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Magnesium in PDB 3q1k: The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp

Enzymatic activity of The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp

All present enzymatic activity of The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp:
6.3.2.4;

Protein crystallography data

The structure of The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp, PDB code: 3q1k was solved by R.Zhang, N.Maltseva, L.Papazisi, W.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.54 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.153, 85.813, 230.893, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp (pdb code 3q1k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp, PDB code: 3q1k:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3q1k

Go back to Magnesium Binding Sites List in 3q1k
Magnesium binding site 1 out of 3 in the The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg372

b:35.3
occ:1.00
 O1B A:ADP370 2.2 44.6 1.0
O A:HOH494 2.3 38.4 1.0
O A:HOH495 2.3 49.5 1.0
O1A A:ADP370 2.4 46.4 1.0
O A:HOH493 2.5 53.4 1.0
OE2 A:GLU315 2.8 79.6 1.0
O A:HOH481 3.3 70.2 1.0
PB A:ADP370 3.4 48.4 1.0
CD A:GLU315 3.6 81.6 1.0
PA A:ADP370 3.7 47.1 1.0
O3B A:ADP370 3.8 53.4 1.0
O3A A:ADP370 3.9 58.9 1.0
OE1 A:GLU315 4.1 88.5 1.0
OD2 A:ASP302 4.2 51.1 1.0
C5' A:ADP370 4.3 53.0 1.0
O3' A:ADP370 4.4 43.2 1.0
O5' A:ADP370 4.5 54.1 1.0
ND2 A:ASN314 4.6 40.7 1.0
CB A:GLU315 4.6 46.0 1.0
CG A:GLU315 4.7 68.2 1.0
O2B A:ADP370 4.7 58.3 1.0
O2A A:ADP370 4.9 52.5 1.0
C3' A:ADP370 5.0 49.4 1.0

Magnesium binding site 2 out of 3 in 3q1k

Go back to Magnesium Binding Sites List in 3q1k
Magnesium binding site 2 out of 3 in the The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg371

b:86.0
occ:1.00
 O1A B:ADP370 2.4 60.8 1.0
OE1 B:GLU315 2.7 70.2 1.0
O3B B:ADP370 2.9 0.9 1.0
CD B:GLU315 3.2 71.3 1.0
OD2 B:ASP302 3.4 58.4 1.0
OE2 B:GLU315 3.8 76.5 1.0
PA B:ADP370 3.8 58.1 1.0
O3' B:ADP370 3.9 66.7 1.0
PB B:ADP370 3.9 0.6 1.0
CG B:GLU315 4.1 57.2 1.0
O2B B:ADP370 4.1 0.1 1.0
ND2 B:ASN314 4.1 50.1 1.0
O3A B:ADP370 4.2 0.7 1.0
CG B:ASP302 4.5 48.5 1.0
NH2 B:ARG300 4.5 40.0 1.0
C3' B:ADP370 4.7 60.7 1.0
O2A B:ADP370 4.7 66.2 1.0
O5' B:ADP370 4.8 59.2 1.0
C5' B:ADP370 4.8 50.1 1.0
CB B:ASP302 4.9 34.5 1.0

Magnesium binding site 3 out of 3 in 3q1k

Go back to Magnesium Binding Sites List in 3q1k
Magnesium binding site 3 out of 3 in the The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg372

b:36.9
occ:1.00
 O1B D:ADP370 2.1 47.0 1.0
O1A D:ADP370 2.4 42.8 1.0
O D:HOH470 2.4 54.6 1.0
O D:HOH472 2.5 40.1 1.0
OE1 D:GLU315 2.5 66.0 1.0
O D:HOH471 2.6 66.9 1.0
CD D:GLU315 3.3 69.7 1.0
PB D:ADP370 3.4 61.0 1.0
OE2 D:GLU315 3.6 72.6 1.0
PA D:ADP370 3.6 47.1 1.0
O3A D:ADP370 3.9 54.9 1.0
O3B D:ADP370 4.0 51.3 1.0
O3' D:ADP370 4.1 40.7 1.0
C5' D:ADP370 4.2 43.3 1.0
OD2 D:ASP302 4.3 54.8 1.0
O5' D:ADP370 4.4 46.4 1.0
ND2 D:ASN314 4.4 46.8 1.0
O2B D:ADP370 4.6 60.3 1.0
CG D:GLU315 4.6 59.8 1.0
CB D:GLU315 4.7 41.1 1.0
C3' D:ADP370 4.8 44.1 1.0
OE2 D:GLU228 4.9 50.5 1.0
O2A D:ADP370 4.9 53.8 1.0

Reference:

R.Zhang, N.Maltseva, L.Papazisi, W.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). The Crystal Structure of the D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed with Adp To Be Published.
Page generated: Mon Dec 14 08:41:15 2020

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