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Calcium in PDB 6xw2: Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein

Protein crystallography data

The structure of Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein, PDB code: 6xw2 was solved by K.M.Boyko, A.Y.Nikolaeva, D.A.Korzhenevskiy, V.A.Lazarenko, O.M.Subach, F.V.Subach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.99 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.900, 65.700, 93.020, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein (pdb code 6xw2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein, PDB code: 6xw2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6xw2

Go back to Calcium Binding Sites List in 6xw2
Calcium binding site 1 out of 4 in the Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein


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 the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:10.0
occ:1.00
 O A:THR173 2.3 10.6 1.0
OD1 A:ASP167 2.3 9.4 1.0
O A:HOH660 2.4 12.3 1.0
OD1 A:ASP171 2.4 11.1 1.0
OD1 A:ASP169 2.4 10.8 1.0
OE2 A:GLU178 2.4 10.6 1.0
OE1 A:GLU178 2.4 10.8 1.0
CD A:GLU178 2.8 9.9 1.0
CG A:ASP169 3.3 11.1 1.0
CG A:ASP171 3.3 10.5 1.0
CG A:ASP167 3.5 10.7 1.0
C A:THR173 3.5 9.4 1.0
OD2 A:ASP169 3.7 11.3 1.0
OD2 A:ASP171 4.0 11.1 1.0
N A:ASP171 4.1 9.8 1.0
N A:THR173 4.1 9.7 1.0
CA A:ASP167 4.2 10.1 1.0
CG A:GLU178 4.3 9.7 1.0
OD2 A:ASP167 4.3 11.8 1.0
CB A:ASP171 4.3 10.2 1.0
N A:ASP169 4.4 11.5 1.0
CB A:ASP167 4.4 11.0 1.0
CA A:THR173 4.4 9.7 1.0
N A:ILE174 4.5 8.3 1.0
C A:ASP167 4.5 11.0 1.0
CA A:ILE174 4.6 8.2 1.0
O A:HOH615 4.6 22.1 1.0
CB A:ASP169 4.6 12.2 1.0
N A:GLY170 4.6 10.8 1.0
CA A:ASP171 4.6 10.2 1.0
CG2 A:THR173 4.6 10.3 1.0
O A:HOH734 4.6 13.9 1.0
N A:LYS168 4.7 11.6 1.0
N A:GLY172 4.7 10.2 1.0
N A:THR175 4.8 9.4 1.0
CG2 A:THR175 4.8 9.9 1.0
CA A:ASP169 4.8 12.5 1.0
C A:ASP171 4.9 9.7 1.0
C A:ASP169 5.0 12.2 1.0
O A:ASP167 5.0 11.3 1.0

Calcium binding site 2 out of 4 in 6xw2

Go back to Calcium Binding Sites List in 6xw2
Calcium binding site 2 out of 4 in the Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein


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 the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:9.4
occ:1.00
 OD1 A:ASP203 2.3 9.1 1.0
O A:HOH851 2.3 8.3 1.0
OD1 A:ASP205 2.4 10.2 1.0
O A:THR209 2.4 9.6 1.0
OD1 A:ASP207 2.4 9.0 1.0
OE1 A:GLU214 2.4 9.4 1.0
OE2 A:GLU214 2.5 9.3 1.0
CD A:GLU214 2.8 9.4 1.0
CG A:ASP205 3.2 12.3 1.0
CG A:ASP203 3.3 8.8 1.0
CG A:ASP207 3.3 11.4 1.0
C A:THR209 3.5 8.8 1.0
OD2 A:ASP205 3.6 15.4 1.0
OD2 A:ASP203 3.9 9.4 1.0
OG1 A:THR209 4.1 10.6 1.0
N A:ASP207 4.1 9.6 1.0
OD2 A:ASP207 4.1 14.6 1.0
N A:THR209 4.2 8.8 1.0
CB A:ASP207 4.3 10.7 1.0
CG A:GLU214 4.3 9.8 1.0
CA A:THR209 4.4 9.6 1.0
CB A:ASP203 4.4 9.2 1.0
N A:ASP205 4.4 10.2 1.0
CB A:ASP205 4.4 11.1 1.0
N A:ASP211 4.4 8.8 1.0
CA A:ASP203 4.4 9.0 1.0
N A:GLY206 4.4 9.7 1.0
N A:LEU210 4.4 9.3 1.0
CA A:LEU210 4.6 9.0 1.0
C A:ASP203 4.6 9.3 1.0
CA A:ASP207 4.7 10.3 1.0
CG A:ASP211 4.7 10.8 1.0
CA A:ASP205 4.7 10.5 1.0
C A:ASP205 4.7 9.6 1.0
N A:GLY208 4.8 9.6 1.0
N A:ALA204 4.8 10.1 1.0
OD1 A:ASP211 4.8 10.5 1.0
OD2 A:ASP211 4.9 11.9 1.0
CB A:THR209 4.9 9.8 1.0
CB A:ASP211 4.9 10.2 1.0
C A:LEU210 5.0 8.9 1.0

