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Sodium in PDB 5vfb: 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid.

Enzymatic activity of 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid.

All present enzymatic activity of 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid.:
2.3.3.9;

Protein crystallography data

The structure of 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid., PDB code: 5vfb was solved by G.Minasov, L.Shuvalova, I.Dubrovska, O.Kiryukhina, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.62 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.385, 111.712, 96.954, 90.00, 100.42, 90.00
R / Rfree (%) 14.3 / 16.8

Other elements in 5vfb:

The structure of 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid. also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid. (pdb code 5vfb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid., PDB code: 5vfb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5vfb

Go back to Sodium Binding Sites List in 5vfb
Sodium binding site 1 out of 2 in the 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:26.0
occ:1.00
 O B:HOH1063 2.2 23.0 1.0
O B:HOH1447 2.3 17.4 0.5
O B:HOH1454 3.7 12.0 0.5
O B:GLN670 4.1 11.2 1.0
O B:HOH1454 4.2 11.4 0.5
O B:HOH994 4.5 14.7 1.0
O B:HOH1843 4.6 23.6 1.0
O B:HOH1995 4.8 45.4 1.0
O B:HOH1760 4.9 29.7 1.0
C B:GLN670 4.9 10.8 1.0
CA B:GLN670 4.9 11.3 1.0

Sodium binding site 2 out of 2 in 5vfb

Go back to Sodium Binding Sites List in 5vfb
Sodium binding site 2 out of 2 in the 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:28.4
occ:1.00
 O B:HOH931 2.4 31.9 1.0
O A:HOH2007 2.4 36.5 1.0
O B:HOH1972 2.5 29.3 1.0
O B:HOH1537 2.5 31.6 1.0
O B:HOH1970 2.5 25.0 1.0
O B:HOH1745 2.5 27.7 0.5
O B:HOH1588 3.4 16.5 0.3
OE1 B:GLU178 3.7 22.3 1.0
O B:HOH1673 4.0 29.3 1.0
O B:HOH1875 4.3 24.0 0.6
O A:HOH1660 4.3 22.6 0.7
O B:HOH1875 4.3 18.2 0.4
O B:HOH1805 4.5 31.5 1.0
O B:HOH1519 4.5 27.1 1.0
O B:HOH1567 4.5 17.7 1.0
OE2 B:GLU178 4.6 19.5 1.0
CD B:GLU178 4.6 17.7 1.0
O B:HOH1588 4.6 29.8 0.7
O B:HOH1918 4.7 27.2 1.0
O B:HOH1852 4.8 40.6 1.0
NZ B:LYS555 4.9 20.2 1.0

Reference:

G.Minasov, L.Shuvalova, I.Dubrovska, O.Kiryukhina, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G From Pseudomonas Aeruginosa in Complex with Glycolic Acid. To Be Published.
Page generated: Tue Oct 8 00:48:03 2024

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