Zinc in PDB 7kwd: Crystal Structure of Thermus Thermophilus Alkaline Phosphatase

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Alkaline Phosphatase, PDB code: 7kwd was solved by G.Gallo, C.Coelho, B.Borges, N.Negri, F.Maiello, L.Hardy, M.Wurtele, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.26 / 2.10
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 163.175, 163.175, 163.175, 90, 90, 90
R / Rfree (%) 16.3 / 20.1

Other elements in 7kwd:

The structure of Crystal Structure of Thermus Thermophilus Alkaline Phosphatase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase (pdb code 7kwd). 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 Thermus Thermophilus Alkaline Phosphatase, PDB code: 7kwd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7kwd

Go back to Zinc Binding Sites List in 7kwd
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:37.0
occ:1.00
OG A:SER95 2.1 36.7 1.0
OD2 A:ASP317 2.2 27.0 1.0
OD1 A:ASP47 2.2 21.9 1.0
NE2 A:HIS318 2.2 26.8 1.0
OD2 A:ASP47 2.7 25.0 1.0
CG A:ASP47 2.7 25.4 1.0
O41 A:TLA601 2.9 43.5 1.0
CG A:ASP317 3.0 22.1 1.0
CD2 A:HIS318 3.1 29.1 1.0
OD1 A:ASP317 3.1 20.1 1.0
CE1 A:HIS318 3.2 23.4 1.0
HD2 A:HIS318 3.2 35.0 1.0
HA A:SER95 3.3 39.0 1.0
CB A:SER95 3.3 38.8 1.0
HE1 A:HIS318 3.4 28.1 1.0
C4 A:TLA601 3.7 40.0 1.0
CA A:SER95 3.8 32.5 1.0
O4 A:TLA601 3.8 43.9 1.0
HB3 A:SER95 3.9 46.6 1.0
HB2 A:SER95 3.9 46.6 1.0
H A:GLY48 3.9 24.5 1.0
O A:HOH717 4.1 23.1 1.0
O A:HOH705 4.1 33.9 1.0
HA A:ASP47 4.1 25.8 1.0
CB A:ASP47 4.1 21.5 1.0
HE1 A:HIS433 4.2 30.6 1.0
CG A:HIS318 4.2 27.9 1.0
ND1 A:HIS318 4.2 21.4 1.0
HB2 A:ASP275 4.2 28.3 1.0
N A:SER95 4.3 30.5 1.0
N A:GLY48 4.3 20.4 1.0
HG1 A:THR148 4.3 26.1 1.0
CB A:ASP317 4.4 22.4 1.0
MG A:MG602 4.4 33.8 1.0
CG A:ASP275 4.4 25.3 1.0
H A:SER95 4.5 36.6 1.0
HB2 A:ASP317 4.5 26.9 1.0
OD2 A:ASP275 4.5 24.3 1.0
OD1 A:ASP275 4.5 20.6 1.0
CA A:ASP47 4.5 21.5 1.0
CE1 A:HIS433 4.5 25.5 1.0
HB3 A:ASP47 4.6 25.9 1.0
HB2 A:ASP47 4.7 25.9 1.0
OG1 A:THR148 4.7 21.7 1.0
C A:ASP47 4.7 22.8 1.0
CB A:ASP275 4.8 23.6 1.0
HB3 A:ASP317 4.8 26.9 1.0
O3 A:TLA601 4.8 53.6 1.0
NE2 A:HIS433 4.8 23.4 1.0
O A:HOH727 4.8 25.0 1.0
HA2 A:GLY48 4.8 29.2 1.0
HB3 A:ALA98 4.8 28.6 1.0
ZN A:ZN604 4.9 30.3 1.0
C3 A:TLA601 4.9 54.6 1.0
O A:HOH712 5.0 36.3 1.0
HB3 A:ASP275 5.0 28.3 1.0
HD1 A:HIS318 5.0 25.7 1.0