Calcium binding site 3 out of 4 in 6xw2

Go back to Calcium Binding Sites List in 6xw2
Calcium binding site 3 out of 4 in the Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein


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 the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:13.2
occ:1.00
 O A:TYR246 2.3 14.9 1.0
OD1 A:ASP240 2.3 13.9 1.0
OD1 A:ASP242 2.3 15.0 1.0
OD1 A:ASN244 2.4 15.4 1.0
OE2 A:GLU251 2.4 12.4 1.0
OE1 A:GLU251 2.4 13.0 1.0
O A:HOH630 2.4 18.0 1.0
CD A:GLU251 2.7 11.7 1.0
CG A:ASP242 3.3 17.4 1.0
CG A:ASN244 3.3 15.7 1.0
CG A:ASP240 3.5 16.3 1.0
C A:TYR246 3.5 13.3 1.0
OD2 A:ASP242 3.6 17.6 1.0
ND2 A:ASN244 3.7 16.4 1.0
CA A:ASP240 4.1 14.8 1.0
N A:ASN244 4.2 18.8 1.0
N A:TYR246 4.2 13.9 1.0
CG A:GLU251 4.2 12.4 1.0
CB A:ASP240 4.3 14.3 1.0
N A:ASP242 4.3 20.0 1.0
OD2 A:ASP240 4.3 15.2 1.0
CA A:TYR246 4.4 15.1 1.0
N A:ILE247 4.4 13.2 1.0
C A:ASP240 4.4 16.5 1.0
CB A:ASN244 4.4 16.6 1.0
CA A:ILE247 4.5 12.6 1.0
CB A:ASP242 4.5 17.9 1.0
N A:GLY243 4.6 17.5 1.0
N A:GLY248 4.6 11.8 1.0
O3 A:SO4501 4.6 23.2 1.0
N A:LYS241 4.6 18.8 1.0
O A:HOH652 4.6 24.6 1.0
CA A:ASN244 4.7 18.1 1.0
CA A:ASP242 4.7 18.7 1.0
CB A:TYR246 4.8 15.7 1.0
C A:ASP242 4.8 18.7 1.0
N A:GLY245 4.8 16.7 1.0
O A:ASP240 4.9 17.2 1.0
O A:HOH789 5.0 15.4 1.0
C A:ASN244 5.0 18.7 1.0

Calcium binding site 4 out of 4 in 6xw2

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Calcium binding site 4 out of 4 in the Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein


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 the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:13.1
occ:1.00
 OD1 A:ASP276 2.3 14.7 1.0
OD1 A:ASP278 2.3 14.1 1.0
O A:GLN282 2.3 15.0 1.0
O A:HOH722 2.3 14.0 1.0
OD1 A:ASP280 2.4 15.6 1.0
OE1 A:GLU287 2.4 13.5 1.0
OE2 A:GLU287 2.5 15.0 1.0
CD A:GLU287 2.8 13.4 1.0
CG A:ASP278 3.3 16.8 1.0
CG A:ASP280 3.3 18.6 1.0
CG A:ASP276 3.5 14.3 1.0
C A:GLN282 3.6 13.9 1.0
OD2 A:ASP278 3.7 17.8 1.0
OD2 A:ASP280 3.8 15.9 1.0
CA A:ASP276 4.1 14.2 1.0
CB A:ASP276 4.2 14.5 1.0
N A:ASP278 4.2 16.0 1.0
N A:ASP280 4.3 17.1 1.0
N A:GLN282 4.3 14.3 1.0
CG A:GLU287 4.3 12.4 1.0
OD2 A:ASP276 4.4 15.3 1.0
CA A:VAL283 4.4 13.0 1.0
N A:VAL283 4.4 12.5 1.0
C A:ASP276 4.4 15.9 1.0
N A:ASN284 4.4 13.2 1.0
N A:GLY279 4.4 15.6 1.0
CB A:ASP278 4.5 16.5 1.0
CB A:ASP280 4.5 18.5 1.0
CA A:GLN282 4.5 14.4 1.0
N A:ILE277 4.6 17.3 1.0
CG A:GLN282 4.7 17.8 1.0
CA A:ASP278 4.7 17.1 1.0
C A:ASP278 4.8 17.7 1.0
CA A:ASP280 4.8 17.6 1.0
ND2 A:ASN284 4.8 16.1 1.0
N A:GLY281 4.8 16.6 1.0
C A:VAL283 4.9 14.2 1.0
CG A:ASN284 4.9 15.2 1.0

Reference:

K.M.Boyko, A.Y.Nikolaeva, D.A.Korzhenevskiy, V.A.Lazarenko, O.M.Subach, F.V.Subach. Crystal Structure of the Bright Genetically Encoded Calcium Indicator NCAMP7 Based on Mneongreen Fluorescent Protein To Be Published.
Page generated: Tue Jul 16 18:18:14 2024

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