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Calcium in PDB 4c08: Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms

Enzymatic activity of Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms

All present enzymatic activity of Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms:
2.1.1.125;

Protein crystallography data

The structure of Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms, PDB code: 4c08 was solved by L.Bonnefond, V.Cura, N.Troffer-Charlier, J.Mailliot, J.M.Wurtz, J.Cavarelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.983 / 1.34
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 79.325, 79.325, 118.411, 90.00, 90.00, 90.00
R / Rfree (%) 14.05 / 16.42

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms (pdb code 4c08). 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 M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms, PDB code: 4c08:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4c08

Go back to Calcium Binding Sites List in 4c08
Calcium binding site 1 out of 6 in the Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms


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 M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1379

b:22.3
occ:0.47
 CA A:CA1379 0.0 22.3 0.5
CA A:CA1379 1.6 23.0 0.5
O A:HOH2125 2.1 34.3 1.0
O A:HOH2126 2.1 22.9 0.9
O A:HOH2129 2.2 36.8 1.0
O A:MET160 2.5 16.4 1.0
OE1 A:GLU158 2.5 21.0 1.0
OE2 A:GLU158 2.9 21.8 1.0
CD A:GLU158 3.0 20.1 1.0
O A:HOH2019 3.0 40.5 1.0
HZ2 A:TRP321 3.3 20.7 1.0
HE1 A:TRP321 3.4 20.2 1.0
C A:MET160 3.6 14.5 1.0
O A:HOH2028 3.7 26.1 0.8
O A:HOH2061 3.8 41.2 1.0
H A:MET160 3.9 17.7 1.0
HE2 A:HIS320 3.9 23.8 1.0
N A:MET160 3.9 14.8 1.0
CZ2 A:TRP321 4.0 17.2 1.0
O A:GLU158 4.1 18.7 1.0
NE1 A:TRP321 4.1 16.9 1.0
HA2 A:GLY161 4.1 18.9 1.0
C A:TRP159 4.3 14.8 1.0
O A:HOH2139 4.3 33.4 0.8
CA A:MET160 4.3 14.3 1.0
HB2 A:MET160 4.4 17.0 1.0
CE2 A:TRP321 4.4 15.8 1.0
C A:GLU158 4.5 15.7 1.0
CG A:GLU158 4.5 17.9 1.0
N A:GLY161 4.6 15.2 1.0
SD A:MET63 4.6 31.6 1.0
HE A:ARG69 4.7 27.0 1.0
HA A:TRP159 4.7 18.2 1.0
NE2 A:HIS320 4.7 19.9 1.0
O A:TRP159 4.7 16.0 1.0
HH21 A:ARG69 4.7 29.6 1.0
N A:TRP159 4.8 14.4 1.0
HE1 A:HIS320 4.8 22.8 1.0
CA A:GLY161 4.8 15.8 1.0
CA A:TRP159 4.8 15.1 1.0
HB3 A:GLU158 4.8 20.4 1.0
HG2 A:GLU158 4.9 21.4 1.0
CB A:MET160 4.9 14.2 1.0
HG3 A:GLU158 5.0 21.4 1.0

Calcium binding site 2 out of 6 in 4c08

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Calcium binding site 2 out of 6 in the Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms


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 M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1379

b:23.0
occ:0.53
 CA A:CA1379 0.0 23.0 0.5
CA A:CA1379 1.6 22.3 0.5
O A:HOH2019 2.3 40.5 1.0
OE2 A:GLU158 2.3 21.8 1.0
O A:HOH2028 2.5 26.1 0.8
O A:HOH2126 2.5 22.9 0.9
O A:HOH2125 2.7 34.3 1.0
CD A:GLU158 2.9 20.1 1.0
OE1 A:GLU158 2.9 21.0 1.0
O A:HOH2129 3.0 36.8 1.0
SD A:MET63 3.3 31.6 1.0
HH21 A:ARG69 3.5 29.6 1.0
HE A:ARG69 3.9 27.0 1.0
O A:GLU158 3.9 18.7 1.0
HE2 A:HIS320 4.0 23.8 1.0
O A:MET160 4.0 16.4 1.0
HZ2 A:TRP321 4.1 20.7 1.0
HB3 A:GLU158 4.2 20.4 1.0
CG A:GLU158 4.2 17.9 1.0
NH2 A:ARG69 4.3 24.7 1.0
HE2 A:MET63 4.4 37.3 1.0
HG2 A:MET63 4.4 30.9 1.0
CE A:MET63 4.5 31.1 1.0
HG3 A:GLU158 4.5 21.4 1.0
C A:GLU158 4.6 15.7 1.0
CG A:MET63 4.6 25.7 1.0
NE A:ARG69 4.6 22.5 1.0
O A:HOH2061 4.7 41.2 1.0
CB A:GLU158 4.7 17.0 1.0
HE1 A:TRP321 4.7 20.2 1.0
NE2 A:HIS320 4.7 19.9 1.0
HE1 A:HIS320 4.7 22.8 1.0
CZ2 A:TRP321 4.8 17.2 1.0
HH22 A:ARG69 4.8 29.6 1.0
O A:HOH2139 4.9 33.4 0.8
HE1 A:MET63 4.9 37.3 1.0
HG2 A:GLU158 4.9 21.4 1.0
O A:HOH2053 4.9 30.2 0.7
H A:MET160 5.0 17.7 1.0
CZ A:ARG69 5.0 23.0 1.0

Calcium binding site 3 out of 6 in 4c08

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Calcium binding site 3 out of 6 in the Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms


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 M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1380

b:32.1
occ:1.00
 O A:GLY275 2.3 21.4 1.0
O A:HOH2241 2.3 44.3 1.0
O A:HOH2242 2.4 45.8 1.0
O A:HOH2228 2.5 33.0 1.0
O A:HOH2236 2.5 33.2 1.0
H A:GLY275 3.4 25.0 1.0
C A:GLY275 3.5 20.1 1.0
HA2 A:GLY276 4.0 24.0 1.0
N A:GLY275 4.2 20.8 1.0
O A:HOH2240 4.2 42.6 1.0
HA3 A:GLY276 4.2 24.0 1.0
OE2 A:GLU269 4.3 45.2 1.0
CA A:GLY275 4.4 22.7 1.0
N A:GLY276 4.4 18.9 1.0
CA A:GLY276 4.4 20.0 1.0
O A:HOH2230 4.5 30.2 1.0
HB3 A:ALA257 4.6 25.7 1.0
O A:PHE256 4.7 20.8 1.0
O A:HOH2293 4.9 54.4 1.0
HA A:ALA257 5.0 22.6 1.0
HA A:VAL274 5.0 23.6 1.0
HA2 A:GLY275 5.0 27.2 1.0

Calcium binding site 4 out of 6 in 4c08

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Calcium binding site 4 out of 6 in the Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms


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 M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1381

b:38.8
occ:1.00
 O A:HOH2224 2.3 46.1 1.0
O A:HOH2225 2.4 50.1 1.0
O A:HOH2223 2.4 38.0 1.0
O A:ARG255 2.4 20.7 1.0
O A:HOH2226 2.6 24.0 0.9
O A:HOH2229 2.6 31.6 1.0
HA A:PHE256 3.1 21.4 1.0
C A:ARG255 3.6 17.4 1.0
CA A:PHE256 4.0 17.8 1.0
O A:ARG277 4.2 21.7 1.0
O A:HOH2227 4.2 38.8 1.0
N A:PHE256 4.3 17.1 1.0
O A:HOH2219 4.3 30.0 1.0
HB3 A:ARG255 4.3 23.8 1.0
C A:PHE256 4.6 18.4 1.0
HG2 A:ARG255 4.7 27.9 1.0
CA A:ARG255 4.8 17.3 1.0
O A:HOH2220 4.8 22.0 0.9
O A:PHE256 4.8 20.8 1.0
H A:ARG255 4.9 20.9 1.0
HE A:ARG255 4.9 47.1 1.0
HB3 A:PHE256 5.0 21.6 1.0
CB A:ARG255 5.0 19.9 1.0
CB A:PHE256 5.0 18.0 1.0

Calcium binding site 5 out of 6 in 4c08

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Calcium binding site 5 out of 6 in the Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms


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 M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1382

b:41.2
occ:1.00
 O A:HOH2141 2.0 36.3 1.0
O A:HOH2137 2.3 39.4 1.0
OE2 A:GLU167 2.3 34.5 1.0
O A:HOH2143 2.4 41.2 1.0
O A:HOH2144 2.6 49.5 1.0
CD A:GLU167 3.3 30.5 1.0
HE2 A:HIS166 3.5 22.9 1.0
OE1 A:GLU167 3.7 32.0 1.0
O A:HOH2142 4.1 42.2 1.0
NE2 A:HIS166 4.3 19.1 1.0
HE1 A:HIS166 4.5 21.6 1.0
CG A:GLU167 4.7 24.0 1.0
O A:HOH2064 4.8 37.0 0.8
HG3 A:GLU167 4.8 28.8 1.0
CE1 A:HIS166 4.8 18.0 1.0
HG2 A:GLU167 4.9 28.8 1.0

Calcium binding site 6 out of 6 in 4c08

Go back to Calcium Binding Sites List in 4c08
Calcium binding site 6 out of 6 in the Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms


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 M. Musculus Protein Arginine Methyltransferase PRMT6 with CACL2 at 1.34 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1383

b:46.9
occ:1.00
 OD1 A:ASP243 2.3 37.0 1.0
O A:HOH2203 2.4 44.1 1.0
O A:HOH2199 2.4 44.4 1.0
OE1 A:GLN242 2.6 44.1 1.0
O A:HOH2200 2.7 37.5 1.0
CG A:ASP243 3.4 34.3 1.0
HE22 A:GLN242 3.5 59.8 1.0
H A:ASP243 3.6 22.8 1.0
CD A:GLN242 3.6 43.2 1.0
HZ3 A:LYS322 3.7 41.7 1.0
OD2 A:ASP243 3.8 39.3 1.0
NE2 A:GLN242 3.9 49.8 1.0
N A:ASP243 4.4 19.0 1.0
HD3 A:LYS322 4.6 30.4 1.0
NZ A:LYS322 4.6 34.8 1.0
O A:ASP243 4.6 24.0 1.0
CB A:ASP243 4.6 25.5 1.0
HA A:GLN242 4.6 24.5 1.0
HE21 A:GLN242 4.8 59.8 1.0
HZ2 A:LYS322 4.8 41.7 1.0
HB3 A:ASP243 4.8 30.6 1.0
HE3 A:LYS322 4.9 36.6 1.0
CG A:GLN242 4.9 36.8 1.0
O A:HOH2202 4.9 50.4 1.0
HG3 A:GLN242 4.9 44.2 1.0
CA A:ASP243 5.0 19.4 1.0

Reference:

L.Bonnefond, V.Cura, N.Troffer-Charlier, J.Mailliot, J.M.Wurtz, J.Cavarelli. Crystal Structure of M. Musculus Protein Arginine Methyltransferase PRMT6 To Be Published.
Page generated: Sat Jul 13 22:54:23 2024

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