Zinc binding site 2 out of 4 in 7kwd

Go back to Zinc Binding Sites List in 7kwd
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:30.3
occ:1.00
H2 A:TLA601 1.6 55.9 1.0
OD2 A:ASP275 2.0 24.3 1.0
NE2 A:HIS433 2.2 23.4 1.0
NE2 A:HIS279 2.2 25.9 1.0
O41 A:TLA601 2.4 43.5 1.0
C2 A:TLA601 2.6 46.6 1.0
CG A:ASP275 2.6 25.3 1.0
OD1 A:ASP275 2.7 20.6 1.0
C4 A:TLA601 3.0 40.0 1.0
CD2 A:HIS279 3.1 20.1 1.0
CD2 A:HIS433 3.1 24.8 1.0
HD2 A:HIS279 3.1 24.1 1.0
CE1 A:HIS433 3.2 25.5 1.0
C3 A:TLA601 3.2 54.6 1.0
CE1 A:HIS279 3.3 25.4 1.0
HD2 A:HIS433 3.3 29.8 1.0
HE1 A:HIS433 3.4 30.6 1.0
O1 A:TLA601 3.4 62.5 1.0
C1 A:TLA601 3.5 62.9 1.0
HE1 A:HIS279 3.5 30.5 1.0
O2 A:TLA601 3.6 54.3 1.0
HE1 A:HIS318 3.6 28.1 1.0
O3 A:TLA601 3.8 53.6 1.0
O A:HOH712 4.1 36.3 1.0
O4 A:TLA601 4.1 43.9 1.0
CB A:ASP275 4.1 23.6 1.0
H3 A:TLA601 4.2 65.5 1.0
HG21 A:THR320 4.2 30.3 1.0
CG A:HIS279 4.3 23.7 1.0
ND1 A:HIS433 4.3 28.2 1.0
CG A:HIS433 4.3 24.1 1.0
HD2 A:HIS276 4.3 32.8 1.0
CE1 A:HIS318 4.3 23.4 1.0
ND1 A:HIS279 4.3 27.6 1.0
HB3 A:ASP275 4.3 28.3 1.0
HA A:TLA601 4.4 65.2 1.0
HE2 B:TYR332 4.5 30.1 1.0
HB2 A:ASP275 4.5 28.3 1.0
HB A:TLA601 4.5 64.3 1.0
OG1 A:THR320 4.6 22.0 1.0
NE2 A:HIS318 4.7 26.8 1.0
O11 A:TLA601 4.7 60.5 1.0
ZN A:ZN603 4.9 37.0 1.0
HG23 A:THR320 4.9 30.3 1.0
CG2 A:THR320 5.0 25.3 1.0
OD1 A:ASP47 5.0 21.9 1.0
HG1 A:THR320 5.0 26.5 1.0
C A:ASP275 5.0 22.7 1.0

Zinc binding site 3 out of 4 in 7kwd

Go back to Zinc Binding Sites List in 7kwd
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:38.5
occ:1.00
OG B:SER95 1.9 44.2 1.0
OD2 B:ASP317 2.2 26.9 1.0
NE2 B:HIS318 2.3 27.9 1.0
OD1 B:ASP47 2.3 26.7 1.0
O4 B:TLA601 2.7 41.3 1.0
OD2 B:ASP47 2.8 28.7 1.0
CG B:ASP47 2.8 24.5 1.0
CG B:ASP317 3.0 29.1 1.0
CD2 B:HIS318 3.1 24.6 1.0
OD1 B:ASP317 3.1 22.7 1.0
HA B:SER95 3.1 40.9 1.0
HD2 B:HIS318 3.2 29.5 1.0
CB B:SER95 3.2 39.4 1.0
CE1 B:HIS318 3.2 27.9 1.0
HE1 B:HIS318 3.5 33.5 1.0
CA B:SER95 3.6 34.1 1.0
HB2 B:SER95 3.7 47.3 1.0
HB3 B:SER95 3.8 47.3 1.0
H B:GLY48 3.9 28.6 1.0
C4 B:TLA601 3.9 42.3 1.0
O B:HOH720 4.0 37.8 1.0
O B:HOH763 4.0 23.6 1.0
HA B:ASP47 4.1 29.0 1.0
N B:SER95 4.2 35.5 1.0
CB B:ASP47 4.2 25.4 1.0
CG B:HIS318 4.2 26.0 1.0
ND1 B:HIS318 4.2 23.8 1.0
H B:SER95 4.3 42.6 1.0
HB2 B:ASP275 4.3 28.9 1.0
N B:GLY48 4.3 23.8 1.0
O3 B:TLA601 4.3 45.8 1.0
HE1 B:HIS433 4.3 33.7 1.0
CB B:ASP317 4.4 19.3 1.0
MG B:MG602 4.4 34.5 1.0
HB2 B:ASP317 4.5 23.1 1.0
O41 B:TLA601 4.5 51.6 1.0
CG B:ASP275 4.5 24.1 1.0
CA B:ASP47 4.6 24.1 1.0
OD1 B:ASP275 4.6 30.2 1.0
CE1 B:HIS433 4.6 28.1 1.0
OD2 B:ASP275 4.7 27.5 1.0
HB2 B:ASP47 4.7 30.5 1.0
HB3 B:ASP47 4.7 30.5 1.0
NE2 B:HIS433 4.7 23.3 1.0
OG1 B:THR148 4.7 27.2 1.0
C B:ASP47 4.8 25.2 1.0
HA2 B:GLY48 4.8 29.9 1.0
HB3 B:ALA98 4.8 33.2 1.0
HB3 B:ASP317 4.8 23.1 1.0
ZN B:ZN604 4.8 33.4 1.0
CB B:ASP275 4.9 24.1 1.0
C3 B:TLA601 4.9 57.8 1.0
O B:HOH726 4.9 28.9 1.0
C B:GLU94 4.9 34.6 1.0
C B:SER95 4.9 30.3 1.0

