Calcium in PDB 6k88: RGLG1 Midas Binds Calcium Ion

Enzymatic activity of RGLG1 Midas Binds Calcium Ion

All present enzymatic activity of RGLG1 Midas Binds Calcium Ion:
2.3.2.27;

Protein crystallography data

The structure of RGLG1 Midas Binds Calcium Ion, PDB code: 6k88 was solved by Q.Wang, Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.00 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.876, 70.727, 146.403, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24

Calcium Binding Sites:

The binding sites of Calcium atom in the RGLG1 Midas Binds Calcium Ion (pdb code 6k88). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the RGLG1 Midas Binds Calcium Ion, PDB code: 6k88:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6k88

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Calcium binding site 1 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:12.1
occ:1.00
O A:LEU209 2.3 10.5 1.0
O A:HOH643 2.4 17.4 1.0
OD1 A:ASP207 2.4 14.2 1.0
OD1 A:ASN156 2.4 19.9 1.0
O A:HOH650 2.4 18.0 1.0
OD1 A:ASP205 2.5 12.6 1.0
OD2 A:ASP205 2.5 11.6 1.0
CG A:ASP205 2.9 15.2 1.0
CG A:ASN156 3.4 24.1 1.0
C A:LEU209 3.5 12.8 1.0
CG A:ASP207 3.5 20.0 1.0
N A:LEU209 3.9 11.1 1.0
CB A:ASN156 3.9 16.2 1.0
OD2 A:ASP207 3.9 20.8 1.0
CA A:LEU209 4.1 13.5 1.0
CA A:ASN156 4.3 13.6 1.0
N A:ASP207 4.4 14.0 1.0
CB A:ASP205 4.4 13.1 1.0
CB A:LEU209 4.4 15.4 1.0
N A:ASN208 4.5 12.2 1.0
N A:LEU157 4.5 13.0 1.0
N A:ILE210 4.6 13.0 1.0
ND2 A:ASN156 4.6 26.1 1.0
CD1 A:ILE210 4.7 15.5 1.0
CB A:ASP207 4.7 18.2 1.0
CD A:PRO211 4.8 12.6 1.0
N A:GLU206 4.8 13.8 1.0
CA A:ILE210 4.8 10.8 1.0
C A:ASN208 4.9 16.4 1.0
CA A:ASP207 4.9 15.8 1.0
C A:ASP207 4.9 19.2 1.0
O A:LEU157 4.9 13.9 1.0
C A:ASN156 4.9 14.9 1.0

Calcium binding site 2 out of 8 in 6k88

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Calcium binding site 2 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:11.4
occ:1.00
OG1 A:THR258 2.3 11.1 1.0
O A:HOH518 2.4 11.6 1.0
O A:HOH568 2.4 13.8 1.0
OG A:SER166 2.5 13.7 1.0
OG1 A:THR164 2.5 10.2 1.0
O A:GLN288 2.6 13.0 1.0
CB A:SER166 3.3 14.2 1.0
CB A:THR258 3.4 13.0 1.0
CB A:THR164 3.5 9.1 1.0
CG2 A:THR258 3.7 10.8 1.0
C A:GLN288 3.8 13.2 1.0
CB A:GLN288 3.9 13.8 1.0
OD1 A:ASP286 4.1 13.6 1.0
CG2 A:THR164 4.2 11.2 1.0
N A:SER166 4.2 9.6 1.0
CA A:GLN288 4.3 12.3 1.0
CA A:SER166 4.4 12.4 1.0
OD2 A:ASP286 4.6 12.6 1.0
OD2 A:ASP162 4.6 17.3 1.0
OD1 A:ASP162 4.7 11.6 1.0
CA A:THR258 4.7 10.3 1.0
CA A:THR164 4.7 10.2 1.0
CG A:ASP286 4.8 13.1 1.0
C A:THR164 4.9 11.5 1.0
N A:VAL289 4.9 10.9 1.0
N A:GLN288 4.9 12.9 1.0
O A:HOH630 4.9 19.8 1.0

Calcium binding site 3 out of 8 in 6k88

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Calcium binding site 3 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:16.3
occ:1.00
OE1 A:GLN350 2.3 14.5 1.0
O A:HOH611 2.3 23.4 1.0
OE2 A:GLU378 2.4 20.6 1.0
O A:HOH549 2.4 21.9 1.0
O A:HOH652 2.4 28.6 1.0
OD2 A:ASP338 2.5 14.6 1.0
OD1 A:ASP338 2.6 16.0 1.0
CG A:ASP338 2.9 15.4 1.0
CD A:GLN350 3.4 14.0 1.0
CD A:GLU378 3.4 17.6 1.0
O A:HOH570 3.7 16.5 1.0
NE2 A:GLN350 3.9 15.1 1.0
CA A:CA404 3.9 15.2 1.0
OD1 A:ASP339 4.0 25.9 1.0
OE1 A:GLU378 4.2 22.1 1.0
CG A:GLU378 4.3 18.1 1.0
CB A:ASP338 4.4 14.1 1.0
N A:PHE351 4.4 10.8 1.0
CA A:GLN350 4.6 12.3 1.0
CG A:GLN350 4.7 10.5 1.0
O A:PHE351 4.7 14.1 1.0
CB A:GLN350 4.9 12.9 1.0

