 49.3 1.0
CG A:LYS85 4.4 61.4 1.0
N A:TRP86 4.4 54.0 1.0
CG A:GLU17 4.6 56.5 1.0
CB A:LYS85 4.7 57.8 1.0
CB A:TRP86 4.8 46.4 1.0
O A:HOH486 4.9 59.9 1.0
N A:THR87 4.9 54.6 1.0
CA A:LYS85 5.0 57.1 1.0

Cadmium binding site 6 out of 9 in 1wvr

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Cadmium binding site 6 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:71.4
occ:1.00
OD1 A:ASP173 2.4 37.2 1.0
O A:HOH518 2.4 53.8 1.0
OD2 A:ASP173 2.6 37.6 1.0
CG A:ASP173 2.8 37.6 1.0
O A:SER172 4.2 41.1 1.0
CB A:ASP173 4.3 37.5 1.0
O A:ASN218 4.3 43.7 1.0
CB A:SER172 4.6 46.8 1.0
C A:SER172 4.6 41.1 1.0
O A:HOH416 4.6 38.6 1.0
ND2 A:ASN218 4.8 52.7 1.0
CB A:ASN181 4.9 34.6 1.0
O A:HOH511 5.0 44.8 1.0

Cadmium binding site 7 out of 9 in 1wvr

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Cadmium binding site 7 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:0.3
occ:1.00
ND1 A:HIS91 2.3 63.0 1.0
O A:HOH424 2.7 55.8 1.0
ND1 A:HIS94 3.0 56.6 1.0
O A:HOH488 3.0 52.7 1.0
CE1 A:HIS91 3.1 64.8 1.0
CG A:HIS91 3.2 62.7 1.0
CB A:HIS91 3.6 59.3 1.0
CE1 A:HIS94 3.8 54.4 1.0
CG A:HIS94 4.0 55.0 1.0
CA A:HIS91 4.1 57.9 1.0
NE2 A:HIS91 4.1 65.3 1.0
CD2 A:HIS91 4.2 64.6 1.0
CB A:HIS94 4.2 53.9 1.0
O A:HIS91 4.4 57.7 1.0
CD2 A:LEU25 4.6 48.7 1.0
C A:HIS91 4.7 57.3 1.0
NE2 A:HIS94 5.0 55.2 1.0

Cadmium binding site 8 out of 9 in 1wvr

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Cadmium binding site 8 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd308

b:0.6
occ:1.00
OD1 A:ASP193 2.0 74.3 1.0
O A:HOH437 2.4 32.5 1.0
CG A:ASP193 2.8 74.4 1.0
OD2 A:ASP193 2.9 76.6 1.0
O A:HOH454 3.2 53.4 1.0
OG A:SER213 3.8 52.9 1.0
CB A:ASP193 4.2 73.3 1.0
OD1 A:ASN187 4.6 53.8 1.0
CB A:SER213 4.8 50.2 1.0
CA A:SER213 4.8 49.7 1.0
CA A:ASP193 4.9 73.6 1.0

Cadmium binding site 9 out of 9 in 1wvr

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Cadmium binding site 9 out of 9 in the Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of A Crisp Family Ca-Channel Blocker Derived From Snake Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd309

b:0.4
occ:1.00
OD1 A:ASP5 2.5 73.2 1.0
OD2 A:ASP5 2.6 74.0 1.0
O A:ASN1 2.8 82.1 1.0
CG A:ASP5 2.9 71.2 1.0
N A:ASN1 3.3 85.0 1.0
C A:ASN1 3.9 83.3 1.0
CA A:ASN1 4.2 84.6 1.0
CB A:ASP5 4.3 69.9 1.0
CD2 A:PHE4 4.6 65.6 1.0
N A:ASP5 4.9 68.1 1.0

Reference:

Y.Shikamoto, K.Suto, Y.Yamazaki, T.Morita, H.Mizuno. Crystal Structure of A Crisp Family CA2+ -Channel Blocker Derived From Snake Venom. J.Mol.Biol. V. 350 735 2005.
ISSN: ISSN 0022-2836
PubMed: 15953617
DOI: 10.1016/J.JMB.2005.05.020
Page generated: Wed Oct 28 09:57:55 2020
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