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Cobalt in PDB 1y6v: Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution

Enzymatic activity of Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution

All present enzymatic activity of Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution:
3.1.3.1;

Protein crystallography data

The structure of Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution, PDB code: 1y6v 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 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.475, 164.257, 192.819, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.2

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution (pdb code 1y6v). 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 E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution, PDB code: 1y6v:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 1y6v

Go back to Cobalt Binding Sites List in 1y6v
Cobalt binding site 1 out of 6 in the Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 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 E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co850

b:11.7
occ:1.00
 OD1 A:ASP327 2.0 15.5 1.0
NE2 A:HIS331 2.0 15.3 1.0
NE2 A:HIS412 2.1 16.8 1.0
O2 A:PO4856 2.2 24.7 1.0
O3 A:PO4856 2.3 18.8 1.0
OD2 A:ASP327 2.4 16.2 1.0
CG A:ASP327 2.5 16.0 1.0
P A:PO4856 2.8 20.9 1.0
CE1 A:HIS412 3.0 20.7 1.0
CE1 A:HIS331 3.0 19.2 1.0
CD2 A:HIS331 3.1 17.8 1.0
CD2 A:HIS412 3.1 17.7 1.0
O4 A:PO4856 3.8 17.3 1.0
O A:HOH1228 3.8 63.0 1.0
NE2 A:HIS372 4.0 15.8 1.0
CO A:CO851 4.0 12.7 1.0
O1 A:PO4856 4.0 18.2 1.0
CB A:ASP327 4.0 14.1 1.0
CE1 A:HIS370 4.1 12.5 1.0
ND1 A:HIS412 4.2 15.7 1.0
ND1 A:HIS331 4.2 18.8 1.0
NE2 A:HIS370 4.2 13.5 1.0
CG A:HIS331 4.2 19.2 1.0
CG A:HIS412 4.2 17.9 1.0
O A:HOH987 4.3 17.4 1.0
OD1 A:ASP51 4.4 14.3 1.0
OG A:SER102 4.5 20.4 1.0
CD2 A:HIS372 4.5 14.1 1.0
O A:HOH1220 4.7 50.7 1.0
O A:ASP327 4.8 16.3 1.0
C A:ASP327 4.9 15.7 1.0
CA A:ASP327 5.0 15.4 1.0

Cobalt binding site 2 out of 6 in 1y6v

Go back to Cobalt Binding Sites List in 1y6v
Cobalt binding site 2 out of 6 in the Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 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 E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co851

b:12.7
occ:1.00
 OG A:SER102 1.7 20.4 1.0
OD1 A:ASP51 1.9 14.3 1.0
NE2 A:HIS370 1.9 13.5 1.0
OD1 A:ASP369 2.0 15.4 1.0
O3 A:PO4856 2.1 18.8 1.0
CG A:ASP51 2.8 13.3 1.0
CE1 A:HIS370 3.0 12.5 1.0
CD2 A:HIS370 3.0 11.9 1.0
CG A:ASP369 3.0 14.8 1.0
OD2 A:ASP51 3.1 13.8 1.0
CB A:SER102 3.1 15.7 1.0
P A:PO4856 3.3 20.9 1.0
OD2 A:ASP369 3.3 15.2 1.0
OD1 A:ASP327 3.6 15.5 1.0
CA A:SER102 3.7 13.6 1.0
O4 A:PO4856 3.8 17.3 1.0
O1 A:PO4856 3.8 18.2 1.0
CG A:ASP327 3.9 16.0 1.0
CO A:CO850 4.0 11.7 1.0
N A:SER102 4.0 12.5 1.0
CE1 A:HIS412 4.1 20.7 1.0
ND1 A:HIS370 4.1 13.6 1.0
CB A:ASP51 4.1 13.2 1.0
CG A:HIS370 4.2 12.1 1.0
NE2 A:HIS412 4.2 16.8 1.0
N A:GLY52 4.3 13.7 1.0
CB A:ASP369 4.4 12.0 1.0
O A:HOH908 4.4 13.7 1.0
OD2 A:ASP327 4.4 16.2 1.0
CB A:ASP327 4.4 14.1 1.0
O2 A:PO4856 4.5 24.7 1.0
O A:HOH888 4.5 13.6 1.0
CA A:ASP51 4.6 12.7 1.0
C A:ASP51 4.7 14.2 1.0
CO A:CO852 4.7 15.0 1.0
C A:ASP101 4.8 13.8 1.0
O A:HOH987 4.9 17.4 1.0
ND1 A:HIS412 5.0 15.7 1.0

