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Gadolinium in PDB 3q4i: Crystal Structure of Cdp-Chase in Complex with GD3+

Protein crystallography data

The structure of Crystal Structure of Cdp-Chase in Complex with GD3+, PDB code: 3q4i was solved by K.C.Duong-Ly, S.B.Gabelli, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.90 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.005, 70.855, 111.793, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 28.8

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Crystal Structure of Cdp-Chase in Complex with GD3+ (pdb code 3q4i). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 3 binding sites of Gadolinium where determined in the Crystal Structure of Cdp-Chase in Complex with GD3+, PDB code: 3q4i:
Jump to Gadolinium binding site number: 1; 2; 3;

Gadolinium binding site 1 out of 3 in 3q4i

Go back to Gadolinium Binding Sites List in 3q4i
Gadolinium binding site 1 out of 3 in the Crystal Structure of Cdp-Chase in Complex with GD3+


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of Cdp-Chase in Complex with GD3+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd301

b:79.6
occ:0.50
O A:GLY96 2.3 46.9 1.0
OE2 A:GLU116 2.4 53.2 1.0
O A:HOH212 2.8 52.6 1.0
OE1 A:GLU112 3.4 57.7 1.0
C A:GLY96 3.5 47.1 1.0
CD A:GLU116 3.5 52.5 1.0
CA A:GLY97 4.1 46.8 1.0
OE1 A:GLU116 4.1 51.4 1.0
OE1 A:GLU86 4.2 75.5 1.0
N A:GLY97 4.2 47.1 1.0
N A:GLY96 4.5 46.9 1.0
CA A:GLY96 4.6 47.0 1.0
CG A:GLU116 4.6 51.4 1.0
CD A:GLU112 4.6 56.4 1.0
O A:HOH222 4.9 58.4 1.0

Gadolinium binding site 2 out of 3 in 3q4i

Go back to Gadolinium Binding Sites List in 3q4i
Gadolinium binding site 2 out of 3 in the Crystal Structure of Cdp-Chase in Complex with GD3+


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure of Cdp-Chase in Complex with GD3+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd302

b:86.2
occ:0.50
O B:GLY96 2.4 45.8 1.0
OE2 B:GLU116 2.8 50.8 1.0
O B:HOH214 3.0 47.4 1.0
OE1 B:GLU112 3.1 51.9 1.0
CD B:GLU116 3.4 49.1 1.0
C B:GLY96 3.5 45.3 1.0
O B:HOH211 3.6 63.0 1.0
OE1 B:GLU116 3.7 51.9 1.0
O B:HOH223 4.1 68.0 1.0
CA B:GLY97 4.1 44.2 1.0
OE2 B:GLU86 4.2 70.5 1.0
N B:GLY97 4.3 45.0 1.0
CD B:GLU112 4.3 52.4 1.0
N B:GLY96 4.5 44.9 1.0
CG B:GLU116 4.5 47.5 1.0
CA B:GLY96 4.6 45.1 1.0
NH1 B:ARG72 4.9 39.8 1.0
CD B:GLU86 4.9 70.1 1.0

Gadolinium binding site 3 out of 3 in 3q4i

Go back to Gadolinium Binding Sites List in 3q4i
Gadolinium binding site 3 out of 3 in the Crystal Structure of Cdp-Chase in Complex with GD3+


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Crystal Structure of Cdp-Chase in Complex with GD3+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd303

b:0.3
occ:0.50
OE2 B:GLU163 2.2 76.0 1.0
O B:HOH223 2.3 68.0 1.0
OE2 B:GLU30 2.9 67.2 1.0
CD B:GLU163 3.1 75.5 1.0
O B:HOH211 3.1 63.0 1.0
O B:HOH220 3.2 52.0 1.0
OE1 B:GLU163 3.2 75.3 1.0
O B:HOH212 3.5 59.7 1.0
CD B:GLU30 3.8 66.4 1.0
OE1 B:GLU115 4.1 54.7 1.0
OE1 B:GLU30 4.1 67.5 1.0
OE2 B:GLU112 4.4 54.6 1.0
CG B:GLU163 4.5 73.0 1.0
OE1 B:GLU112 4.9 51.9 1.0

Reference:

K.C.Duong-Ly, S.B.Gabelli, W.Xu, C.A.Dunn, A.J.Schoeffield, M.J.Bessman, L.M.Amzel. The Nudix Hydrolase Cdp-Chase, A Cdp-Choline Pyrophosphatase, Is An Asymmetric Dimer with Two Distinct Enzymatic Activities. J.Bacteriol. V. 193 3175 2011.
ISSN: ISSN 0021-9193
PubMed: 21531795
DOI: 10.1128/JB.00089-11
Page generated: Sun Dec 13 18:59:27 2020

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