Calcium binding site 4 out of 8 in 6k88

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Calcium binding site 4 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:15.2
occ:1.00
OD1 A:ASP338 2.3 16.0 1.0
OE1 A:GLU378 2.3 22.1 1.0
O A:ASP338 2.4 16.9 1.0
OD1 A:ASP347 2.4 18.7 1.0
O A:PHE349 2.4 16.7 1.0
O A:HOH570 2.4 16.5 1.0
OD2 A:ASP347 2.5 24.1 1.0
OE2 A:GLU378 2.7 20.6 1.0
CG A:ASP347 2.8 23.2 1.0
CD A:GLU378 2.8 17.6 1.0
C A:ASP338 3.3 19.4 1.0
CG A:ASP338 3.5 15.4 1.0
C A:PHE349 3.6 14.7 1.0
CA A:ASP338 3.8 14.7 1.0
CA A:CA403 3.9 16.3 1.0
CB A:ASP338 4.2 14.1 1.0
O A:HOH538 4.2 24.9 1.0
CB A:ASP347 4.3 22.6 1.0
CG A:GLU378 4.3 18.1 1.0
CA A:GLN350 4.3 12.3 1.0
OD1 A:ASP339 4.4 25.9 1.0
N A:GLN350 4.4 10.2 1.0
OD2 A:ASP338 4.4 14.6 1.0
N A:ASP339 4.4 16.9 1.0
O A:HOH509 4.5 31.0 1.0
OE1 A:GLN350 4.5 14.5 1.0
NH2 A:ARG344 4.5 20.4 1.0
N A:PHE349 4.6 15.8 1.0
CA A:PHE349 4.6 14.3 1.0
CA A:ASP339 4.8 19.3 1.0
CB A:GLU378 5.0 17.7 1.0

Calcium binding site 5 out of 8 in 6k88

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Calcium binding site 5 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:18.1
occ:1.00
OD1 B:ASP338 2.3 21.2 1.0
O B:ASP338 2.4 17.0 1.0
OE1 B:GLU378 2.4 22.9 1.0
O B:PHE349 2.4 13.0 1.0
OD1 B:ASP347 2.5 20.0 1.0
OD2 B:ASP347 2.5 21.3 1.0
O B:HOH548 2.6 23.0 1.0
OE2 B:GLU378 2.6 25.6 1.0
CG B:ASP347 2.8 23.9 1.0
CD B:GLU378 2.8 22.2 1.0
C B:ASP338 3.3 18.2 1.0
CG B:ASP338 3.5 19.4 1.0
C B:PHE349 3.6 14.1 1.0
CA B:ASP338 3.8 15.8 1.0
CA B:CA402 4.0 21.3 1.0
CB B:ASP338 4.2 15.9 1.0
CB B:ASP347 4.3 20.9 1.0
CG B:GLU378 4.3 22.0 1.0
CA B:GLN350 4.4 13.2 1.0
OD1 B:ASP339 4.4 25.7 1.0
N B:GLN350 4.4 14.5 1.0
N B:ASP339 4.4 19.0 1.0
O B:HOH555 4.4 23.5 1.0
NH2 B:ARG344 4.4 19.2 1.0
OD2 B:ASP338 4.5 14.8 1.0
N B:PHE349 4.5 16.6 1.0
CA B:PHE349 4.6 16.2 1.0
OE1 B:GLN350 4.6 16.0 1.0
O A:HOH676 4.7 34.2 1.0
CA B:ASP339 4.8 21.2 1.0
O B:HOH632 4.9 31.4 1.0

Calcium binding site 6 out of 8 in 6k88

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Calcium binding site 6 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:21.3
occ:1.00
OE1 B:GLN350 2.3 16.0 1.0
O B:HOH606 2.3 30.5 1.0
O B:HOH639 2.4 28.3 1.0
OE2 B:GLU378 2.4 25.6 1.0
O B:HOH534 2.4 22.6 1.0
OD2 B:ASP338 2.5 14.8 1.0
OD1 B:ASP338 2.6 21.2 1.0
CG B:ASP338 2.9 19.4 1.0
CD B:GLN350 3.4 16.0 1.0
O A:HOH616 3.5 34.7 1.0
CD B:GLU378 3.5 22.2 1.0
O B:HOH548 3.7 23.0 1.0
NE2 B:GLN350 3.9 18.2 1.0
O B:HOH632 3.9 31.4 1.0
CA B:CA401 4.0 18.1 1.0
OD1 B:ASP339 4.1 25.7 1.0
CG B:GLU378 4.3 22.0 1.0
OE1 B:GLU378 4.4 22.9 1.0
CB B:ASP338 4.4 15.9 1.0
N B:PHE351 4.5 12.2 1.0
O A:HOH676 4.6 34.2 1.0
CA B:GLN350 4.7 13.2 1.0
CG B:GLN350 4.7 14.7 1.0
O B:PHE351 4.7 14.7 1.0
O B:HOH650 4.8 34.2 1.0
O A:HOH660 4.9 34.6 1.0
CB B:GLN350 4.9 13.0 1.0

Calcium binding site 7 out of 8 in 6k88

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Calcium binding site 7 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:17.7
occ:1.00
O B:LEU209 2.3 18.6 1.0
OD1 B:ASP207 2.3 15.3 1.0
O B:HOH583 2.4 15.4 1.0
O B:HOH611 2.4 19.4 1.0
OD2 B:ASP205 2.4 23.2 1.0
OD1 B:ASP205 2.5 23.3 1.0
OD1 B:ASN156 2.6 23.4 1.0
CG B:ASP205 2.8 26.3 1.0
CG B:ASP207 3.4 25.3 1.0
C B:LEU209 3.5 19.2 1.0
CG B:ASN156 3.6 26.9 1.0
OD2 B:ASP207 3.9 23.6 1.0
N B:LEU209 3.9 22.6 1.0
CB B:ASN156 4.0 23.5 1.0
CA B:LEU209 4.1 23.6 1.0
O B:HOH649 4.2 29.7 1.0
CB B:ASP205 4.2 21.4 1.0
CB B:LEU209 4.3 21.7 1.0
N B:ASP207 4.4 24.2 1.0
N B:ASN208 4.5 24.2 1.0
N B:LEU157 4.5 14.8 1.0
N B:ILE210 4.5 20.2 1.0
CA B:ASN156 4.6 16.5 1.0
O B:LEU157 4.6 16.4 1.0
CD B:PRO211 4.7 17.5 1.0
CB B:ASP207 4.7 23.4 1.0
ND2 B:ASN156 4.7 23.0 1.0
CA B:ILE210 4.8 18.0 1.0
C B:ASN208 4.8 24.3 1.0
N B:GLU206 4.9 28.4 1.0
C B:ASP207 4.9 20.9 1.0
CA B:ASP205 4.9 27.4 1.0
CA B:ASP207 4.9 21.8 1.0
CD1 B:ILE210 4.9 18.2 1.0
C B:ASP205 4.9 28.2 1.0

Calcium binding site 8 out of 8 in 6k88

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Calcium binding site 8 out of 8 in the RGLG1 Midas Binds Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of RGLG1 Midas Binds Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:10.9
occ:1.00
OG B:SER166 2.4 8.9 1.0
O B:HOH529 2.4 9.0 1.0
OG1 B:THR258 2.4 11.1 1.0
OG1 B:THR164 2.5 11.3 1.0
O B:HOH586 2.6 15.0 1.0
O B:GLN288 2.6 11.1 1.0
CB B:SER166 3.3 11.2 1.0
CB B:THR258 3.4 12.0 1.0
CB B:THR164 3.5 11.4 1.0
CG2 B:THR258 3.7 11.6 1.0
C B:GLN288 3.8 10.4 1.0
CB B:GLN288 3.9 9.6 1.0
CG2 B:THR164 4.1 11.6 1.0
OD1 B:ASP286 4.1 10.7 1.0
N B:SER166 4.3 8.8 1.0
CA B:SER166 4.4 12.6 1.0
CA B:GLN288 4.4 10.6 1.0
OD2 B:ASP162 4.6 17.8 1.0
OD2 B:ASP286 4.6 11.2 1.0
OD1 B:ASP162 4.6 13.2 1.0
CA B:THR164 4.7 12.0 1.0
CA B:THR258 4.8 10.4 1.0
CG B:ASP286 4.8 13.5 1.0
C B:THR164 4.8 12.0 1.0
N B:VAL289 4.9 8.3 1.0
N B:GLN288 4.9 8.9 1.0
O B:HOH614 5.0 13.6 1.0

Reference:

Q.Wang, Y.Wu. RGLG1 Midas Binds Calcium Ion To Be Published.
Page generated: Sat Dec 12 06:16:06 2020

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