Zinc binding site 4 out of 4 in 7kwd

Go back to Zinc Binding Sites List in 7kwd
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:33.4
occ:1.00
H2 B:TLA601 1.6 67.7 1.0
OD2 B:ASP275 2.1 27.5 1.0
NE2 B:HIS433 2.2 23.3 1.0
NE2 B:HIS279 2.2 26.1 1.0
C2 B:TLA601 2.6 56.4 1.0
OD1 B:ASP275 2.7 30.2 1.0
CG B:ASP275 2.7 24.1 1.0
O4 B:TLA601 3.0 41.3 1.0
CD2 B:HIS279 3.0 25.8 1.0
HD2 B:HIS279 3.0 31.0 1.0
C4 B:TLA601 3.1 42.3 1.0
CD2 B:HIS433 3.1 27.4 1.0
CE1 B:HIS433 3.1 28.1 1.0
O2 B:TLA601 3.2 59.3 1.0
C3 B:TLA601 3.2 57.8 1.0
HD2 B:HIS433 3.3 32.9 1.0
CE1 B:HIS279 3.3 29.4 1.0
HE1 B:HIS433 3.3 33.7 1.0
HA B:TLA601 3.3 71.2 1.0
O3 B:TLA601 3.5 45.8 1.0
HE1 B:HIS318 3.6 33.5 1.0
HE1 B:HIS279 3.6 35.4 1.0
C1 B:TLA601 3.8 70.8 1.0
HB B:TLA601 3.8 54.9 1.0
O41 B:TLA601 3.8 51.6 1.0
O11 B:TLA601 4.0 60.2 1.0
CB B:ASP275 4.2 24.1 1.0
H3 B:TLA601 4.2 69.4 1.0
CG B:HIS279 4.2 29.8 1.0
HD2 B:HIS276 4.2 39.3 1.0
ND1 B:HIS433 4.3 29.1 1.0
CG B:HIS433 4.3 21.1 1.0
CE1 B:HIS318 4.3 27.9 1.0
HG1 B:THR320 4.3 32.8 1.0
ND1 B:HIS279 4.3 28.9 1.0
HG21 B:THR320 4.3 28.8 1.0
HB3 B:ASP275 4.4 28.9 1.0
HB2 B:ASP275 4.6 28.9 1.0
OG1 B:THR320 4.6 27.3 1.0
HE2 A:TYR332 4.6 36.6 1.0
NE2 B:HIS318 4.7 27.9 1.0
ZN B:ZN603 4.8 38.5 1.0
O1 B:TLA601 4.9 68.0 1.0
OD1 B:ASP47 4.9 26.7 1.0

Reference:

B.Borges, G.Gallo, C.Coelho, N.Negri, F.Maiello, L.Hardy, M.Wurtele. Dynamic Cross Correlation Analysis of Thermus Thermophilus Alkaline Phosphatase and Determinants of Thermostability. Biochim Biophys Acta Gen 29895 2021SUBJ.
ISSN: ISSN 1872-8006
PubMed: 33781823
DOI: 10.1016/J.BBAGEN.2021.129895
Page generated: Sat Apr 17 17:48:42 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy