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Zinc in PDB 3tg0: E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate

Enzymatic activity of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate

All present enzymatic activity of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate:
3.1.3.1;

Protein crystallography data

The structure of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate, PDB code: 3tg0 was solved by E.Bobyr, J.K.Lassila, H.I.Wiersma-Koch, T.D.Fenn, J.J.Lee, I.Nikolic-Hughes, K.O.Hodgson, D.C.Rees, B.Hedman, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.963, 98.457, 152.146, 90.00, 94.61, 90.00
R / Rfree (%) 14.8 / 16.9

Other elements in 3tg0:

The structure of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate (pdb code 3tg0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate, PDB code: 3tg0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 1 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:11.3
occ:1.00
 OD1 A:ASP51 2.0 9.5 1.0
OG A:SER102 2.0 17.4 1.0
OD2 A:ASP369 2.0 10.6 1.0
O2 A:PO4504 2.0 18.7 0.7
NE2 A:HIS370 2.1 9.4 1.0
CG A:ASP51 2.7 8.7 1.0
OD2 A:ASP51 2.9 10.0 1.0
CG A:ASP369 2.9 9.5 1.0
CD2 A:HIS370 3.0 8.8 1.0
CE1 A:HIS370 3.1 9.6 1.0
OD1 A:ASP369 3.1 9.3 1.0
CB A:SER102 3.1 13.0 1.0
P A:PO4504 3.5 13.2 0.7
OD1 A:ASP327 3.7 10.5 1.0
CA A:SER102 3.7 11.5 1.0
O3 A:PO4504 4.1 13.1 0.7
O1 A:PO4504 4.1 12.9 0.7
CG A:ASP327 4.1 10.4 1.0
N A:SER102 4.1 10.5 1.0
CB A:ASP51 4.1 9.1 1.0
ZN A:ZN502 4.1 10.9 1.0
CG A:HIS370 4.2 8.4 1.0
ND1 A:HIS370 4.2 9.1 1.0
CE1 A:HIS412 4.2 10.2 1.0
O A:HOH5162 4.2 12.3 1.0
CB A:ASP369 4.3 8.9 1.0
N A:GLY52 4.3 8.4 1.0
O4 A:PO4504 4.3 13.6 0.7
NE2 A:HIS412 4.4 10.6 1.0
O A:HOH5275 4.4 12.8 1.0
CA A:ASP51 4.6 8.4 1.0
CB A:ASP327 4.6 9.7 1.0
OD2 A:ASP327 4.6 12.4 1.0
MG A:MG503 4.7 8.9 1.0
C A:ASP51 4.7 8.6 1.0
C A:ASP101 4.9 9.8 1.0

Zinc binding site 2 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 2 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:10.9
occ:1.00
 O4 A:PO4504 1.8 13.6 0.7
NE2 A:HIS331 2.1 10.7 1.0
NE2 A:HIS412 2.1 10.6 1.0
OD1 A:ASP327 2.1 10.5 1.0
OD2 A:ASP327 2.6 12.4 1.0
O2 A:PO4504 2.6 18.7 0.7
CG A:ASP327 2.7 10.4 1.0
P A:PO4504 2.8 13.2 0.7
CD2 A:HIS331 3.0 10.3 1.0
CE1 A:HIS412 3.0 10.2 1.0
CE1 A:HIS331 3.1 11.7 1.0
CD2 A:HIS412 3.1 8.3 1.0
O3 A:PO4504 3.7 13.1 0.7
O A:HOH6450 3.9 33.9 1.0
O1 A:PO4504 3.9 12.9 0.7
NE2 A:HIS372 4.0 10.5 1.0
O A:HOH6264 4.0 36.6 1.0
ZN A:ZN501 4.1 11.3 1.0
ND1 A:HIS331 4.2 11.7 1.0
CE1 A:HIS370 4.2 9.6 1.0
CB A:ASP327 4.2 9.7 1.0
CG A:HIS331 4.2 10.7 1.0
ND1 A:HIS412 4.2 9.8 1.0
OG A:SER102 4.2 17.4 1.0
NE2 A:HIS370 4.2 9.4 1.0
CG A:HIS412 4.2 8.6 1.0
O A:HOH5189 4.3 11.6 1.0
CD2 A:HIS372 4.5 9.7 1.0
OD1 A:ASP51 4.5 9.5 1.0
O A:ASP327 4.8 9.8 1.0
O A:HOH6413 5.0 36.1 1.0

