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Cobalt in PDB 1y7a: Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution

Enzymatic activity of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution

All present enzymatic activity of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution:
3.1.3.1;

Protein crystallography data

The structure of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution, PDB code: 1y7a was solved by J.Wang, K.Stieglitz, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.77
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.208, 164.564, 192.636, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.8

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution (pdb code 1y7a). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution, PDB code: 1y7a:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 1y7a

Go back to Cobalt Binding Sites List in 1y7a
Cobalt binding site 1 out of 6 in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1450

b:31.4
occ:1.00
 O2 A:PO41456 2.0 67.7 0.6
NE2 A:HIS331 2.1 25.3 1.0
NE2 A:HIS412 2.1 27.3 1.0
OD2 A:ASP327 2.2 26.0 1.0
O3 A:PO41456 2.3 69.5 0.6
P A:PO41456 2.5 67.9 0.6
OD1 A:ASP327 2.5 28.9 1.0
CG A:ASP327 2.7 25.8 1.0
O A:HOH1833 2.8 44.8 1.0
CE1 A:HIS412 2.9 27.2 1.0
CD2 A:HIS331 3.0 26.0 1.0
O4 A:PO41456 3.2 65.8 0.6
CE1 A:HIS331 3.2 28.4 1.0
CD2 A:HIS412 3.3 27.6 1.0
O1 A:PO41456 4.0 67.2 0.6
O A:HOH1571 4.0 52.8 1.0
ND1 A:HIS412 4.1 26.4 1.0
CG A:HIS331 4.2 26.6 1.0
OG A:SER102 4.2 26.2 1.0
CB A:ASP327 4.2 26.0 1.0
ND1 A:HIS331 4.2 25.3 1.0
NE2 A:HIS370 4.3 22.0 1.0
CO A:CO1451 4.3 36.6 1.0
CG A:HIS412 4.3 27.1 1.0
CE1 A:HIS370 4.3 22.4 1.0
NE2 A:HIS372 4.3 23.7 1.0
O A:HOH1831 4.4 50.6 1.0
OD2 A:ASP51 4.5 21.6 1.0
O A:HOH1817 4.6 50.4 1.0
CD2 A:HIS372 4.9 22.4 1.0
O A:ASP327 5.0 27.7 1.0

Cobalt binding site 2 out of 6 in 1y7a

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Cobalt binding site 2 out of 6 in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1451

b:36.6
occ:1.00
 OG A:SER102 2.0 26.2 1.0
OD1 A:ASP369 2.0 20.5 1.0
OD2 A:ASP51 2.0 21.6 1.0
NE2 A:HIS370 2.2 22.0 1.0
O3 A:PO41456 2.5 69.5 0.6
CG A:ASP51 2.6 27.5 1.0
OD1 A:ASP51 2.7 27.5 1.0
CG A:ASP369 2.9 19.9 1.0
CD2 A:HIS370 3.0 21.5 1.0
CB A:SER102 3.1 19.9 1.0
OD2 A:ASP369 3.2 21.3 1.0
CE1 A:HIS370 3.3 22.4 1.0
CA A:SER102 3.6 19.0 1.0
OD1 A:ASP327 4.0 28.9 1.0
P A:PO41456 4.0 67.9 0.6
CE1 A:HIS412 4.0 27.2 1.0
CG A:ASP327 4.0 25.8 1.0
CB A:ASP51 4.1 23.8 1.0
N A:SER102 4.1 17.4 1.0
CG A:HIS370 4.2 21.7 1.0
CB A:ASP369 4.2 16.9 1.0
O A:HOH1570 4.2 23.4 1.0
OD2 A:ASP327 4.2 26.0 1.0
CO A:CO1450 4.3 31.4 1.0
ND1 A:HIS370 4.3 22.8 1.0
NE2 A:HIS412 4.3 27.3 1.0
N A:GLY52 4.3 19.8 1.0
CO A:CO1452 4.5 30.5 1.0
CA A:ASP51 4.5 21.9 1.0
O1 A:PO41456 4.5 67.2 0.6
O A:HOH1571 4.6 52.8 1.0
CB A:ASP327 4.6 26.0 1.0
C A:ASP51 4.7 22.4 1.0
O4 A:PO41456 4.7 65.8 0.6
OG1 A:THR155 4.9 22.9 1.0
C A:ASP101 4.9 18.5 1.0
ND1 A:HIS412 4.9 26.4 1.0
C A:SER102 4.9 18.4 1.0
O2 A:PO41456 5.0 67.7 0.6

