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Nickel 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:

Chlorine (Cl) 10 atoms
Sodium (Na) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel 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 Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5vfb

Go back to Nickel Binding Sites List in 5vfb
Nickel 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 Nickel with other atoms in the Ni 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
A:Ni801

b:7.2
occ:1.00
 O2 A:GOA807 2.0 8.8 1.0
OD2 A:ASP460 2.1 5.7 1.0
O A:HOH976 2.1 9.1 1.0
O11 A:GOA807 2.1 6.3 1.0
O A:HOH1054 2.1 7.2 1.0
OE2 A:GLU432 2.1 5.2 1.0
C1 A:GOA807 2.9 7.5 1.0
C2 A:GOA807 2.9 8.0 1.0
CG A:ASP460 3.1 5.3 1.0
CD A:GLU432 3.1 4.7 1.0
OE1 A:GLU432 3.5 4.9 1.0
CB A:ASP460 3.6 5.1 1.0
NH1 A:ARG340 3.9 7.4 1.0
O12 A:GOA807 4.1 7.3 1.0
O A:HOH1447 4.1 14.8 1.0
NZ A:LYS397 4.1 6.5 1.0
OD2 A:ASP275 4.1 9.3 1.0
OD1 A:ASP460 4.2 5.9 1.0
CB A:ALA633 4.4 6.5 1.0
CG A:GLU432 4.4 4.6 1.0
OE1 A:GLU274 4.5 6.8 1.0
N A:ASP460 4.6 5.0 1.0
CA A:ASP460 4.7 5.0 1.0
CB A:GLU432 4.7 4.7 1.0
CE A:MET430 4.8 6.1 1.0
CG A:ASP275 4.9 8.7 1.0
CZ A:ARG340 4.9 7.1 1.0
CA A:GLY457 5.0 4.8 1.0

Nickel binding site 2 out of 2 in 5vfb

Go back to Nickel Binding Sites List in 5vfb
Nickel 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 Nickel with other atoms in the Ni 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:Ni801

b:7.4
occ:1.00
 O2 B:GOA809 2.0 6.6 0.8
OD2 B:ASP460 2.1 6.0 1.0
OE2 B:GLU432 2.1 5.7 1.0
O B:HOH954 2.1 10.0 1.0
O11 B:GOA809 2.1 5.4 0.8
O B:HOH1093 2.1 6.8 1.0
O11 B:GOA809 2.2 11.3 0.2
C1 B:GOA809 2.9 6.2 0.8
C2 B:GOA809 2.9 6.7 0.8
C1 B:GOA809 3.1 11.7 0.2
CD B:GLU432 3.1 4.9 1.0
CG B:ASP460 3.1 5.4 1.0
C2 B:GOA809 3.3 12.2 0.2
OE1 B:GLU432 3.5 5.0 1.0
CB B:ASP460 3.5 5.1 1.0
NH1 B:ARG340 3.9 7.1 1.0
O12 B:GOA809 4.1 6.2 0.8
OD2 B:ASP275 4.1 9.0 1.0
NZ B:LYS397 4.1 6.8 1.0
O2 B:GOA809 4.2 12.5 0.2
O B:HOH920 4.2 18.2 1.0
OD1 B:ASP460 4.2 5.9 1.0
O12 B:GOA809 4.2 11.7 0.2
CB B:ALA633 4.4 6.8 1.0
CG B:GLU432 4.4 4.7 1.0
OE1 B:GLU274 4.5 7.8 1.0
N B:ASP460 4.5 5.0 1.0
CA B:ASP460 4.7 5.0 1.0
CB B:GLU432 4.7 4.6 1.0
CE B:MET430 4.7 6.0 1.0
CZ B:ARG340 4.9 6.8 1.0
CG B:ASP275 4.9 8.0 1.0
CA B:GLY457 4.9 5.0 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: Wed Dec 16 01:49:21 2020

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