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Calcium in PDB 4n1g: Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution, PDB code: 4n1g was solved by P.V.Natashin, S.V.Markova, J.Lee, E.S.Vysotski, Z.J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.54 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.920, 85.127, 90.088, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution (pdb code 4n1g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution, PDB code: 4n1g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4n1g

Go back to Calcium Binding Sites List in 4n1g
Calcium binding site 1 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:16.2
occ:1.00
 OD1 A:ASP30 2.3 19.4 1.0
O A:HOH376 2.3 16.6 1.0
O A:LYS36 2.3 17.4 1.0
OD1 A:ASN32 2.4 20.9 1.0
OE2 A:GLU41 2.4 18.9 1.0
OD1 A:ASN34 2.5 19.7 1.0
OE1 A:GLU41 2.6 16.1 1.0
CD A:GLU41 2.9 16.1 1.0
CG A:ASN32 3.3 21.4 1.0
CG A:ASN34 3.4 20.6 1.0
CG A:ASP30 3.4 19.3 1.0
C A:LYS36 3.6 15.0 1.0
ND2 A:ASN32 3.7 20.7 1.0
ND2 A:ASN34 3.8 26.0 1.0
N A:ASN34 4.2 20.5 1.0
CA A:ASP30 4.2 17.5 1.0
N A:LYS36 4.3 16.9 1.0
OD2 A:ASP30 4.3 20.6 1.0
N A:ASN32 4.3 22.3 1.0
CB A:ASP30 4.3 18.8 1.0
CG A:GLU41 4.3 11.7 1.0
CA A:LYS36 4.4 16.6 1.0
CA A:ILE37 4.4 14.8 1.0
N A:ILE37 4.4 13.8 1.0
C A:ASP30 4.5 19.0 1.0
CB A:ASN34 4.5 22.9 1.0
N A:GLY33 4.6 24.9 1.0
CB A:ASN32 4.6 24.5 1.0
OE1 A:GLU82 4.6 35.9 1.0
N A:ILE31 4.7 22.4 1.0
CA A:ASN34 4.7 20.2 1.0
CB A:LYS36 4.7 17.5 1.0
CA A:ASN32 4.8 22.1 1.0
C A:ASN32 4.8 23.6 1.0
N A:GLY35 4.9 18.4 1.0
O A:HOH341 4.9 19.5 1.0
O A:ASP30 5.0 21.7 1.0
C A:ASN34 5.0 22.1 1.0

Calcium binding site 2 out of 6 in 4n1g

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Calcium binding site 2 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:16.4
occ:1.00
 OD1 A:ASP123 2.3 15.7 1.0
O A:THR129 2.3 17.2 1.0
OD1 A:ASP125 2.3 19.5 1.0
O A:HOH312 2.4 19.7 1.0
OE1 A:GLU134 2.4 13.8 1.0
OG A:SER127 2.5 18.8 1.0
OE2 A:GLU134 2.6 15.4 1.0
CD A:GLU134 2.9 14.6 1.0
CG A:ASP125 3.3 23.5 1.0
CG A:ASP123 3.4 15.7 1.0
C A:THR129 3.6 14.6 1.0
CB A:SER127 3.6 20.0 1.0
OD2 A:ASP125 3.6 29.0 1.0
N A:SER127 4.0 23.9 1.0
O A:HOH422 4.2 31.6 1.0
CA A:ASP123 4.2 12.2 1.0
OD2 A:ASP123 4.3 20.3 1.0
CA A:ILE130 4.3 12.7 0.4
CA A:SER127 4.3 21.7 1.0
CB A:ASP123 4.4 13.0 1.0
N A:THR129 4.4 18.9 1.0
N A:ILE130 4.4 12.0 0.4
CA A:ILE130 4.4 12.9 0.6
N A:ILE130 4.4 11.4 0.6
N A:ASP125 4.4 20.9 1.0
CG A:GLU134 4.4 15.1 1.0
C A:ASP123 4.5 12.4 1.0
N A:THR131 4.5 10.5 1.0
OG1 A:THR131 4.6 17.1 1.0
CB A:ASP125 4.6 21.0 1.0
CA A:THR129 4.6 12.5 1.0
N A:GLY126 4.7 19.8 1.0
N A:GLY128 4.7 16.2 1.0
N A:LYS124 4.7 13.1 1.0
CA A:ASP125 4.9 20.4 1.0
C A:SER127 4.9 19.8 1.0
CD1 A:ILE130 4.9 13.0 0.6
OG1 A:THR129 4.9 23.4 1.0
C A:ILE130 4.9 11.9 0.4
C A:ASP125 4.9 20.9 1.0
O A:HOH326 4.9 22.6 1.0
C A:ILE130 4.9 11.5 0.6

