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Cadmium in PDB 4fmk: Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2

Protein crystallography data

The structure of Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2, PDB code: 4fmk was solved by O.J.Harrison, J.Brasch, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.56
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 68.666, 68.666, 159.605, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 26.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2 (pdb code 4fmk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2, PDB code: 4fmk:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 4fmk

Go back to Cadmium Binding Sites List in 4fmk
Cadmium binding site 1 out of 4 in the Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2


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 Mouse Nectin-2 Extracellular Fragment D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd312

b:73.5
occ:1.00
NE2 A:HIS156 2.6 85.8 1.0
OE2 A:GLU158 2.6 99.6 1.0
OE1 A:GLU158 2.7 84.7 1.0
CD A:GLU158 2.7 87.7 1.0
NH1 A:ARG173 2.8 0.2 1.0
CE1 A:HIS156 3.1 81.6 1.0
CD2 A:HIS156 3.6 83.4 1.0
CG A:GLU158 3.8 80.7 1.0
CZ A:ARG173 3.9 0.1 1.0
NH2 A:ARG173 4.3 0.7 1.0
ND1 A:HIS156 4.3 79.5 1.0
CG A:HIS156 4.6 77.2 1.0
CG2 A:VAL175 4.6 67.9 1.0

Cadmium binding site 2 out of 4 in 4fmk

Go back to Cadmium Binding Sites List in 4fmk
Cadmium binding site 2 out of 4 in the Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2


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 Mouse Nectin-2 Extracellular Fragment D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd313

b:80.1
occ:1.00
O A:HOH419 1.9 53.6 1.0
O A:HOH418 2.1 62.1 1.0
ND1 A:HIS252 2.2 0.8 1.0
OD2 A:ASP223 2.2 88.3 1.0
OD1 A:ASP223 2.3 88.5 1.0
CG A:ASP223 2.6 90.6 1.0
CE1 A:HIS252 2.9 98.5 1.0
CG A:HIS252 3.4 0.2 1.0
CB A:HIS252 3.9 0.1 1.0
CB A:ASP223 4.1 91.5 1.0
NE2 A:HIS252 4.2 0.8 1.0
O A:HIS251 4.3 1.0 1.0
CA A:HIS252 4.4 0.2 1.0
CD2 A:HIS252 4.4 0.2 1.0
O A:LEU246 4.5 83.9 1.0
ND1 A:HIS253 4.5 0.9 1.0
N A:GLY224 4.6 83.5 1.0
CE1 A:HIS253 4.7 0.9 1.0
CA A:SER247 4.8 83.3 1.0
C A:ASP223 4.9 88.9 1.0
CA A:ASP223 4.9 89.9 1.0

Cadmium binding site 3 out of 4 in 4fmk

Go back to Cadmium Binding Sites List in 4fmk
Cadmium binding site 3 out of 4 in the Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2


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 Mouse Nectin-2 Extracellular Fragment D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd314

b:0.2
occ:1.00
OD2 A:ASP113 2.7 72.9 1.0
CE1 A:HIS55 3.0 80.5 1.0
CG A:ASP113 3.6 64.3 1.0
ND1 A:HIS55 3.7 75.1 1.0
NE2 A:HIS55 4.2 78.6 1.0
CB A:ASP113 4.2 60.4 1.0
O A:HOH410 4.3 66.9 1.0
CB A:ALA103 4.4 0.5 1.0
OD1 A:ASP113 4.5 60.3 1.0
O A:HOH414 4.6 66.6 1.0
CG A:HIS55 4.9 73.1 1.0

Cadmium binding site 4 out of 4 in 4fmk

Go back to Cadmium Binding Sites List in 4fmk
Cadmium binding site 4 out of 4 in the Crystal Structure of Mouse Nectin-2 Extracellular Fragment D1-D2


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 Mouse Nectin-2 Extracellular Fragment D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd315

b:0.8
occ:1.00
ND1 A:HIS251 2.5 0.2 1.0
O A:HOH433 2.7 59.6 1.0
CE1 A:HIS251 3.1 0.5 1.0
CG A:HIS251 3.2 0.3 1.0
CB A:HIS251 3.7 0.1 1.0
NE2 A:HIS251 4.0 0.6 1.0
CD2 A:HIS251 4.0 0.9 1.0
CA A:HIS251 4.4 0.1 1.0
O A:TYR250 4.9 0.7 1.0

Reference:

O.J.Harrison, J.Vendome, J.Brasch, X.Jin, S.Hong, P.S.Katsamba, G.Ahlsen, R.B.Troyanovsky, S.M.Troyanovsky, B.Honig, L.Shapiro. Nectin Ectodomain Structures Reveal A Canonical Adhesive Interface. Nat.Struct.Mol.Biol. V. 19 906 2012.
ISSN: ISSN 1545-9993
PubMed: 22902367
DOI: 10.1038/NSMB.2366
Page generated: Sat Dec 12 08:24:32 2020

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