Magnesium in PDB 5jmv: Crystal Structure of MJKAE1-PFUPCC1 Complex

Enzymatic activity of Crystal Structure of MJKAE1-PFUPCC1 Complex

All present enzymatic activity of Crystal Structure of MJKAE1-PFUPCC1 Complex:
2.3.1.234; 2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of MJKAE1-PFUPCC1 Complex, PDB code: 5jmv was solved by L.Wan, F.Sicheri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.24 / 3.39
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.913, 121.913, 310.613, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of MJKAE1-PFUPCC1 Complex (pdb code 5jmv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of MJKAE1-PFUPCC1 Complex, PDB code: 5jmv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5jmv

Go back to Magnesium Binding Sites List in 5jmv
Magnesium binding site 1 out of 3 in the Crystal Structure of MJKAE1-PFUPCC1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of MJKAE1-PFUPCC1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:38.1
occ:1.00
OD1 A:ASP284 2.0 81.2 1.0
OH A:TYR127 2.2 57.0 1.0
NE2 A:HIS110 2.4 58.5 1.0
NE2 A:HIS106 2.5 67.0 1.0
CG A:ASP284 3.1 82.9 1.0
CE1 A:HIS110 3.2 66.6 1.0
CD2 A:HIS110 3.3 52.1 1.0
O2P A:AMP401 3.3 59.9 1.0
CE1 A:HIS106 3.4 55.4 1.0
CZ A:TYR127 3.4 51.5 1.0
CD2 A:HIS106 3.5 70.1 1.0
OD2 A:ASP284 3.6 83.0 1.0
OG A:SER129 3.7 80.5 1.0
CE1 A:TYR127 3.9 38.0 1.0
CB A:SER129 4.2 73.0 1.0
ND1 A:HIS110 4.3 60.0 1.0
CG A:HIS110 4.4 58.2 1.0
CB A:ASP284 4.4 78.0 1.0
N A:ASP284 4.5 51.6 1.0
ND1 A:HIS106 4.5 56.9 1.0
CA A:ASP284 4.5 58.3 1.0
P A:AMP401 4.5 87.2 1.0
CE2 A:TYR127 4.6 58.9 1.0
CG A:HIS106 4.6 60.2 1.0
O3P A:AMP401 4.8 92.9 1.0
CE A:MET288 4.9 53.5 1.0
ND2 A:ASN132 5.0 61.0 1.0

Magnesium binding site 2 out of 3 in 5jmv

Go back to Magnesium Binding Sites List in 5jmv
Magnesium binding site 2 out of 3 in the Crystal Structure of MJKAE1-PFUPCC1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of MJKAE1-PFUPCC1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:36.4
occ:1.00
OD1 B:ASP284 2.1 80.0 1.0
OH B:TYR127 2.4 32.6 1.0
NE2 B:HIS110 2.6 68.5 1.0
NE2 B:HIS106 2.9 64.4 1.0
CG B:ASP284 3.1 78.8 1.0
CE1 B:HIS110 3.3 68.5 1.0
OG B:SER129 3.3 67.1 1.0
OD2 B:ASP284 3.5 75.9 1.0
CZ B:TYR127 3.5 42.1 1.0
CD2 B:HIS110 3.6 62.9 1.0
O2P B:AMP401 3.6 78.1 1.0
CE1 B:TYR127 3.7 44.9 1.0
CB B:SER129 3.7 63.9 1.0
CE1 B:HIS106 3.8 55.9 1.0
O3P B:AMP401 3.9 98.3 1.0
CD2 B:HIS106 3.9 63.5 1.0
P B:AMP401 4.1 95.5 1.0
N B:ASP284 4.3 56.0 1.0
ND1 B:HIS110 4.4 62.2 1.0
CB B:ASP284 4.4 74.9 1.0
CA B:ASP284 4.5 62.0 1.0
CG B:HIS110 4.6 55.2 1.0
O1P B:AMP401 4.6 92.2 1.0
CE2 B:TYR127 4.7 43.8 1.0
CA B:SER129 4.9 65.0 1.0
C B:GLY283 5.0 62.8 1.0
ND1 B:HIS106 5.0 53.5 1.0

Magnesium binding site 3 out of 3 in 5jmv

Go back to Magnesium Binding Sites List in 5jmv
Magnesium binding site 3 out of 3 in the Crystal Structure of MJKAE1-PFUPCC1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of MJKAE1-PFUPCC1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:18.5
occ:1.00
OD1 C:ASP284 2.2 92.1 1.0
NE2 C:HIS106 2.4 61.2 1.0
NE2 C:HIS110 2.4 46.5 1.0
OH C:TYR127 2.5 54.4 1.0
CE1 C:HIS106 3.3 58.4 1.0
CG C:ASP284 3.3 86.0 1.0
CE1 C:HIS110 3.3 53.6 1.0
CD2 C:HIS110 3.3 46.2 1.0
OG C:SER129 3.4 81.7 1.0
CD2 C:HIS106 3.4 67.9 1.0
CZ C:TYR127 3.6 60.9 1.0
O2P C:AMP401 3.7 57.6 1.0
OD2 C:ASP284 3.7 99.2 1.0
CE1 C:TYR127 4.0 61.7 1.0
CB C:SER129 4.0 61.5 1.0
P C:AMP401 4.3 71.0 1.0
O1P C:AMP401 4.3 78.0 1.0
ND1 C:HIS110 4.3 49.4 1.0
CG C:HIS110 4.4 48.2 1.0
ND1 C:HIS106 4.4 61.2 1.0
CG C:HIS106 4.5 67.6 1.0
CB C:ASP284 4.5 61.5 1.0
O3P C:AMP401 4.7 66.7 1.0
N C:ASP284 4.7 57.2 1.0
CA C:ASP284 4.7 51.5 1.0
CE2 C:TYR127 4.8 52.8 1.0
CE C:MET288 4.9 80.5 1.0
ND2 C:ASN132 5.0 0.5 1.0

Reference:

L.C.Wan, M.C.Pillon, N.Thevakumaran, Y.Sun, A.Chakrabartty, A.Guarne, I.Kurinov, D.Durocher, F.Sicheri. Structural and Functional Characterization of Keops Dimerization By PCC1 and Its Role in T6A Biosynthesis. Nucleic Acids Res. V. 44 6971 2016.
ISSN: ESSN 1362-4962
PubMed: 27302132
DOI: 10.1093/NAR/GKW542
Page generated: Mon Dec 14 20:34:18 2020

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