Zinc binding site 3 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 3 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:10.1
occ:1.00
 O1 B:PO4508 1.8 12.5 0.8
NE2 B:HIS412 2.1 9.2 1.0
NE2 B:HIS331 2.1 9.3 1.0
OD1 B:ASP327 2.1 9.6 1.0
OD2 B:ASP327 2.6 10.5 1.0
O2 B:PO4508 2.7 16.0 0.8
CG B:ASP327 2.7 10.2 1.0
P B:PO4508 2.8 11.4 0.8
CE1 B:HIS412 3.0 9.5 1.0
CE1 B:HIS331 3.0 10.3 1.0
CD2 B:HIS412 3.1 8.8 1.0
CD2 B:HIS331 3.1 9.6 1.0
O4 B:PO4508 3.8 12.4 0.8
O3 B:PO4508 4.0 11.3 0.8
O B:HOH6503 4.0 42.2 1.0
NE2 B:HIS372 4.0 10.1 1.0
O B:HOH6160 4.1 31.9 1.0
ZN B:ZN506 4.1 10.6 1.0
ND1 B:HIS331 4.2 11.2 1.0
ND1 B:HIS412 4.2 10.1 1.0
CB B:ASP327 4.2 9.8 1.0
CE1 B:HIS370 4.2 9.7 1.0
CG B:HIS412 4.2 9.0 1.0
CG B:HIS331 4.2 10.0 1.0
O B:HOH5054 4.2 10.8 1.0
NE2 B:HIS370 4.3 9.7 1.0
CD2 B:HIS372 4.5 9.2 1.0
OG B:SER102 4.5 20.1 1.0
OD1 B:ASP51 4.6 8.5 1.0
O B:ASP327 4.9 8.9 1.0

Zinc binding site 4 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 4 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:10.6
occ:1.00
 OG B:SER102 1.9 20.1 1.0
OD1 B:ASP51 2.0 8.5 1.0
O2 B:PO4508 2.0 16.0 0.8
OD2 B:ASP369 2.0 9.8 1.0
NE2 B:HIS370 2.1 9.7 1.0
CG B:ASP51 2.8 8.1 1.0
CG B:ASP369 2.9 8.6 1.0
OD2 B:ASP51 2.9 9.3 1.0
CD2 B:HIS370 3.0 8.0 1.0
CE1 B:HIS370 3.1 9.7 1.0
OD1 B:ASP369 3.1 8.6 1.0
CB B:SER102 3.2 13.2 1.0
P B:PO4508 3.4 11.4 0.8
OD1 B:ASP327 3.7 9.6 1.0
CA B:SER102 3.7 11.5 1.0
O4 B:PO4508 4.0 12.4 0.8
N B:SER102 4.1 10.2 1.0
CG B:ASP327 4.1 10.2 1.0
O3 B:PO4508 4.1 11.3 0.8
ZN B:ZN505 4.1 10.1 1.0
ND1 B:HIS370 4.1 9.1 1.0
CG B:HIS370 4.1 8.0 1.0
CE1 B:HIS412 4.2 9.5 1.0
CB B:ASP51 4.2 8.5 1.0
O B:HOH5220 4.3 12.2 1.0
CB B:ASP369 4.3 8.4 1.0
NE2 B:HIS412 4.3 9.2 1.0
O1 B:PO4508 4.3 12.5 0.8
N B:GLY52 4.3 8.2 1.0
O B:HOH5117 4.5 11.3 1.0
CB B:ASP327 4.5 9.8 1.0
CA B:ASP51 4.6 8.2 1.0
OD2 B:ASP327 4.6 10.5 1.0
C B:ASP51 4.7 8.6 1.0
MG B:MG507 4.7 8.2 1.0
C B:ASP101 4.9 10.3 1.0
ND1 B:HIS412 5.0 10.1 1.0

