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Magnesium in PDB 5c1o: Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis

Enzymatic activity of Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis

All present enzymatic activity of Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5c1o was solved by H.T.Tran, L.W.Kang, M.K.Hong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.69 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.029, 106.795, 212.012, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.3

Other elements in 5c1o:

The structure of Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis also contains other interesting chemical elements:

Sodium (Na) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis (pdb code 5c1o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis, PDB code: 5c1o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5c1o

Go back to Magnesium Binding Sites List in 5c1o
Magnesium binding site 1 out of 4 in the Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:77.0
occ:1.00
 O1B A:ANP401 2.2 80.0 1.0
O1A A:ANP401 2.2 83.8 1.0
O2G A:ANP401 2.2 0.7 1.0
O1G A:ANP401 2.2 0.1 1.0
OE1 A:GLU270 2.3 69.5 1.0
PG A:ANP401 2.7 0.9 1.0
CD A:GLU270 3.1 72.1 1.0
OE2 A:GLU270 3.1 82.3 1.0
PB A:ANP401 3.1 93.2 1.0
N3B A:ANP401 3.2 98.0 1.0
PA A:ANP401 3.5 74.1 1.0
O3A A:ANP401 3.7 86.7 1.0
NZ A:LYS97 3.8 93.8 1.0
O3G A:ANP401 4.2 0.1 1.0
C5' A:ANP401 4.3 58.4 1.0
O5' A:ANP401 4.4 70.5 1.0
O2B A:ANP401 4.5 89.9 1.0
CE A:LYS97 4.6 91.2 1.0
CG A:GLU270 4.6 65.2 1.0
O2A A:ANP401 4.7 70.7 1.0

Magnesium binding site 2 out of 4 in 5c1o

Go back to Magnesium Binding Sites List in 5c1o
Magnesium binding site 2 out of 4 in the Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:88.0
occ:1.00
 OE1 B:GLU270 2.2 78.4 1.0
O2G B:ANP401 2.2 85.5 1.0
O2B B:ANP401 2.2 92.7 1.0
OE1 B:GLU148 2.2 0.9 1.0
OE2 B:GLU148 2.2 81.8 1.0
O2A B:ANP401 2.2 87.0 1.0
OE2 B:GLU270 2.2 76.2 1.0
CD B:GLU270 2.5 68.7 1.0
CD B:GLU148 2.6 89.2 1.0
PG B:ANP401 3.3 91.2 1.0
NZ B:LYS97 3.5 81.4 1.0
PB B:ANP401 3.5 97.3 1.0
O1G B:ANP401 3.5 87.0 1.0
PA B:ANP401 3.6 78.7 1.0
N3B B:ANP401 3.9 89.6 1.0
O3A B:ANP401 4.0 78.1 1.0
CG B:GLU270 4.1 58.4 1.0
CG B:GLU148 4.1 79.8 1.0
O3G B:ANP401 4.6 97.4 1.0
O5' B:ANP401 4.6 68.9 1.0
O1A B:ANP401 4.6 61.8 1.0
CE B:LYS97 4.8 75.7 1.0
CB B:GLU270 4.8 45.4 1.0
O1B B:ANP401 4.8 0.9 1.0
C5' B:ANP401 4.8 63.5 1.0
CB B:GLU148 5.0 75.6 1.0

Magnesium binding site 3 out of 4 in 5c1o

Go back to Magnesium Binding Sites List in 5c1o
Magnesium binding site 3 out of 4 in the Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


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 Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:63.8
occ:1.00
 O2G C:ANP401 1.8 69.0 1.0
OE2 C:GLU148 2.2 71.8 1.0
O2A C:ANP401 2.2 67.4 1.0
O2B C:ANP401 2.2 66.3 1.0
OE2 C:GLU270 2.2 72.4 1.0
OE1 C:GLU270 2.2 64.2 1.0
CD C:GLU270 2.6 59.1 1.0
CD C:GLU148 3.0 73.0 1.0
PG C:ANP401 3.2 78.8 1.0
OE1 C:GLU148 3.4 74.0 1.0
PA C:ANP401 3.5 56.8 1.0
PB C:ANP401 3.6 72.0 1.0
O1G C:ANP401 3.7 68.0 1.0
N3B C:ANP401 3.9 68.9 1.0
CG C:GLU270 4.1 51.4 1.0
O3A C:ANP401 4.1 53.7 1.0
CG C:GLU148 4.2 73.6 1.0
O3G C:ANP401 4.3 77.0 1.0
O1A C:ANP401 4.4 55.9 1.0
O5' C:ANP401 4.5 55.6 1.0
CE C:LYS97 4.6 63.7 1.0
C5' C:ANP401 4.8 43.4 1.0
NZ C:LYS215 4.8 71.8 1.0
CB C:GLU270 4.9 45.6 1.0
O1B C:ANP401 4.9 61.3 1.0

Magnesium binding site 4 out of 4 in 5c1o

Go back to Magnesium Binding Sites List in 5c1o
Magnesium binding site 4 out of 4 in the Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Amp-Pnp Complexed D-Alanine-D-Alanine Ligase(Ddl) From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:76.4
occ:1.00
 OE2 D:GLU270 2.2 72.0 1.0
O1G D:ANP401 2.2 74.0 1.0
O1B D:ANP401 2.2 73.9 1.0
OE1 D:GLU270 2.2 74.0 1.0
OE1 D:GLU148 2.2 89.9 1.0
O1A D:ANP401 2.2 78.1 1.0
CD D:GLU270 2.5 62.9 1.0
CD D:GLU148 3.3 0.5 1.0
PG D:ANP401 3.4 86.2 1.0
PB D:ANP401 3.5 80.3 1.0
PA D:ANP401 3.6 74.0 1.0
OE2 D:GLU148 3.8 98.3 1.0
O2G D:ANP401 3.8 75.3 1.0
N3B D:ANP401 3.9 73.2 1.0
CG D:GLU270 4.0 56.6 1.0
O3A D:ANP401 4.0 72.1 1.0
CE D:LYS97 4.3 66.4 1.0
NZ D:LYS97 4.4 71.2 1.0
CG D:GLU148 4.4 1.0 1.0
O2A D:ANP401 4.6 56.1 1.0
O3G D:ANP401 4.6 82.3 1.0
O5' D:ANP401 4.7 71.1 1.0
CB D:GLU270 4.7 54.9 1.0
O2B D:ANP401 4.7 75.4 1.0
C5' D:ANP401 4.9 70.0 1.0

Reference:

H.T.Tran, M.K.Hong, H.P.Ngo, K.H.Huynh, Y.J.Ahn, Z.Wang, L.W.Kang. Structure of D-Alanine-D-Alanine Ligase From Yersinia Pestis: Nucleotide Phosphate Recognition By the Serine Loop. Acta Crystallogr D Struct V. 72 12 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894530
DOI: 10.1107/S2059798315021671
Page generated: Sun Sep 29 01:52:01 2024

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