Calcium binding site 3 out of 6 in 4n1g

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Calcium binding site 3 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:12.1
occ:1.00
 O A:HOH336 2.3 21.1 1.0
OD1 A:ASP159 2.4 14.6 1.0
OG A:SER163 2.4 13.2 1.0
OD1 A:ASP161 2.4 12.9 1.0
O A:ASP165 2.4 12.5 1.0
OE2 A:GLU170 2.5 13.1 1.0
OE1 A:GLU170 2.6 12.3 1.0
CD A:GLU170 2.9 11.3 1.0
CG A:ASP161 3.4 20.8 1.0
CB A:SER163 3.5 13.6 1.0
CG A:ASP159 3.5 12.9 1.0
C A:ASP165 3.7 11.6 1.0
OD2 A:ASP161 3.8 22.9 1.0
N A:SER163 4.0 14.1 1.0
OD1 A:ASP165 4.1 19.6 1.0
OD2 A:ASP159 4.3 14.6 1.0
CA A:ASP159 4.3 10.7 1.0
CA A:LEU166 4.3 11.4 1.0
CA A:SER163 4.3 13.0 1.0
O A:HOH552 4.4 49.2 1.0
CG A:GLU170 4.4 9.5 1.0
CB A:ASP159 4.4 12.3 1.0
N A:ASP165 4.5 12.0 1.0
N A:LEU166 4.5 11.2 1.0
N A:ASP161 4.5 15.0 1.0
OD2 A:ASP167 4.6 22.0 1.0
N A:ASP167 4.6 11.1 1.0
C A:ASP159 4.6 11.1 1.0
CB A:ASP161 4.6 17.5 1.0
CA A:ASP165 4.7 14.5 1.0
O A:HOH458 4.7 22.6 1.0
N A:ASN162 4.8 13.4 1.0
N A:LEU160 4.8 12.1 1.0
N A:GLY164 4.8 13.6 1.0
C A:LEU166 4.9 11.0 1.0
CA A:ASP161 4.9 15.9 1.0
C A:ASP161 4.9 16.1 1.0
C A:SER163 5.0 14.2 1.0

Calcium binding site 4 out of 6 in 4n1g

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Calcium binding site 4 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:14.2
occ:1.00
 OD1 B:ASP159 2.3 14.0 1.0
O B:HOH313 2.3 17.9 1.0
O B:ASP165 2.4 14.8 1.0
OD1 B:ASP161 2.4 15.0 1.0
OG B:SER163 2.5 14.9 1.0
OE1 B:GLU170 2.5 12.6 1.0
OE2 B:GLU170 2.5 14.3 1.0
CD B:GLU170 2.9 12.9 1.0
CG B:ASP161 3.3 19.9 1.0
CG B:ASP159 3.5 17.4 1.0
CB B:SER163 3.6 18.4 1.0
C B:ASP165 3.6 15.8 1.0
OD2 B:ASP161 3.8 23.3 1.0
N B:SER163 4.0 18.1 1.0
OD1 B:ASP165 4.1 25.3 1.0
CA B:LEU166 4.3 11.7 1.0
CA B:ASP159 4.3 14.2 1.0
OD2 B:ASP159 4.3 19.1 1.0
CG B:GLU170 4.3 12.5 1.0
CA B:SER163 4.4 20.0 1.0
N B:ASP161 4.4 18.4 1.0
OD2 B:ASP167 4.4 22.0 1.0
N B:ASP165 4.4 15.3 1.0
CB B:ASP159 4.4 14.1 1.0
O B:HOH354 4.4 29.2 1.0
N B:LEU166 4.4 12.5 1.0
N B:ASP167 4.5 14.3 1.0
C B:ASP159 4.6 13.2 1.0
CB B:ASP161 4.6 18.2 1.0
CA B:ASP165 4.6 14.3 1.0
O B:HOH523 4.6 50.6 1.0
O B:HOH428 4.7 31.0 1.0
N B:LEU160 4.7 15.0 1.0
N B:ASN162 4.7 17.3 1.0
CA B:ASP161 4.8 20.1 1.0
C B:LEU166 4.8 13.4 1.0
N B:GLY164 4.8 16.3 1.0
C B:ASP161 4.8 18.6 1.0
C B:SER163 4.9 15.7 1.0
CD2 B:LEU166 5.0 15.7 1.0