Cobalt binding site 3 out of 6 in 1y7a

Go back to Cobalt Binding Sites List in 1y7a
Cobalt binding site 3 out of 6 in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1452

b:30.5
occ:1.00
 OD1 A:ASP51 1.9 27.5 1.0
NE2 A:HIS153 2.0 28.6 1.0
OE2 A:GLU322 2.0 19.9 1.0
O A:HOH1816 2.3 28.0 1.0
OG1 A:THR155 2.3 22.9 1.0
CD2 A:HIS153 2.8 25.5 1.0
CG A:ASP51 2.9 27.5 1.0
CD A:GLU322 3.0 20.7 1.0
CE1 A:HIS153 3.1 28.1 1.0
CB A:THR155 3.3 21.3 1.0
CB A:ASP51 3.4 23.8 1.0
OE1 A:GLU322 3.4 21.9 1.0
O A:HOH1571 3.9 52.8 1.0
CG A:HIS153 4.0 25.6 1.0
OD2 A:ASP51 4.1 21.6 1.0
ND1 A:HIS153 4.1 26.8 1.0
N A:THR155 4.2 18.4 1.0
CG A:GLU322 4.2 19.7 1.0
O A:HOH1570 4.3 23.4 1.0
CG2 A:THR155 4.3 19.5 1.0
CA A:THR155 4.4 19.2 1.0
OG A:SER102 4.4 26.2 1.0
CB A:ALA324 4.5 23.0 1.0
CO A:CO1451 4.5 36.6 1.0
OD1 A:ASP369 4.6 20.5 1.0
O A:ALA324 4.6 25.3 1.0
CB A:SER102 4.6 19.9 1.0
CA A:ASP51 4.7 21.9 1.0
CA A:ALA324 4.8 22.8 1.0

Cobalt binding site 4 out of 6 in 1y7a

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Cobalt binding site 4 out of 6 in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1950

b:38.3
occ:1.00
 O3 B:PO41956 2.0 73.6 0.6
NE2 B:HIS412 2.0 32.3 1.0
OD2 B:ASP327 2.1 29.7 1.0
NE2 B:HIS331 2.2 30.8 1.0
O2 B:PO41956 2.3 75.0 0.6
OD1 B:ASP327 2.4 34.5 1.0
P B:PO41956 2.5 74.8 0.6
CG B:ASP327 2.6 33.3 1.0
CE1 B:HIS412 2.9 30.5 1.0
CD2 B:HIS331 3.0 31.9 1.0
CD2 B:HIS412 3.2 30.3 1.0
CE1 B:HIS331 3.3 35.3 1.0
O4 B:PO41956 3.3 71.9 0.6
O1 B:PO41956 3.7 75.1 0.6
ND1 B:HIS412 4.1 30.1 1.0
CB B:ASP327 4.1 32.3 1.0
CO B:CO1951 4.2 46.5 1.0
NE2 B:HIS370 4.2 25.3 1.0
NE2 B:HIS372 4.2 29.9 1.0
CG B:HIS331 4.2 32.5 1.0
CG B:HIS412 4.3 29.4 1.0
CE1 B:HIS370 4.3 25.8 1.0
OD1 B:ASP51 4.3 31.4 1.0
ND1 B:HIS331 4.4 32.5 1.0
OG B:SER102 4.5 33.2 1.0
CD2 B:HIS372 4.8 27.3 1.0
O B:HOH2201 4.8 55.4 1.0
O B:ASP327 4.9 31.4 1.0

