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Zinc 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
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers, PDB code: 3tol:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3tol

Go back to Zinc Binding Sites List in 3tol
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn107

b:18.7
occ:1.00
NE2 A:HIS77 2.0 20.0 1.0
NE2 B:HIS63 2.1 25.8 1.0
NE2 A:HIS73 2.1 20.1 1.0
CE1 A:HIS73 2.9 20.8 1.0
CE1 A:HIS77 2.9 21.7 1.0
CD2 A:HIS77 3.0 17.7 1.0
CE1 B:HIS63 3.0 27.8 1.0
CD2 B:HIS63 3.1 24.9 1.0
CD2 A:HIS73 3.2 18.9 1.0
ND1 A:HIS77 4.1 17.7 1.0
ND1 A:HIS73 4.1 19.5 1.0
CG A:HIS77 4.1 17.1 1.0
ND1 B:HIS63 4.2 28.0 1.0
CG B:HIS63 4.2 24.7 1.0
CG A:HIS73 4.2 17.9 1.0
CG1 B:ILE67 4.3 20.8 1.0
O A:HOH135 4.6 31.7 1.0
O A:HOH118 4.7 33.7 1.0
CD1 B:ILE67 4.7 24.0 1.0

Zinc binding site 2 out of 4 in 3tol

Go back to Zinc Binding Sites List in 3tol
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn107

b:20.5
occ:1.00
NE2 C:HIS73 2.0 27.0 1.0
NE2 C:HIS77 2.0 27.3 1.0
NE2 D:HIS63 2.0 26.9 1.0
CE1 C:HIS73 2.9 29.8 1.0
CD2 D:HIS63 2.9 26.2 1.0
CD2 C:HIS77 3.0 24.7 1.0
CE1 C:HIS77 3.0 29.6 1.0
CD2 C:HIS73 3.1 27.4 1.0
CE1 D:HIS63 3.1 27.9 1.0
ND1 C:HIS73 4.0 27.9 1.0
ND1 C:HIS77 4.1 27.7 1.0
CG D:HIS63 4.1 27.0 1.0
CG C:HIS77 4.1 25.8 1.0
ND1 D:HIS63 4.1 27.9 1.0
CG C:HIS73 4.2 26.4 1.0
O C:HOH337 4.3 35.7 1.0
O C:HOH314 4.9 40.1 1.0

Zinc binding site 3 out of 4 in 3tol

Go back to Zinc Binding Sites List in 3tol
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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
D:Zn107

b:25.1
occ:1.00
NE2 D:HIS77 1.9 24.2 1.0
OE2 B:GLU81 2.0 25.9 1.0
NE2 D:HIS73 2.0 26.9 1.0
NE2 C:HIS63 2.1 27.9 1.0
OE1 B:GLU81 2.5 28.2 1.0
CD B:GLU81 2.5 22.2 1.0
CD2 D:HIS77 2.8 24.4 1.0
CE1 D:HIS73 2.9 28.4 1.0
CE1 D:HIS77 3.0 28.1 1.0
CE1 C:HIS63 3.0 27.6 1.0
CD2 C:HIS63 3.1 25.6 1.0
CD2 D:HIS73 3.1 24.1 1.0
CG D:HIS77 4.0 23.9 1.0
ND1 D:HIS77 4.0 26.5 1.0
CG B:GLU81 4.0 22.0 1.0
ND1 D:HIS73 4.1 28.0 1.0
ND1 C:HIS63 4.1 26.0 1.0
CG C:HIS63 4.2 25.8 1.0
CG D:HIS73 4.2 23.6 1.0
O D:HOH357 4.3 29.5 1.0
O B:HOH138 4.5 32.3 1.0
CG1 C:ILE67 4.7 24.3 1.0
O D:HOH108 4.8 26.5 1.0
CB B:GLU81 4.9 21.4 1.0
OD1 B:ASN80 4.9 26.4 1.0
CA B:GLU81 5.0 21.3 1.0

Zinc binding site 4 out of 4 in 3tol

Go back to Zinc Binding Sites List in 3tol
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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
B:Zn107

b:22.0
occ:1.00
NE2 B:HIS77 1.9 23.2 1.0
NE2 A:HIS63 2.1 21.6 1.0
NE2 B:HIS73 2.1 19.9 1.0
OE2 D:GLU81 2.2 27.6 1.0
OE1 D:GLU81 2.2 32.0 1.0
CD D:GLU81 2.5 26.7 1.0
CD2 B:HIS77 2.8 20.7 1.0
CE1 B:HIS77 2.9 25.6 1.0
CD2 A:HIS63 3.0 21.1 1.0
CE1 A:HIS63 3.1 23.4 1.0
CD2 B:HIS73 3.1 18.2 1.0
CE1 B:HIS73 3.1 22.4 1.0
CG B:HIS77 3.9 20.4 1.0
ND1 B:HIS77 4.0 23.0 1.0
CG D:GLU81 4.0 26.0 1.0
ND1 A:HIS63 4.2 23.6 1.0
CG A:HIS63 4.2 21.8 1.0
ND1 B:HIS73 4.2 19.7 1.0
CG B:HIS73 4.2 18.2 1.0
O B:HOH140 4.5 29.2 1.0
O D:HOH221 4.5 37.8 1.0
O B:HOH340 4.6 44.9 1.0
CG1 A:ILE67 4.6 19.2 1.0
O B:HOH137 4.6 30.9 1.0
O D:HOH127 4.8 34.4 1.0
CD1 A:ILE67 4.9 21.6 1.0
CB D:GLU81 5.0 25.8 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: Wed Dec 16 04:52:32 2020

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