Calcium binding site 5 out of 6 in 4n1g

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Calcium binding site 5 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:19.3
occ:1.00
 OD1 B:ASP123 2.3 18.7 1.0
O B:HOH317 2.3 24.4 1.0
O B:THR129 2.3 19.0 1.0
OD1 B:ASP125 2.4 20.7 1.0
OG B:SER127 2.4 23.1 1.0
OE1 B:GLU134 2.5 17.4 1.0
OE2 B:GLU134 2.6 20.1 1.0
CD B:GLU134 2.9 18.0 1.0
CG B:ASP125 3.3 31.0 1.0
CG B:ASP123 3.4 15.2 1.0
CB B:SER127 3.5 24.8 1.0
C B:THR129 3.5 16.7 1.0
OD2 B:ASP125 3.6 35.9 1.0
N B:SER127 4.0 22.4 1.0
CA B:ASP123 4.2 16.9 1.0
CB B:ASP123 4.3 13.5 1.0
OD2 B:ASP123 4.3 18.4 1.0
CA B:SER127 4.3 20.9 1.0
OG1 B:THR129 4.3 26.6 1.0
N B:THR129 4.4 19.9 1.0
CA B:ILE130 4.4 12.4 1.0
CG B:GLU134 4.4 20.0 1.0
N B:ILE130 4.4 14.7 1.0
N B:ASP125 4.4 21.4 1.0
C B:ASP123 4.5 19.3 1.0
CA B:THR129 4.5 15.7 1.0
CB B:ASP125 4.6 25.0 1.0
N B:THR131 4.6 13.1 1.0
N B:GLY126 4.6 20.4 1.0
N B:LYS124 4.7 16.6 1.0
N B:GLY128 4.8 20.2 1.0
OG1 B:THR131 4.8 25.2 1.0
CA B:ASP125 4.9 24.6 1.0
O B:HOH329 4.9 21.9 1.0
C B:ASP125 4.9 26.7 1.0
C B:SER127 4.9 21.7 1.0
CG2 B:THR131 5.0 19.6 1.0
C B:ILE130 5.0 14.0 1.0

Calcium binding site 6 out of 6 in 4n1g

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Calcium binding site 6 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:20.7
occ:1.00
 O B:HOH330 2.3 25.6 1.0
OD1 B:ASP30 2.3 25.3 1.0
O B:LYS36 2.3 20.7 1.0
OD1 B:ASN32 2.4 28.2 1.0
OD1 B:ASN34 2.4 25.4 1.0
OE2 B:GLU41 2.6 24.2 1.0
OE1 B:GLU41 2.6 21.2 1.0
CD B:GLU41 2.9 24.3 1.0
CG B:ASN32 3.4 31.4 1.0
CG B:ASN34 3.4 27.2 1.0
CG B:ASP30 3.4 25.7 1.0
C B:LYS36 3.5 17.1 1.0
ND2 B:ASN32 3.8 33.3 1.0
ND2 B:ASN34 3.9 29.5 1.0
OD2 B:ASP30 4.2 25.5 1.0
CA B:ASP30 4.3 23.6 1.0
N B:ASN34 4.3 28.9 1.0
N B:LYS36 4.3 20.5 1.0
CB B:ASP30 4.4 24.2 1.0
N B:ILE37 4.4 13.7 1.0
N B:ASN32 4.4 24.1 1.0
CA B:ILE37 4.4 15.4 1.0
CA B:LYS36 4.4 16.5 1.0
C B:ASP30 4.5 25.1 1.0
CG B:GLU41 4.5 15.2 1.0
OE2 B:GLU82 4.5 44.4 1.0
CB B:ASN34 4.5 26.4 1.0
N B:ILE31 4.6 25.1 1.0
CB B:ASN32 4.6 26.1 1.0
N B:GLY33 4.6 32.0 1.0
CB B:LYS36 4.7 22.2 1.0
O B:HOH388 4.7 36.4 1.0
O B:HOH384 4.7 28.6 1.0
CA B:ASN34 4.8 27.6 1.0
CA B:ASN32 4.8 27.8 1.0
C B:ASN32 4.9 34.7 1.0
N B:GLY35 4.9 24.6 1.0

Reference:

P.V.Natashin, S.V.Markova, J.Lee, E.S.Vysotski, Z.J.Liu. Crystal Structures of the F88Y Obelin Mutant Before and After Bioluminescence Provide Molecular Insight Into Spectral Tuning Among Hydromedusan Photoproteins Febs J. V. 281 1432 2014.
ISSN: ISSN 1742-464X
PubMed: 24418253
DOI: 10.1111/FEBS.12715
Page generated: Sun Jul 14 10:41:44 2024

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