Zinc binding site 5 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 5 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn509

b:14.7
occ:1.00
 O4 C:PO4512 1.9 19.1 0.7
OD1 C:ASP51 1.9 12.5 1.0
OG C:SER102 2.0 20.9 1.0
OD2 C:ASP369 2.0 12.6 1.0
NE2 C:HIS370 2.1 12.3 1.0
CG C:ASP51 2.7 11.5 1.0
CG C:ASP369 2.9 11.6 1.0
OD2 C:ASP51 2.9 13.3 1.0
CD2 C:HIS370 3.0 11.8 1.0
CE1 C:HIS370 3.1 12.1 1.0
OD1 C:ASP369 3.1 12.6 1.0
CB C:SER102 3.3 15.3 1.0
P C:PO4512 3.4 16.2 0.7
OD1 C:ASP327 3.7 14.2 1.0
CA C:SER102 3.8 14.6 1.0
O3 C:PO4512 4.1 15.1 0.7
O1 C:PO4512 4.1 15.6 0.7
CG C:ASP327 4.1 13.2 1.0
ZN C:ZN510 4.1 15.2 1.0
N C:SER102 4.1 14.2 1.0
ND1 C:HIS370 4.1 12.6 1.0
CG C:HIS370 4.1 11.6 1.0
CB C:ASP51 4.2 11.3 1.0
CE1 C:HIS412 4.2 12.8 1.0
CB C:ASP369 4.3 11.5 1.0
N C:GLY52 4.3 11.2 1.0
O C:HOH5380 4.3 16.6 1.0
NE2 C:HIS412 4.3 12.4 1.0
O2 C:PO4512 4.3 16.2 0.7
O C:HOH6210 4.5 17.5 1.0
CB C:ASP327 4.5 12.3 1.0
CA C:ASP51 4.6 10.9 1.0
OD2 C:ASP327 4.6 14.4 1.0
C C:ASP51 4.7 10.8 1.0
MG C:MG511 4.7 12.7 1.0
C C:ASP101 4.9 13.8 1.0
ND1 C:HIS412 5.0 13.2 1.0

Zinc binding site 6 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 6 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn510

b:15.2
occ:1.00
 O2 C:PO4512 1.9 16.2 0.7
NE2 C:HIS412 2.1 12.4 1.0
OD1 C:ASP327 2.1 14.2 1.0
NE2 C:HIS331 2.1 12.8 1.0
OD2 C:ASP327 2.6 14.4 1.0
CG C:ASP327 2.7 13.2 1.0
O4 C:PO4512 2.8 19.1 0.7
P C:PO4512 2.8 16.2 0.7
CE1 C:HIS412 3.0 12.8 1.0
CD2 C:HIS331 3.1 12.8 1.0
CD2 C:HIS412 3.1 12.1 1.0
CE1 C:HIS331 3.1 13.9 1.0
O1 C:PO4512 3.8 15.6 0.7
O C:HOH6614 3.9 41.8 1.0
O3 C:PO4512 4.0 15.1 0.7
NE2 C:HIS372 4.0 13.3 1.0
O C:HOH6497 4.1 38.4 1.0
ZN C:ZN509 4.1 14.7 1.0
ND1 C:HIS412 4.1 13.2 1.0
CB C:ASP327 4.2 12.3 1.0
CE1 C:HIS370 4.2 12.1 1.0
ND1 C:HIS331 4.2 15.2 1.0
CG C:HIS412 4.2 12.4 1.0
CG C:HIS331 4.2 13.5 1.0
O C:HOH5330 4.3 15.1 1.0
NE2 C:HIS370 4.3 12.3 1.0
OG C:SER102 4.4 20.9 1.0
CD2 C:HIS372 4.5 12.1 1.0
OD1 C:ASP51 4.6 12.5 1.0
O C:HOH6498 4.6 44.1 1.0
O C:ASP327 4.9 11.8 1.0