Cobalt binding site 3 out of 6 in 1y6v

Go back to Cobalt Binding Sites List in 1y6v
Cobalt binding site 3 out of 6 in the Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 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 E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co852

b:15.0
occ:1.00
 OD2 A:ASP51 1.9 13.8 1.0
OE2 A:GLU322 2.0 11.2 1.0
O A:HOH1265 2.0 15.0 1.0
O A:HOH888 2.1 13.6 1.0
OG1 A:THR155 2.2 13.2 1.0
O A:HOH1242 2.2 13.2 1.0
CG A:ASP51 3.0 13.3 1.0
CD A:GLU322 3.0 10.2 1.0
CB A:THR155 3.1 13.8 1.0
OE1 A:GLU322 3.3 13.3 1.0
CB A:ASP51 3.6 13.2 1.0
OD2 A:ASP153 3.7 14.2 1.0
O A:HOH987 4.1 17.4 1.0
N A:THR155 4.1 14.3 1.0
CG2 A:THR155 4.1 10.8 1.0
OD1 A:ASP51 4.1 14.3 1.0
OG A:SER102 4.1 20.4 1.0
O A:HOH908 4.2 13.7 1.0
CA A:THR155 4.2 12.3 1.0
CB A:SER102 4.4 15.7 1.0
CG A:GLU322 4.4 12.9 1.0
O1 A:PO4856 4.4 18.2 1.0
CB A:ALA324 4.4 13.6 1.0
CG A:ASP153 4.6 15.2 1.0
CA A:ALA324 4.7 14.5 1.0
O A:ALA324 4.7 14.6 1.0
CO A:CO851 4.7 12.7 1.0
OD1 A:ASP369 4.9 15.4 1.0
CA A:ASP51 4.9 12.7 1.0

Cobalt binding site 4 out of 6 in 1y6v

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Cobalt binding site 4 out of 6 in the Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 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 E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co950

b:19.9
occ:1.00
 O2 B:PO4956 2.0 31.1 1.0
NE2 B:HIS331 2.0 26.7 1.0
OD1 B:ASP327 2.1 22.6 1.0
NE2 B:HIS412 2.1 20.6 1.0
O3 B:PO4956 2.4 31.6 1.0
OD2 B:ASP327 2.4 21.4 1.0
CG B:ASP327 2.6 23.9 1.0
P B:PO4956 2.8 27.2 1.0
CD2 B:HIS331 3.0 29.1 1.0
CD2 B:HIS412 3.1 21.3 1.0
CE1 B:HIS331 3.1 30.1 1.0
CE1 B:HIS412 3.1 22.4 1.0
O4 B:PO4956 3.7 28.7 1.0
O1 B:PO4956 3.9 28.6 1.0
NE2 B:HIS372 3.9 17.6 1.0
CO B:CO951 3.9 19.7 1.0
CE1 B:HIS370 4.1 17.7 1.0
NE2 B:HIS370 4.1 17.8 1.0
O B:HOH1024 4.1 21.2 1.0
CB B:ASP327 4.1 21.4 1.0
CG B:HIS331 4.2 27.5 1.0
ND1 B:HIS412 4.2 19.2 1.0
ND1 B:HIS331 4.2 27.9 1.0
CG B:HIS412 4.2 20.6 1.0
O B:HOH1168 4.3 38.5 1.0
OD1 B:ASP51 4.4 18.9 1.0
CD2 B:HIS372 4.5 17.8 1.0
O B:ASP327 4.7 17.7 1.0
OG B:SER102 4.8 25.3 1.0
C B:ASP327 4.9 19.2 1.0
CE1 B:HIS372 5.0 18.0 1.0

Cobalt binding site 5 out of 6 in 1y6v

Go back to Cobalt Binding Sites List in 1y6v
Cobalt binding site 5 out of 6 in the Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 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 E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co951

b:19.7
occ:1.00
 O3 B:PO4956 1.9 31.6 1.0
NE2 B:HIS370 2.0 17.8 1.0
OD1 B:ASP51 2.0 18.9 1.0
OD1 B:ASP369 2.0 16.2 1.0
OG B:SER102 2.1 25.3 1.0
CG B:ASP51 2.8 21.9 1.0
OD2 B:ASP51 2.9 21.2 1.0
CG B:ASP369 3.0 16.7 1.0
CD2 B:HIS370 3.0 16.8 1.0
CE1 B:HIS370 3.0 17.7 1.0
P B:PO4956 3.2 27.2 1.0
OD2 B:ASP369 3.3 17.0 1.0
CB B:SER102 3.4 23.0 1.0
OD1 B:ASP327 3.7 22.6 1.0
CA B:SER102 3.7 19.0 1.0
O1 B:PO4956 3.8 28.6 1.0
O4 B:PO4956 3.8 28.7 1.0
CO B:CO950 3.9 19.9 1.0
CG B:ASP327 3.9 23.9 1.0
N B:SER102 4.0 18.9 1.0
ND1 B:HIS370 4.1 18.7 1.0
CG B:HIS370 4.1 18.1 1.0
CE1 B:HIS412 4.2 22.4 1.0
NE2 B:HIS412 4.2 20.6 1.0
CB B:ASP51 4.2 17.5 1.0
O B:HOH1017 4.2 23.1 1.0
CB B:ASP369 4.3 16.9 1.0
O2 B:PO4956 4.3 31.1 1.0
N B:GLY52 4.3 17.4 1.0
OD2 B:ASP327 4.4 21.4 1.0
CB B:ASP327 4.4 21.4 1.0
O B:HOH1022 4.5 20.9 1.0
CA B:ASP51 4.7 17.7 1.0
CO B:CO952 4.7 19.8 1.0
C B:ASP51 4.8 18.0 1.0
O B:HOH1024 4.8 21.2 1.0
C B:ASP101 4.8 18.9 1.0

Cobalt binding site 6 out of 6 in 1y6v

Go back to Cobalt Binding Sites List in 1y6v
Cobalt binding site 6 out of 6 in the Structure of E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 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 E. Coli Alkaline Phosphatase in Presence of Cobalt at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co952

b:19.8
occ:1.00
 OE2 B:GLU322 1.8 21.0 1.0
OD2 B:ASP51 2.0 21.2 1.0
O B:HOH1262 2.0 20.7 1.0
O B:HOH1022 2.1 20.9 1.0
O B:HOH970 2.1 17.6 1.0
OG1 B:THR155 2.1 19.0 1.0
CD B:GLU322 2.9 24.8 1.0
CB B:THR155 3.1 22.7 1.0
CG B:ASP51 3.1 21.9 1.0
OE1 B:GLU322 3.4 17.3 1.0
OD2 B:ASP153 3.6 23.5 1.0
CB B:ASP51 3.7 17.5 1.0
OG B:SER102 3.8 25.3 1.0
CG2 B:THR155 4.0 20.7 1.0
N B:THR155 4.0 21.2 1.0
O B:HOH1024 4.1 21.2 1.0
CG B:GLU322 4.1 25.6 1.0
OD1 B:ASP51 4.1 18.9 1.0
CA B:THR155 4.2 21.3 1.0
O B:HOH1017 4.3 23.1 1.0
O1 B:PO4956 4.3 28.6 1.0
CB B:ALA324 4.4 22.6 1.0
CB B:SER102 4.4 23.0 1.0
CG B:ASP153 4.6 22.6 1.0
O B:ALA324 4.6 21.5 1.0
CO B:CO951 4.7 19.7 1.0
CA B:ALA324 4.7 21.4 1.0
OD1 B:ASP369 4.8 16.2 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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