Cobalt binding site 5 out of 6 in 1y7a

Go back to Cobalt Binding Sites List in 1y7a
Cobalt binding site 5 out of 6 in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1951

b:46.5
occ:1.00
 OD2 B:ASP369 1.9 25.5 1.0
OD1 B:ASP51 2.1 31.4 1.0
NE2 B:HIS370 2.2 25.3 1.0
OG B:SER102 2.3 33.2 1.0
O2 B:PO41956 2.7 75.0 0.6
OD2 B:ASP51 2.7 35.5 1.0
CG B:ASP51 2.7 32.1 1.0
CG B:ASP369 2.8 27.2 1.0
CD2 B:HIS370 2.9 26.5 1.0
OD1 B:ASP369 3.1 27.2 1.0
CE1 B:HIS370 3.3 25.8 1.0
CB B:SER102 3.5 29.1 1.0
CA B:SER102 3.7 25.0 1.0
O B:HOH2026 3.9 37.7 1.0
OD1 B:ASP327 4.0 34.5 1.0
CG B:ASP327 4.1 33.3 1.0
CB B:ASP369 4.1 24.9 1.0
CG B:HIS370 4.1 26.7 1.0
CE1 B:HIS412 4.1 30.5 1.0
CO B:CO1950 4.2 38.3 1.0
P B:PO41956 4.2 74.8 0.6
CB B:ASP51 4.2 29.1 1.0
N B:SER102 4.2 23.3 1.0
ND1 B:HIS370 4.3 27.4 1.0
OD2 B:ASP327 4.3 29.7 1.0
N B:GLY52 4.4 24.1 1.0
NE2 B:HIS412 4.4 32.3 1.0
CO B:CO1952 4.5 37.2 1.0
CB B:ASP327 4.6 32.3 1.0
CA B:ASP51 4.6 26.3 1.0
O1 B:PO41956 4.7 75.1 0.6
O4 B:PO41956 4.7 71.9 0.6
C B:ASP51 4.8 24.9 1.0
ND1 B:HIS412 4.9 30.1 1.0
OG1 B:THR155 4.9 26.7 1.0
C B:SER102 5.0 25.0 1.0
C B:ASP101 5.0 23.6 1.0

Cobalt binding site 6 out of 6 in 1y7a

Go back to Cobalt Binding Sites List in 1y7a
Cobalt binding site 6 out of 6 in the Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of D153H/K328W E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.77 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1952

b:37.2
occ:1.00
 OE2 B:GLU322 1.8 24.1 1.0
NE2 B:HIS153 2.0 29.3 1.0
OD2 B:ASP51 2.0 35.5 1.0
O B:HOH2027 2.4 29.6 1.0
OG1 B:THR155 2.5 26.7 1.0
CD2 B:HIS153 2.8 27.7 1.0
CG B:ASP51 3.0 32.1 1.0
CD B:GLU322 3.0 26.2 1.0
CE1 B:HIS153 3.1 30.7 1.0
CB B:THR155 3.2 26.0 1.0
CB B:ASP51 3.5 29.1 1.0
OE1 B:GLU322 3.6 27.5 1.0
OD1 B:ASP51 4.0 31.4 1.0
CG B:HIS153 4.1 28.9 1.0
CG2 B:THR155 4.1 26.6 1.0
OG B:SER102 4.1 33.2 1.0
ND1 B:HIS153 4.1 29.6 1.0
CG B:GLU322 4.2 25.7 1.0
O B:HOH2026 4.2 37.7 1.0
N B:THR155 4.2 24.8 1.0
CB B:ALA324 4.4 31.1 1.0
CA B:THR155 4.4 25.0 1.0
CO B:CO1951 4.5 46.5 1.0
OD2 B:ASP369 4.6 25.5 1.0
O B:ALA324 4.6 32.9 1.0
CA B:ALA324 4.7 30.7 1.0
CA B:ASP51 4.8 26.3 1.0
CB B:SER102 4.9 29.1 1.0

Reference:

J.Wang, K.A.Stieglitz, E.R.Kantrowitz. Metal Specificity Is Correlated with Two Crucial Active Site Residues in Escherichia Coli Alkaline Phosphatase(,). Biochemistry V. 44 8378 2005.
ISSN: ISSN 0006-2960
PubMed: 15938627
DOI: 10.1021/BI050155P
Page generated: Tue Jul 30 14:49:40 2024

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