Zinc binding site 7 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 7 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn513

b:12.4
occ:1.00
 OD1 D:ASP51 1.9 10.1 1.0
OD2 D:ASP369 2.0 11.1 1.0
OG D:SER102 2.0 20.2 1.0
O1 D:PO4516 2.0 17.2 0.7
NE2 D:HIS370 2.1 11.2 1.0
CG D:ASP51 2.7 9.1 1.0
OD2 D:ASP51 2.9 11.9 1.0
CG D:ASP369 2.9 9.5 1.0
CD2 D:HIS370 3.0 10.1 1.0
CE1 D:HIS370 3.1 11.4 1.0
OD1 D:ASP369 3.1 10.6 1.0
CB D:SER102 3.2 14.3 1.0
P D:PO4516 3.4 12.1 0.7
OD1 D:ASP327 3.7 11.6 1.0
CA D:SER102 3.7 12.8 1.0
O4 D:PO4516 4.0 11.9 0.7
O2 D:PO4516 4.0 11.7 0.7
CG D:ASP327 4.1 11.5 1.0
N D:SER102 4.1 11.8 1.0
ZN D:ZN514 4.1 12.2 1.0
ND1 D:HIS370 4.1 10.4 1.0
CG D:HIS370 4.1 10.0 1.0
CB D:ASP51 4.2 10.0 1.0
CE1 D:HIS412 4.2 11.6 1.0
O D:HOH5181 4.3 12.6 1.0
N D:GLY52 4.3 9.8 1.0
CB D:ASP369 4.3 9.2 1.0
NE2 D:HIS412 4.3 10.1 1.0
O3 D:PO4516 4.4 14.2 0.7
O D:HOH5158 4.5 13.3 1.0
CB D:ASP327 4.5 11.1 1.0
CA D:ASP51 4.6 9.5 1.0
OD2 D:ASP327 4.6 13.2 1.0
C D:ASP51 4.7 10.4 1.0
MG D:MG515 4.7 9.8 1.0
C D:ASP101 4.9 11.1 1.0

Zinc binding site 8 out of 8 in 3tg0

Go back to Zinc Binding Sites List in 3tg0
Zinc binding site 8 out of 8 in the E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of E. Coli Alkaline Phosphatase with Bound Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn514

b:12.2
occ:1.00
 O3 D:PO4516 1.9 14.2 0.7
NE2 D:HIS331 2.1 11.5 1.0
NE2 D:HIS412 2.1 10.1 1.0
OD1 D:ASP327 2.1 11.6 1.0
OD2 D:ASP327 2.6 13.2 1.0
O1 D:PO4516 2.6 17.2 0.7
CG D:ASP327 2.7 11.5 1.0
P D:PO4516 2.8 12.1 0.7
CE1 D:HIS331 3.1 12.3 1.0
CE1 D:HIS412 3.1 11.6 1.0
CD2 D:HIS331 3.1 11.8 1.0
CD2 D:HIS412 3.1 10.7 1.0
O4 D:PO4516 3.8 11.9 0.7
O2 D:PO4516 4.0 11.7 0.7
O D:HOH6411 4.0 38.8 1.0
NE2 D:HIS372 4.0 11.8 1.0
ZN D:ZN513 4.1 12.4 1.0
CE1 D:HIS370 4.2 11.4 1.0
CB D:ASP327 4.2 11.1 1.0
ND1 D:HIS331 4.2 13.1 1.0
O D:HOH6715 4.2 42.0 1.0
ND1 D:HIS412 4.2 11.0 1.0
CG D:HIS331 4.2 12.4 1.0
NE2 D:HIS370 4.3 11.2 1.0
CG D:HIS412 4.3 10.6 1.0
O D:HOH5096 4.3 12.4 1.0
OG D:SER102 4.4 20.2 1.0
O D:HOH6761 4.5 64.5 1.0
CD2 D:HIS372 4.5 11.3 1.0
OD1 D:ASP51 4.6 10.1 1.0
O D:ASP327 4.9 11.3 1.0

Reference:

E.Bobyr, J.K.Lassila, H.I.Wiersma-Koch, T.D.Fenn, J.J.Lee, I.Nikolic-Hughes, K.O.Hodgson, D.C.Rees, B.Hedman, D.Herschlag. High-Resolution Analysis of Zn(2+) Coordination in the Alkaline Phosphatase Superfamily By Exafs and X-Ray Crystallography. J.Mol.Biol. V. 415 102 2012.
ISSN: ISSN 0022-2836
PubMed: 22056344
DOI: 10.1016/J.JMB.2011.10.040
Page generated: Wed Dec 16 04:52:14 2020

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