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Cadmium in PDB 1z98: Crystal Structure of the Spinach Aquaporin SOPIP2;1 in A Closed Conformation

Protein crystallography data

The structure of Crystal Structure of the Spinach Aquaporin SOPIP2;1 in A Closed Conformation, PDB code: 1z98 was solved by S.Tornroth-Horsefield, K.Hedfalk, U.Johanson, M.Karlsson, R.Neutze, P.Kjellbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 90.097, 90.097, 189.181, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Spinach Aquaporin SOPIP2;1 in A Closed Conformation (pdb code 1z98). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of the Spinach Aquaporin SOPIP2;1 in A Closed Conformation, PDB code: 1z98:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1z98

Go back to Cadmium Binding Sites List in 1z98
Cadmium binding site 1 out of 2 in the Crystal Structure of the Spinach Aquaporin SOPIP2;1 in A Closed Conformation


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 the Spinach Aquaporin SOPIP2;1 in A Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:31.1
occ:1.00
OD1 A:ASP28 2.3 29.5 1.0
OE2 A:GLU31 2.3 29.5 1.0
O A:HOH1002 2.4 27.1 1.0
O A:HOH1005 2.5 29.8 1.0
OD2 A:ASP28 2.5 32.4 1.0
CG A:ASP28 2.8 31.3 1.0
OE1 A:GLU31 2.8 22.8 1.0
CD A:GLU31 2.9 28.3 1.0
NE A:ARG118 4.1 22.5 1.0
O A:HOH1063 4.1 39.5 1.0
O A:HOH1039 4.2 40.8 1.0
CB A:ASP28 4.3 31.4 1.0
CA A:GLY30 4.3 27.5 1.0
OG A:SER115 4.3 27.4 1.0
NH2 A:ARG118 4.4 23.9 1.0
CG A:GLU31 4.4 27.9 1.0
N A:GLU31 4.4 27.9 1.0
N A:GLY30 4.5 27.6 1.0
CB A:SER115 4.5 27.7 1.0
C A:GLY30 4.6 27.8 1.0
N A:ASP28 4.7 35.2 1.0
CZ A:ARG118 4.7 25.9 1.0
N A:SER115 4.8 27.4 1.0
CA A:ASP28 4.9 32.1 1.0
O A:ASP28 5.0 29.9 1.0

Cadmium binding site 2 out of 2 in 1z98

Go back to Cadmium Binding Sites List in 1z98
Cadmium binding site 2 out of 2 in the Crystal Structure of the Spinach Aquaporin SOPIP2;1 in A Closed Conformation


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 the Spinach Aquaporin SOPIP2;1 in A Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd2001

b:30.0
occ:1.00
OE2 M:GLU31 2.2 25.1 1.0
OD2 M:ASP28 2.3 31.0 1.0
O M:HOH2005 2.4 29.4 1.0
OD1 M:ASP28 2.4 30.8 1.0
O M:HOH2003 2.5 29.6 1.0
CG M:ASP28 2.7 30.7 1.0
CD M:GLU31 2.9 28.5 1.0
OE1 M:GLU31 2.9 25.1 1.0
O M:HOH2057 4.1 42.6 1.0
NE M:ARG118 4.1 21.6 1.0
CB M:ASP28 4.2 30.8 1.0
OG M:SER115 4.2 26.3 1.0
CG M:GLU31 4.3 27.6 1.0
CA M:GLY30 4.4 28.4 1.0
N M:GLU31 4.4 27.9 1.0
CB M:SER115 4.5 26.9 1.0
NH2 M:ARG118 4.5 20.8 1.0
N M:GLY30 4.5 28.3 1.0
C M:GLY30 4.6 27.9 1.0
N M:ASP28 4.7 33.5 1.0
CZ M:ARG118 4.8 24.4 1.0
N M:SER115 4.9 27.1 1.0
CA M:ASP28 4.9 30.9 1.0
C M:ASP28 5.0 29.7 1.0
CD M:ARG118 5.0 22.5 1.0

Reference:

S.Tornroth-Horsefield, Y.Wang, K.Hedfalk, U.Johanson, M.Karlsson, E.Tajkhorshid, R.Neutze, P.Kjellbom. Structural Mechanism of Plant Aquaporin Gating Nature V. 439 688 2006.
ISSN: ISSN 0028-0836
PubMed: 16340961
DOI: 10.1038/NATURE04316
Page generated: Fri Aug 28 12:44:53 2020
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