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Magnesium in PDB 5jda: Bacillus Cereus Coth Kinase Plus MG2+/Amp

Enzymatic activity of Bacillus Cereus Coth Kinase Plus MG2+/Amp

All present enzymatic activity of Bacillus Cereus Coth Kinase Plus MG2+/Amp:
2.7.11.1;

Protein crystallography data

The structure of Bacillus Cereus Coth Kinase Plus MG2+/Amp, PDB code: 5jda was solved by D.R.Tomchick, V.S.Tagliabracci, A.Sreelatha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.28 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.757, 63.516, 118.284, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 18.4

Other elements in 5jda:

The structure of Bacillus Cereus Coth Kinase Plus MG2+/Amp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bacillus Cereus Coth Kinase Plus MG2+/Amp (pdb code 5jda). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Bacillus Cereus Coth Kinase Plus MG2+/Amp, PDB code: 5jda:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5jda

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Magnesium binding site 1 out of 5 in the Bacillus Cereus Coth Kinase Plus MG2+/Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacillus Cereus Coth Kinase Plus MG2+/Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:19.8
occ:1.00
 OD1 A:ASP279 1.9 23.6 1.0
O A:HOH524 2.0 21.1 1.0
O A:HOH560 2.0 19.9 1.0
O A:HOH578 2.1 22.6 1.0
O A:HOH746 2.1 25.3 1.0
CG A:ASP279 3.0 22.2 1.0
OD2 A:ASP279 3.4 23.3 1.0
HA A:ASP279 4.0 22.7 1.0
O A:HOH753 4.2 22.6 1.0
O A:ALA275 4.2 16.4 1.0
CB A:ASP279 4.3 21.2 1.0
O A:LEU278 4.4 26.2 1.0
CA A:ASP279 4.5 18.9 1.0
N A:ASP279 4.6 18.8 1.0
HB1 A:ALA275 4.6 17.7 1.0
C A:LEU278 4.7 23.3 1.0
HB3 A:ASP279 4.8 25.5 1.0
HB2 A:ASP279 4.8 25.5 1.0
HA A:ALA275 4.9 16.8 1.0
H A:ASP279 5.0 22.6 1.0

Magnesium binding site 2 out of 5 in 5jda

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Magnesium binding site 2 out of 5 in the Bacillus Cereus Coth Kinase Plus MG2+/Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacillus Cereus Coth Kinase Plus MG2+/Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:24.6
occ:1.00
 O A:HOH503 2.0 28.1 1.0
O A:HOH665 2.0 39.4 1.0
O A:HOH745 2.1 32.4 1.0
OD2 A:ASP246 2.1 26.5 1.0
O A:HOH538 2.1 26.8 1.0
O A:HOH620 2.3 37.9 1.0
CG A:ASP246 3.0 28.4 1.0
OD1 A:ASP246 3.2 31.4 1.0
HE1 A:HIS48 3.8 23.0 1.0
O A:HOH751 4.0 33.6 1.0
HD21 A:ASN228 4.2 33.2 1.0
OD1 A:ASP248 4.2 18.4 1.0
O A:HOH731 4.2 27.7 1.0
OD1 A:ASN228 4.3 20.7 1.0
O1P A:AMP401 4.4 32.2 1.0
CB A:ASP246 4.4 15.7 1.0
O A:HOH601 4.4 19.3 1.0
O A:HOH635 4.4 25.1 1.0
O A:HOH650 4.5 29.3 1.0
HB3 A:ASP246 4.5 18.8 1.0
HG12 A:VAL255 4.7 24.3 1.0
O A:ASP246 4.7 14.2 1.0
CE1 A:HIS48 4.7 19.1 1.0
ND2 A:ASN228 4.8 27.7 1.0
HB2 A:ASP246 4.9 18.8 1.0
CG A:ASN228 5.0 20.1 1.0

Magnesium binding site 3 out of 5 in 5jda

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Magnesium binding site 3 out of 5 in the Bacillus Cereus Coth Kinase Plus MG2+/Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacillus Cereus Coth Kinase Plus MG2+/Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:29.8
occ:0.48
 O3P A:AMP401 1.9 31.4 1.0
HH12 A:ARG45 1.9 16.4 1.0
O A:HOH731 2.2 27.7 1.0
O A:HOH617 2.2 22.6 1.0
NH1 A:ARG45 2.7 13.6 1.0
HD21 A:ASN76 2.8 15.8 1.0
HH11 A:ARG45 2.9 16.4 1.0
O A:HOH739 3.0 17.5 1.0
HD13 A:ILE49 3.1 16.5 1.0
P A:AMP401 3.1 33.7 1.0
ND2 A:ASN76 3.5 13.1 1.0
O1P A:AMP401 3.5 32.2 1.0
HH22 A:ARG45 3.6 18.8 1.0
HD11 A:ILE49 3.7 16.5 1.0
CZ A:ARG45 3.8 14.6 1.0
CD1 A:ILE49 3.8 13.8 1.0
OD1 A:ASN76 4.0 13.5 1.0
HD22 A:ASN76 4.0 15.8 1.0
O A:HOH702 4.0 17.6 1.0
OD1 A:ASP246 4.0 31.4 1.0
NH2 A:ARG45 4.1 15.6 1.0
O A:HOH538 4.1 26.8 1.0
CG A:ASN76 4.1 13.2 1.0
O5' A:AMP401 4.1 36.1 1.0
HD12 A:ILE49 4.1 16.5 1.0
O2P A:AMP401 4.2 39.0 1.0
CG A:ASP246 4.3 28.4 1.0
HB2 A:ASP246 4.3 18.8 1.0
HG21 A:ILE49 4.5 16.9 1.0
HE1 A:TRP245 4.5 16.5 1.0
HA3 A:GLY46 4.5 17.9 1.0
HA2 A:GLY46 4.6 17.9 1.0
OD2 A:ASP246 4.6 26.5 1.0
O A:HOH603 4.7 18.7 1.0
CB A:ASP246 4.8 15.7 1.0
HG3 A:ARG45 4.9 15.2 1.0
HH21 A:ARG45 4.9 18.8 1.0
HZ2 A:TRP245 4.9 18.4 1.0
HA A:ASP246 5.0 15.3 1.0
NE A:ARG45 5.0 13.1 1.0
O A:HOH687 5.0 17.1 1.0
HD3 A:ARG45 5.0 15.6 1.0

Magnesium binding site 4 out of 5 in 5jda

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Magnesium binding site 4 out of 5 in the Bacillus Cereus Coth Kinase Plus MG2+/Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacillus Cereus Coth Kinase Plus MG2+/Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:25.0
occ:0.49
 HE2 A:HIS233 1.7 26.6 1.0
O A:HOH501 1.8 29.2 1.0
O A:ASN238 2.0 23.8 1.0
OD1 A:ASN238 2.1 36.5 0.5
O A:HOH675 2.3 26.3 1.0
O A:HOH616 2.3 19.1 1.0
HB3 A:ASN238 2.5 38.5 0.5
NE2 A:HIS233 2.5 22.2 1.0
C A:ASN238 2.9 23.6 1.0
CG A:ASN238 3.0 37.6 0.5
HB3 A:ASN238 3.1 38.5 0.5
HA A:ASN238 3.2 30.4 0.5
HD2 A:HIS233 3.2 26.3 1.0
CD2 A:HIS233 3.2 21.9 1.0
CB A:ASN238 3.2 32.1 0.5
HA A:ASN238 3.2 30.3 0.5
CB A:ASN238 3.3 32.1 0.5
CA A:ASN238 3.4 25.2 0.5
CA A:ASN238 3.4 25.3 0.5
O A:HOH504 3.5 24.2 1.0
CE1 A:HIS233 3.6 23.0 1.0
HE1 A:HIS233 3.8 27.6 1.0
HB2 A:ASN238 4.0 38.5 0.5
HA A:PHE203 4.0 23.8 1.0
CG A:ASN238 4.0 38.2 0.5
N A:LEU239 4.0 21.6 1.0
HA A:LEU239 4.1 23.8 1.0
OD1 A:ASN238 4.2 41.4 0.5
OE2 A:GLU183 4.2 27.6 0.5
HB2 A:ASN238 4.3 38.5 0.5
ND2 A:ASN238 4.3 44.4 0.5
HD1 A:PHE203 4.4 25.1 1.0
HG2 A:GLN180 4.4 26.0 1.0
CG A:HIS233 4.5 19.2 1.0
CA A:LEU239 4.6 19.8 1.0
HD21 A:ASN238 4.6 53.3 0.5
ND1 A:HIS233 4.6 21.1 1.0
O A:LYS202 4.6 22.4 1.0
HB3 A:GLN180 4.6 25.4 1.0
HD23 A:LEU239 4.6 25.4 1.0
HD2 A:PHE240 4.7 20.1 1.0
H A:LEU239 4.7 26.0 1.0
N A:ASN238 4.8 23.5 1.0
HE2 A:PHE240 4.9 22.3 1.0
O A:PHE203 4.9 20.2 1.0
CA A:PHE203 4.9 19.9 1.0
HD22 A:ASN238 4.9 53.3 0.5

Magnesium binding site 5 out of 5 in 5jda

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Magnesium binding site 5 out of 5 in the Bacillus Cereus Coth Kinase Plus MG2+/Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bacillus Cereus Coth Kinase Plus MG2+/Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:43.3
occ:1.00
 O A:HOH530 2.0 25.7 1.0
O A:PHE61 2.0 20.6 1.0
O A:HOH695 2.2 31.6 1.0
O A:HOH634 2.3 30.8 1.0
O A:HOH680 2.3 32.2 1.0
HA A:TYR62 3.1 22.0 1.0
C A:PHE61 3.2 17.9 1.0
HB2 A:LYS71 3.8 24.6 1.0
CA A:TYR62 3.9 18.3 1.0
HA A:LYS65 4.0 26.8 1.0
N A:TYR62 4.0 16.4 1.0
O A:HOH526 4.2 30.1 1.0
O A:LYS65 4.3 23.5 1.0
CA A:PHE61 4.3 15.3 1.0
O A:LYS71 4.4 16.0 1.0
H A:PHE61 4.4 18.2 1.0
N A:PHE61 4.4 15.2 1.0
HD1 A:TYR62 4.4 27.1 1.0
HB3 A:LYS65 4.5 31.4 1.0
HB2 A:PHE61 4.5 20.0 1.0
O A:TYR62 4.5 20.6 1.0
HB3 A:MET60 4.6 20.2 1.0
C A:TYR62 4.7 18.7 1.0
HD2 A:LYS71 4.7 33.5 1.0
CA A:LYS65 4.8 22.4 1.0
CB A:LYS71 4.8 20.5 1.0
HG2 A:LYS65 4.8 38.4 1.0
H A:TYR62 4.9 19.6 1.0
CB A:PHE61 4.9 16.7 1.0
HB2 A:TYR62 4.9 24.6 1.0
C A:MET60 5.0 14.8 1.0
C A:LYS65 5.0 20.9 1.0

Reference:

K.B.Nguyen, A.Sreelatha, E.S.Durrant, J.Lopez-Garrido, A.Muszewska, M.Dudkiewicz, M.Grynberg, S.Yee, K.Pogliano, D.R.Tomchick, K.Pawowski, J.E.Dixon, V.S.Tagliabracci. Phosphorylation of Spore Coat Proteins By A Family of Atypical Protein Kinases. Proc.Natl.Acad.Sci.Usa V. 113 E3482 2016.
ISSN: ESSN 1091-6490
PubMed: 27185916
DOI: 10.1073/PNAS.1605917113
Page generated: Sun Sep 29 17:44:08 2024

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