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Zinc in PDB 1ajd: Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity

Enzymatic activity of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity

All present enzymatic activity of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity:
3.1.3.1;

Protein crystallography data

The structure of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity, PDB code: 1ajd was solved by C.G.Dealwis, L.Chen, C.Abad-Zapatero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 195.020, 166.930, 76.440, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / n/a

Other elements in 1ajd:

The structure of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity (pdb code 1ajd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity, PDB code: 1ajd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ajd

Go back to Zinc Binding Sites List in 1ajd
Zinc binding site 1 out of 4 in the Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:5.8
occ:1.00
 NE2 A:HIS412 1.9 2.0 1.0
NE2 A:HIS331 2.2 4.2 1.0
OD1 A:ASP327 2.2 2.0 1.0
OD2 A:ASP327 2.3 2.3 1.0
CG A:ASP327 2.6 2.0 1.0
CE1 A:HIS412 2.9 2.0 1.0
CD2 A:HIS412 3.0 2.2 1.0
CD2 A:HIS331 3.1 2.0 1.0
CE1 A:HIS331 3.2 8.9 1.0
OG A:SER102 3.9 12.6 1.0
NE2 A:HIS372 3.9 2.0 1.0
ND1 A:HIS412 4.0 3.0 1.0
ZN A:ZN451 4.0 3.6 1.0
CG A:HIS412 4.1 2.0 1.0
CB A:ASP327 4.1 2.2 1.0
CE1 A:HIS370 4.2 2.5 1.0
CG A:HIS331 4.3 3.0 1.0
ND1 A:HIS331 4.3 3.5 1.0
NE2 A:HIS370 4.5 2.0 1.0
OD1 A:ASP51 4.6 2.0 1.0
CD2 A:HIS372 4.6 2.0 1.0
O A:ASP327 4.6 2.0 1.0
CE1 A:HIS372 4.9 2.0 1.0
C A:ASP327 4.9 2.0 1.0

Zinc binding site 2 out of 4 in 1ajd

Go back to Zinc Binding Sites List in 1ajd
Zinc binding site 2 out of 4 in the Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:3.6
occ:1.00
 OG A:SER102 2.1 12.6 1.0
NE2 A:HIS370 2.1 2.0 1.0
OD2 A:ASP369 2.1 2.6 1.0
OD1 A:ASP51 2.5 2.0 1.0
CE1 A:HIS370 3.0 2.5 1.0
CB A:SER102 3.0 6.7 1.0
OD2 A:ASP51 3.1 2.0 1.0
CG A:ASP51 3.2 3.0 1.0
CG A:ASP369 3.2 4.4 1.0
CD2 A:HIS370 3.2 2.0 1.0
CA A:SER102 3.4 2.0 1.0
CE1 A:HIS412 3.6 2.0 1.0
OD1 A:ASP369 3.7 2.9 1.0
OD2 A:ASP327 3.7 2.3 1.0
NE2 A:HIS412 4.0 2.0 1.0
N A:SER102 4.0 2.0 1.0
ZN A:ZN450 4.0 5.8 1.0
CG A:ASP327 4.1 2.0 1.0
ND1 A:HIS370 4.2 2.0 1.0
CG A:HIS370 4.3 2.0 1.0
CB A:ASP369 4.4 2.0 1.0
O A:ASP101 4.4 2.0 1.0
OD1 A:ASP327 4.4 2.0 1.0
C A:ASP101 4.4 4.0 1.0
ND1 A:HIS412 4.5 3.0 1.0
MG A:MG452 4.6 2.0 1.0
CB A:ASP51 4.6 2.0 1.0
CB A:ASP327 4.7 2.2 1.0
C A:SER102 4.7 4.6 1.0
O A:HOH456 4.8 2.0 1.0
OG1 A:THR155 4.8 2.0 1.0
N A:GLY52 4.9 2.0 1.0
CD2 A:HIS412 5.0 2.2 1.0

