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Zinc in PDB 4mca: Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A

Enzymatic activity of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A

All present enzymatic activity of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A:
1.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A, PDB code: 4mca was solved by P.M.Musille, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.60 / 1.90
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 117.507, 117.507, 259.863, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.5

Other elements in 4mca:

The structure of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A (pdb code 4mca). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A, PDB code: 4mca:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4mca

Go back to Zinc Binding Sites List in 4mca
Zinc binding site 1 out of 4 in the Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:21.9
occ:1.00
NE2 A:HIS254 1.9 14.2 1.0
OD1 A:ASP171 2.0 20.4 1.0
NE2 A:HIS271 2.2 19.7 1.0
O1 A:GOL1002 2.2 32.4 1.0
O3 A:GOL1002 2.4 42.5 1.0
OD2 A:ASP171 2.6 20.0 1.0
CG A:ASP171 2.7 18.5 1.0
C1 A:GOL1002 2.9 38.4 1.0
CE1 A:HIS254 2.9 16.5 1.0
CD2 A:HIS254 3.0 15.4 1.0
CD2 A:HIS271 3.1 21.2 1.0
CE1 A:HIS271 3.2 22.4 1.0
C3 A:GOL1002 3.5 47.6 1.0
C2 A:GOL1002 3.6 45.2 1.0
OD1 A:ASP121 4.0 29.3 1.0
O2 A:GOL1002 4.0 51.5 1.0
ND1 A:HIS254 4.0 14.9 1.0
CG2 A:VAL275 4.1 20.2 1.0
CG A:HIS254 4.1 15.4 1.0
CB A:ASP171 4.2 17.1 1.0
CG A:HIS271 4.2 21.8 1.0
ND1 A:HIS271 4.2 22.6 1.0
NA A:NA1004 4.5 43.8 1.0
CG A:ASP121 4.7 28.2 1.0
OD2 A:ASP121 4.8 34.5 1.0
CA A:ASP171 4.8 17.1 1.0
CG1 A:VAL275 4.9 20.1 1.0
CB A:VAL275 5.0 17.8 1.0

Zinc binding site 2 out of 4 in 4mca

Go back to Zinc Binding Sites List in 4mca
Zinc binding site 2 out of 4 in the Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:96.0
occ:1.00
SG A:CYS85 2.2 64.7 1.0
NE2 A:HIS31 2.6 60.5 1.0
CE1 A:HIS31 2.9 59.0 1.0
CB A:HIS83 3.1 70.4 1.0
CB A:CYS85 3.3 54.9 1.0
CD2 A:HIS31 3.6 60.5 1.0
CB A:HIS60 3.6 57.8 1.0
CA A:CYS85 3.7 48.5 1.0
N A:CYS85 3.8 57.4 1.0
O A:HIS83 3.8 60.8 1.0
C A:HIS83 3.9 61.7 1.0
ND1 A:HIS31 4.0 57.5 1.0
CG A:HIS83 4.1 81.0 1.0
CA A:HIS83 4.1 65.4 1.0
CG A:HIS31 4.3 54.4 1.0
CG A:HIS60 4.4 71.5 1.0
O A:TYR32 4.5 40.6 1.0
N A:GLY84 4.5 62.2 1.0
C A:GLY84 4.5 58.5 1.0
N A:HIS60 4.6 55.2 1.0
ND1 A:HIS83 4.7 84.5 1.0
C A:TYR32 4.7 34.2 1.0
CD2 A:HIS60 4.8 77.1 1.0
N A:LEU33 4.8 34.2 1.0
CA A:HIS60 4.8 57.1 1.0
O A:LEU80 4.8 46.1 1.0
N A:HIS83 5.0 68.9 1.0

Zinc binding site 3 out of 4 in 4mca

Go back to Zinc Binding Sites List in 4mca
Zinc binding site 3 out of 4 in the Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1000

b:21.7
occ:1.00
OD1 B:ASP171 2.0 17.2 1.0
NE2 B:HIS254 2.1 17.7 1.0
O3 B:GOL1001 2.1 31.4 1.0
NE2 B:HIS271 2.2 22.0 1.0
O1 B:GOL1001 2.3 34.1 1.0
CG B:ASP171 2.7 19.2 1.0
OD2 B:ASP171 2.8 24.9 1.0
CE1 B:HIS254 3.0 16.4 1.0
CD2 B:HIS271 3.1 21.2 1.0
CD2 B:HIS254 3.1 17.2 1.0
C3 B:GOL1001 3.1 37.2 1.0
CE1 B:HIS271 3.2 23.5 1.0
C1 B:GOL1001 3.6 39.6 1.0
C2 B:GOL1001 3.8 40.7 1.0
OD1 B:ASP121 4.0 29.1 1.0
CG2 B:VAL275 4.0 17.0 1.0
O2 B:GOL1001 4.1 46.3 1.0
ND1 B:HIS254 4.1 15.9 1.0
CB B:ASP171 4.2 16.4 1.0
CG B:HIS254 4.2 16.9 1.0
CG B:HIS271 4.3 22.6 1.0
ND1 B:HIS271 4.3 21.9 1.0
NA B:NA1004 4.5 48.9 1.0
OD2 B:ASP121 4.6 37.2 1.0
CG B:ASP121 4.6 32.2 1.0
CA B:ASP171 4.8 16.9 1.0
CG1 B:VAL275 4.9 19.2 1.0
CB B:VAL275 4.9 17.9 1.0

Zinc binding site 4 out of 4 in 4mca

Go back to Zinc Binding Sites List in 4mca
Zinc binding site 4 out of 4 in the Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Glycerol Dehydrogenase From Serratia to 1.9A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:80.3
occ:1.00
SG B:CYS85 2.2 58.6 1.0
NE2 B:HIS31 2.6 51.8 1.0
CB B:HIS83 3.1 56.3 1.0
CB B:CYS85 3.2 45.2 1.0
CE1 B:HIS31 3.2 53.9 1.0
CD2 B:HIS31 3.3 50.4 1.0
O B:HIS83 3.6 47.6 1.0
CA B:CYS85 3.6 39.9 1.0
CB B:HIS60 3.7 44.5 1.0
N B:CYS85 3.8 38.8 1.0
C B:HIS83 3.8 46.8 1.0
CA B:HIS83 4.1 51.3 1.0
ND1 B:HIS31 4.1 52.5 1.0
CG B:HIS83 4.2 69.2 1.0
CG B:HIS31 4.2 46.8 1.0
CG B:HIS60 4.4 55.8 1.0
C B:GLY84 4.4 45.0 1.0
CD2 B:HIS60 4.4 61.4 1.0
O B:TYR32 4.5 28.5 1.0
N B:GLY84 4.5 43.8 1.0
C B:TYR32 4.7 25.5 1.0
O B:LEU80 4.7 36.3 1.0
CD2 B:HIS83 4.8 70.7 1.0
N B:LEU33 4.8 23.2 1.0
N B:HIS60 4.9 42.9 1.0
O B:GLY84 4.9 38.9 1.0
CA B:HIS60 5.0 47.5 1.0

Reference:

P.M.Musille, E.A.Ortlund. Structure of Glycerol Dehydrogenase From Serratia Acta Crystallogr.,Sect.F 2014.
ISSN: ESSN 1744-3091
Page generated: Wed Dec 16 05:34:25 2020

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