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Calcium in PDB 4gf6: Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151

Protein crystallography data

The structure of Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151, PDB code: 4gf6 was solved by J.Dong, X.Liu, J.Li, J.Wang, W.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.827, 63.052, 70.369, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 17.9

Other elements in 4gf6:

The structure of Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151 also contains other interesting chemical elements:

Copper (Cu) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151 (pdb code 4gf6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151, PDB code: 4gf6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4gf6

Go back to Calcium Binding Sites List in 4gf6
Calcium binding site 1 out of 5 in the Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151


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 Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:5.2
occ:0.62
O B:HOH452 2.4 12.2 1.0
O B:HOH476 2.4 12.5 1.0
O B:HOH459 2.4 12.7 1.0
O B:HOH419 2.4 8.5 1.0
OD1 B:ASP197 2.4 11.2 1.0
OD2 B:ASP197 2.6 9.9 1.0
CG B:ASP197 2.9 9.1 1.0
O B:HOH471 4.3 13.5 1.0
CB B:ASP197 4.4 9.1 1.0
O B:HOH553 4.6 18.4 1.0
O B:HOH616 4.7 20.6 1.0
CE1 B:HIS81 4.9 10.9 1.0

Calcium binding site 2 out of 5 in 4gf6

Go back to Calcium Binding Sites List in 4gf6
Calcium binding site 2 out of 5 in the Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151


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 Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:6.8
occ:1.00
NE2 B:HIS243 2.0 11.2 1.0
NE2 B:HIS245 2.0 9.3 1.0
O B:HOH418 2.1 8.8 1.0
O B:HOH461 2.6 13.0 1.0
O B:HOH435 2.6 12.1 1.0
CE1 B:HIS245 3.0 10.5 1.0
CE1 B:HIS243 3.0 13.0 1.0
CD2 B:HIS243 3.0 11.4 1.0
CD2 B:HIS245 3.0 8.7 1.0
ND1 B:HIS243 4.1 14.5 1.0
ND1 B:HIS245 4.1 9.7 1.0
CG B:HIS243 4.2 11.9 1.0
CG B:HIS245 4.2 8.6 1.0

Calcium binding site 3 out of 5 in 4gf6

Go back to Calcium Binding Sites List in 4gf6
Calcium binding site 3 out of 5 in the Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:8.0
occ:1.00
NE2 B:HIS246 2.0 11.0 1.0
NE2 B:HIS244 2.0 9.5 1.0
OE1 B:GLU240 2.1 12.6 1.0
OE2 B:GLU240 2.5 15.6 1.0
CD B:GLU240 2.6 13.0 1.0
CE1 B:HIS244 3.0 9.8 1.0
CE1 B:HIS246 3.0 11.7 1.0
CD2 B:HIS246 3.0 11.2 1.0
CD2 B:HIS244 3.0 9.5 1.0
ND1 B:HIS246 4.1 12.5 1.0
ND1 B:HIS244 4.1 9.5 1.0
CG B:GLU240 4.1 13.8 1.0
O B:HOH567 4.1 28.7 1.0
CG B:HIS246 4.1 11.7 1.0
CG B:HIS244 4.2 9.3 1.0
O B:HOH673 4.4 21.5 1.0
CB B:GLU240 4.9 13.0 1.0

Calcium binding site 4 out of 5 in 4gf6

Go back to Calcium Binding Sites List in 4gf6
Calcium binding site 4 out of 5 in the Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:7.2
occ:1.00
ND1 B:HIS242 2.0 9.8 1.0
N B:HIS241 2.0 12.0 1.0
O B:LEU239 2.0 11.8 1.0
N B:HIS242 2.0 11.8 1.0
C B:HIS241 2.8 12.8 1.0
CA B:HIS241 2.9 12.7 1.0
CE1 B:HIS242 2.9 9.6 1.0
CG B:HIS242 3.0 9.8 1.0
C B:GLU240 3.0 11.7 1.0
C B:LEU239 3.0 11.8 1.0
CA B:HIS242 3.1 10.8 1.0
CA B:GLU240 3.2 12.3 1.0
CB B:HIS242 3.3 11.1 1.0
O B:HIS242 3.5 10.3 1.0
N B:GLU240 3.5 11.9 1.0
C B:HIS242 3.7 10.6 1.0
CD2 B:HIS241 3.8 13.3 1.0
CG B:HIS241 3.8 13.2 1.0
CB B:HIS241 3.9 12.4 1.0
O B:HOH609 4.0 20.6 1.0
O B:HIS241 4.0 14.6 1.0
NE2 B:HIS242 4.1 10.1 1.0
CD2 B:HIS242 4.1 10.3 1.0
ND1 B:HIS244 4.1 9.5 1.0
O B:GLU240 4.1 13.2 1.0
CA B:LEU239 4.2 11.8 1.0
CE1 B:HIS244 4.3 9.8 1.0
CB B:LEU239 4.4 11.6 1.0
CG B:ASP234 4.6 11.8 1.0
NE2 B:HIS241 4.6 13.9 1.0
CB B:ASP234 4.6 11.7 1.0
ND1 B:HIS241 4.6 13.3 1.0
CB B:GLU240 4.7 13.0 1.0
OD2 B:ASP234 4.7 14.0 1.0
N B:LEU239 4.9 12.1 1.0
O B:HOH673 4.9 21.5 1.0
OD1 B:ASP234 5.0 13.5 1.0
N B:HIS243 5.0 10.6 1.0

Calcium binding site 5 out of 5 in 4gf6

Go back to Calcium Binding Sites List in 4gf6
Calcium binding site 5 out of 5 in the Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Gfp with Cuprum Bound at the Incorporated Metal Chelating Amino Acid PYZ151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:9.9
occ:1.00
OE1 B:GLU34 2.1 18.2 1.0
OE2 B:GLU34 2.4 18.1 1.0
CD B:GLU34 2.6 15.9 1.0
CG B:GLU34 4.1 13.1 1.0
CB B:GLU34 5.0 10.0 1.0

Reference:

X.Liu, J.Li, J.Dong, C.Hu, W.Gong, J.Wang. Genetic Incorporation of A Metal-Chelating Amino Acid As A Probe For Protein Electron Transfer. Angew.Chem.Int.Ed.Engl. V. 51 10261 2012.
ISSN: ISSN 1433-7851
PubMed: 22936654
DOI: 10.1002/ANIE.201204962
Page generated: Sat Dec 12 04:47:46 2020

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