Zinc binding site 3 out of 4 in 1ajd

Go back to Zinc Binding Sites List in 1ajd
Zinc binding site 3 out of 4 in the Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn950

b:7.0
occ:1.00
 NE2 B:HIS412 2.0 8.9 1.0
NE2 B:HIS331 2.1 2.0 1.0
OD1 B:ASP327 2.2 6.6 1.0
OD2 B:ASP327 2.4 12.0 1.0
CG B:ASP327 2.6 7.5 1.0
CE1 B:HIS412 2.8 5.8 1.0
CE1 B:HIS331 3.1 10.2 1.0
CD2 B:HIS331 3.1 2.0 1.0
CD2 B:HIS412 3.1 4.7 1.0
OG B:SER102 3.8 13.3 1.0
ND1 B:HIS412 4.0 3.8 1.0
CB B:ASP327 4.1 7.4 1.0
ND1 B:HIS331 4.2 8.9 1.0
CG B:HIS412 4.2 4.5 1.0
CG B:HIS331 4.2 5.3 1.0
CE1 B:HIS370 4.3 2.5 1.0
NE2 B:HIS370 4.3 2.0 1.0
NE2 B:HIS372 4.3 9.2 1.0
ZN B:ZN951 4.3 9.4 1.0
OD1 B:ASP51 4.4 5.3 1.0
O B:ASP327 4.7 3.0 1.0
C B:ASP327 4.9 2.0 1.0

Zinc binding site 4 out of 4 in 1ajd

Go back to Zinc Binding Sites List in 1ajd
Zinc binding site 4 out of 4 in the Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three-Dimensional Structure of the D153G Mutant of E. Coli Alkaline Phosphatase: A Mutant with Weaker Magnesium Binding and Increased Catalytic Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn951

b:9.4
occ:1.00
 OD1 B:ASP51 1.9 5.3 1.0
NE2 B:HIS370 2.0 2.0 1.0
OG B:SER102 2.1 13.3 1.0
OD2 B:ASP369 2.2 5.9 1.0
CG B:ASP51 2.7 6.6 1.0
CD2 B:HIS370 2.7 2.0 1.0
CG B:ASP369 2.8 6.6 1.0
OD1 B:ASP369 3.0 8.6 1.0
OD2 B:ASP51 3.0 2.8 1.0
CE1 B:HIS370 3.1 2.5 1.0
CB B:SER102 3.1 12.1 1.0
CA B:SER102 3.6 4.2 1.0
OD2 B:ASP327 3.7 12.0 1.0
CG B:HIS370 4.0 2.0 1.0
CB B:ASP51 4.0 2.0 1.0
CE1 B:HIS412 4.1 5.8 1.0
ND1 B:HIS370 4.1 2.0 1.0
CG B:ASP327 4.1 7.5 1.0
N B:SER102 4.1 6.3 1.0
N B:GLY52 4.2 2.0 1.0
CB B:ASP369 4.2 2.0 1.0
ZN B:ZN950 4.3 7.0 1.0
CA B:ASP51 4.4 4.8 1.0
NE2 B:HIS412 4.4 8.9 1.0
C B:ASP51 4.4 2.3 1.0
CB B:ASP327 4.5 7.4 1.0
OD1 B:ASP327 4.7 6.6 1.0
O B:HOH956 4.8 8.8 1.0
ND1 B:HIS412 4.8 3.8 1.0
CA B:GLY52 4.9 2.0 1.0
MG B:MG952 4.9 2.0 1.0
C B:SER102 5.0 4.4 1.0

Reference:

C.G.Dealwis, C.Brennan, K.Christianson, W.Mandecki, C.Abad-Zapatero. Crystallographic Analysis of Reversible Metal Binding Observed in A Mutant (ASP153-->Gly) of Escherichia Coli Alkaline Phosphatase. Biochemistry V. 34 13967 1995.
ISSN: ISSN 0006-2960
PubMed: 7577993
DOI: 10.1021/BI00043A001
Page generated: Sat Oct 12 22:04:35 2024

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