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Calcium in PDB 3tol: Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers

Protein crystallography data

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers, PDB code: 3tol was solved by J.B.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.28 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.546, 69.506, 126.567, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.5

Other elements in 3tol:

The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers (pdb code 3tol). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers, PDB code: 3tol:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3tol

Go back to Calcium Binding Sites List in 3tol
Calcium binding site 1 out of 2 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca108

b:29.8
occ:1.00
O A:HOH121 2.2 35.6 1.0
OD1 A:ASP21 2.2 41.5 1.0
O A:LYS19 2.3 32.3 1.0
O A:HOH363 2.6 33.5 1.0
CG A:ASP21 3.5 40.1 1.0
C A:LYS19 3.5 31.7 1.0
OD2 A:ASP21 4.1 42.6 1.0
CB A:LYS19 4.2 34.1 1.0
CA A:LYS19 4.3 32.1 1.0
C A:ALA20 4.3 30.6 1.0
O A:ALA20 4.5 30.8 1.0
N A:ASP21 4.5 31.8 1.0
N A:ALA20 4.5 28.8 1.0
CB A:ASP21 4.6 36.8 1.0
CA A:ALA20 4.7 28.9 1.0
CA A:ASP21 4.7 34.5 1.0
O A:HOH109 4.7 28.5 1.0

Calcium binding site 2 out of 2 in 3tol

Go back to Calcium Binding Sites List in 3tol
Calcium binding site 2 out of 2 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca108

b:59.1
occ:1.00
O C:HOH316 2.2 52.3 1.0
OD1 C:ASP5 2.6 42.8 1.0
OE1 C:GLU8 2.9 47.8 1.0
CD C:GLU8 3.3 46.6 1.0
OE2 C:GLU8 3.4 50.6 1.0
CG C:ASP5 3.5 41.3 1.0
OD2 C:ASP5 4.0 44.8 1.0
O C:HOH119 4.2 55.3 1.0
O C:HOH109 4.2 46.3 1.0
CG C:GLU8 4.5 40.3 1.0
CB C:ASP5 4.6 37.6 1.0
CA C:ASP5 4.6 35.5 1.0
O C:HOH228 4.8 44.9 1.0
O C:HOH282 4.9 47.1 1.0
CB C:GLU8 4.9 35.8 1.0

Reference:

J.D.Brodin, X.I.Ambroggio, C.Tang, K.N.Parent, T.S.Baker, F.A.Tezcan. Metal-Directed, Chemically Tunable Assembly of One-, Two- and Three-Dimensional Crystalline Protein Arrays. Nat Chem V. 4 375 2012.
PubMed: 22522257
DOI: 10.1038/NCHEM.1290
Page generated: Sat Dec 12 04:31:50 2020

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