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Calcium in PDB 5n7d: Magi-1 Complexed with A RSK1 Peptide

Enzymatic activity of Magi-1 Complexed with A RSK1 Peptide

All present enzymatic activity of Magi-1 Complexed with A RSK1 Peptide:
2.7.11.1;

Protein crystallography data

The structure of Magi-1 Complexed with A RSK1 Peptide, PDB code: 5n7d was solved by G.Gogl, L.Nyitray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 195.810, 60.680, 99.710, 90.00, 98.81, 90.00
R / Rfree (%) 19.1 / 22.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Magi-1 Complexed with A RSK1 Peptide (pdb code 5n7d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Magi-1 Complexed with A RSK1 Peptide, PDB code: 5n7d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5n7d

Go back to Calcium Binding Sites List in 5n7d
Calcium binding site 1 out of 7 in the Magi-1 Complexed with A RSK1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Magi-1 Complexed with A RSK1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:89.6
occ:1.00
 OE2 A:GLU592 2.4 89.9 1.0
O A:VAL590 2.4 58.8 1.0
O A:GLY589 2.9 0.2 1.0
CD A:GLU592 3.1 79.2 1.0
OE1 A:GLU592 3.1 87.0 1.0
C A:GLY589 3.2 81.5 1.0
C A:VAL590 3.5 49.9 1.0
N A:VAL590 3.7 69.4 1.0
CA A:GLY589 4.0 69.8 1.0
CA A:VAL590 4.1 63.9 1.0
CG A:GLU592 4.5 63.8 1.0
CB A:VAL590 4.6 54.3 1.0
N A:ASP591 4.6 50.9 1.0
O A:HOH1151 4.9 65.4 1.0
N A:GLU592 4.9 44.5 1.0

Calcium binding site 2 out of 7 in 5n7d

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Calcium binding site 2 out of 7 in the Magi-1 Complexed with A RSK1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Magi-1 Complexed with A RSK1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:54.4
occ:1.00
 O A:GLY746 2.4 44.8 1.0
O A:HOH1090 2.4 58.3 1.0
O A:ARG744 2.4 52.7 1.0
O A:GLY741 2.4 45.0 1.0
O A:HOH1155 2.4 51.3 1.0
OE1 A:GLU786 2.5 49.5 1.0
OE2 A:GLU786 2.5 52.2 1.0
CD A:GLU786 2.8 52.1 1.0
C A:GLY741 3.2 43.3 1.0
C A:GLY746 3.5 51.1 1.0
C A:ARG744 3.6 51.6 1.0
N A:GLY746 3.7 47.8 1.0
CA A:GLY741 4.0 41.9 1.0
N A:VAL742 4.0 37.7 1.0
C A:LYS745 4.1 60.0 1.0
CA A:VAL742 4.1 45.6 1.0
CA A:GLY746 4.1 49.8 1.0
OG1 A:THR747 4.2 50.1 1.0
CG A:GLU786 4.3 46.9 1.0
O A:HOH1027 4.3 58.8 1.0
C A:VAL742 4.3 41.1 1.0
CA A:LYS745 4.4 58.0 1.0
O A:VAL742 4.4 55.5 1.0
N A:ARG744 4.4 50.1 1.0
N A:LYS745 4.4 56.7 1.0
N A:THR747 4.6 50.9 1.0
CA A:ARG744 4.6 46.9 1.0
CG A:ARG744 4.6 50.1 1.0
CA A:THR747 4.8 49.3 1.0
O A:LYS745 4.8 67.3 1.0

Calcium binding site 3 out of 7 in 5n7d

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Calcium binding site 3 out of 7 in the Magi-1 Complexed with A RSK1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Magi-1 Complexed with A RSK1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:36.6
occ:1.00
 OG A:SER773 2.4 38.8 1.0
O A:HOH1095 2.4 31.3 1.0
CB A:SER773 3.5 26.1 1.0
CA A:SER773 4.0 35.8 1.0
NH1 A:ARG770 4.4 36.8 1.0
O A:HOH1034 4.4 39.6 1.0
O A:SER773 4.4 41.3 1.0
C A:SER773 4.7 38.6 1.0

Calcium binding site 4 out of 7 in 5n7d

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Calcium binding site 4 out of 7 in the Magi-1 Complexed with A RSK1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Magi-1 Complexed with A RSK1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:89.0
occ:1.00
 O A:HOH1172 3.0 68.4 1.0
O A:ASP815 3.1 31.7 1.0
N A:GLY819 3.3 36.2 1.0
O A:SER816 3.5 38.0 1.0
CA A:GLY819 3.7 40.4 1.0
C A:SER816 3.7 22.6 1.0
O A:HOH1177 3.9 63.2 1.0
C A:GLY819 3.9 41.4 1.0
N A:LYS818 4.0 29.8 1.0
N A:MET817 4.0 32.4 1.0
C A:MET817 4.1 34.5 1.0
O A:LYS820 4.1 36.8 1.0
C A:ASP815 4.2 31.1 1.0
O A:GLY819 4.2 36.0 1.0
CA A:MET817 4.3 27.4 1.0
C A:LYS818 4.4 32.3 1.0
CA A:SER816 4.4 27.7 1.0
O A:GLY821 4.4 32.8 1.0
N A:LYS820 4.5 41.3 1.0
CG A:LYS818 4.5 25.8 1.0
O A:MET817 4.6 25.2 1.0
CA A:LYS818 4.7 32.2 1.0
N A:SER816 4.8 31.7 1.0
N A:ARG823 4.8 29.1 1.0
C A:LYS820 4.9 41.2 1.0
C A:GLY821 4.9 33.9 1.0
CA A:THR822 5.0 35.5 1.0

Calcium binding site 5 out of 7 in 5n7d

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Calcium binding site 5 out of 7 in the Magi-1 Complexed with A RSK1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Magi-1 Complexed with A RSK1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:0.5
occ:1.00
 OE2 B:GLU786 2.4 0.2 1.0
O B:HOH1007 2.5 76.5 1.0
O B:ARG744 2.5 0.1 1.0
OE1 B:GLU786 2.6 0.5 1.0
O B:GLY741 2.7 98.8 1.0
CD B:GLU786 2.8 0.7 1.0
O B:HOH1018 3.0 69.7 1.0
O B:GLY746 3.1 92.0 1.0
O B:VAL742 3.6 0.9 1.0
C B:ARG744 3.7 0.1 1.0
C B:GLY741 3.7 87.7 1.0
O B:HOH1005 3.7 77.8 1.0
CA B:VAL742 3.8 98.5 1.0
C B:VAL742 3.9 0.3 1.0
N B:GLY746 4.1 95.4 1.0
N B:VAL742 4.2 84.4 1.0
C B:GLY746 4.2 93.5 1.0
CG B:GLU786 4.3 0.3 1.0
N B:ARG744 4.4 0.5 1.0
N B:LYS745 4.5 0.0 1.0
CA B:LYS745 4.5 0.1 1.0
CA B:ARG744 4.6 0.9 1.0
C B:LYS745 4.7 0.0 1.0
CA B:GLY746 4.7 91.9 1.0
N B:LYS743 4.8 0.4 1.0
CA B:GLY741 4.9 86.9 1.0
OG1 B:THR747 4.9 0.0 1.0
C B:LYS743 5.0 0.2 1.0

Calcium binding site 6 out of 7 in 5n7d

Go back to Calcium Binding Sites List in 5n7d
Calcium binding site 6 out of 7 in the Magi-1 Complexed with A RSK1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Magi-1 Complexed with A RSK1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:0.5
occ:1.00
 O B:VAL590 2.6 97.8 1.0
O B:GLY589 3.6 0.6 1.0
C B:VAL590 3.7 86.4 1.0
C B:GLY589 4.0 0.5 1.0
CG B:GLU592 4.0 89.5 1.0
CD B:GLU592 4.2 0.7 1.0
N B:VAL590 4.3 93.5 1.0
CA B:VAL590 4.4 84.9 1.0
N B:GLU592 4.5 74.7 1.0
OE2 B:GLU592 4.5 0.2 1.0
OE1 B:GLU592 4.6 0.6 1.0
CB B:GLU592 4.7 76.2 1.0
CB B:VAL590 4.7 82.7 1.0
N B:ASP591 4.8 86.2 1.0
CA B:GLY589 4.9 0.3 1.0

Calcium binding site 7 out of 7 in 5n7d

Go back to Calcium Binding Sites List in 5n7d
Calcium binding site 7 out of 7 in the Magi-1 Complexed with A RSK1 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Magi-1 Complexed with A RSK1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:59.5
occ:1.00
 OD2 B:ASP861 2.1 83.0 1.0
O B:HOH1014 2.4 60.3 1.0
O B:MET817 2.4 57.0 1.0
O B:GLY821 2.4 58.6 1.0
O B:GLY819 2.5 63.4 1.0
CG B:ASP861 3.0 74.8 1.0
OD1 B:ASP861 3.1 76.2 1.0
C B:MET817 3.3 57.4 1.0
C B:GLY821 3.6 64.7 1.0
C B:GLY819 3.7 70.4 1.0
CA B:MET817 3.9 59.5 1.0
N B:GLY821 4.0 72.8 1.0
N B:GLY819 4.1 63.9 1.0
C B:LYS818 4.2 57.0 1.0
OG1 B:THR822 4.2 73.4 1.0
N B:LYS818 4.3 58.8 1.0
C B:LYS820 4.3 73.2 1.0
CA B:GLY821 4.3 66.7 1.0
O B:LYS818 4.4 66.9 1.0
CB B:ASP861 4.4 67.8 1.0
CA B:GLY819 4.5 69.0 1.0
CB B:MET817 4.6 55.3 1.0
N B:LYS820 4.6 72.2 1.0
N B:THR822 4.7 65.8 1.0
CA B:LYS818 4.7 53.6 1.0
CA B:LYS820 4.7 67.8 1.0
O B:LYS820 4.8 81.3 1.0
CA B:THR822 4.8 68.0 1.0

Reference:

G.Gogl, B.Biri-Kovacs, A.L.Poti, H.Vadaszi, B.Szeder, A.Bodor, G.Schlosser, A.Acs, L.Turiak, L.Buday, A.Alexa, L.Nyitray, A.Remenyi. Dynamic Control of Rsk Complexes By Phosphoswitch-Based Regulation. Febs J. V. 285 46 2018.
ISSN: ISSN 1742-4658
PubMed: 29083550
DOI: 10.1111/FEBS.14311
Page generated: Mon Jul 15 08:50:34 2024

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