Atomistry » Fluorine » PDB 2z78-3az8 » 2zbd
Atomistry »
  Fluorine »
    PDB 2z78-3az8 »
      2zbd »

Fluorine in PDB 2zbd: Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium

Enzymatic activity of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium

All present enzymatic activity of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium:
3.6.3.8;

Protein crystallography data

The structure of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium, PDB code: 2zbd was solved by C.Toyoshima, H.Nomura, T.Tsuda, H.Ogawa, Y.Norimatsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.900, 75.100, 152.100, 90.00, 109.30, 90.00
R / Rfree (%) 24.6 / 27.1

Other elements in 2zbd:

The structure of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom
Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium (pdb code 2zbd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium, PDB code: 2zbd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2zbd

Go back to Fluorine Binding Sites List in 2zbd
Fluorine binding site 1 out of 4 in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:57.1
occ:1.00
 F1 A:ALF998 0.0 57.1 1.0
AL A:ALF998 1.8 57.0 1.0
OG1 A:THR625 2.4 58.7 1.0
O3B A:ADP1002 2.5 48.9 1.0
F3 A:ALF998 2.5 56.2 1.0
OD1 A:ASP351 2.6 58.7 1.0
F4 A:ALF998 2.6 55.3 1.0
N A:THR353 2.9 61.1 1.0
N A:LYS352 3.0 60.5 1.0
OG1 A:THR353 3.1 61.2 1.0
CB A:THR625 3.1 59.1 1.0
CB A:LYS352 3.4 60.7 1.0
CA A:LYS352 3.4 60.7 1.0
CG A:ASP351 3.4 59.9 1.0
F2 A:ALF998 3.6 55.3 1.0
C A:LYS352 3.6 60.8 1.0
CA A:THR625 3.7 58.8 1.0
CB A:THR353 3.8 61.4 1.0
OD2 A:ASP351 3.9 59.4 1.0
PB A:ADP1002 3.9 52.4 1.0
CA A:THR353 3.9 61.7 1.0
C A:ASP351 4.1 60.8 1.0
N A:GLY626 4.2 57.9 1.0
CE A:LYS352 4.2 63.0 1.0
O A:ILE624 4.4 60.2 1.0
MG A:MG1001 4.4 49.4 1.0
CG A:LYS352 4.4 60.8 1.0
CA A:ASP351 4.5 61.4 1.0
CB A:ASP351 4.5 60.8 1.0
O2B A:ADP1002 4.5 51.5 1.0
C A:THR625 4.5 58.3 1.0
NZ A:LYS684 4.5 60.0 1.0
CG2 A:THR625 4.6 57.0 1.0
O3A A:ADP1002 4.6 53.1 1.0
NZ A:LYS352 4.7 64.1 1.0
CD A:LYS352 4.8 62.0 1.0
N A:THR625 4.8 59.9 1.0
O A:THR353 4.8 62.5 1.0
O A:LYS352 4.8 60.6 1.0
C A:THR353 4.9 62.5 1.0
O1B A:ADP1002 4.9 50.0 1.0
C A:ILE624 5.0 60.7 1.0

Fluorine binding site 2 out of 4 in 2zbd

Go back to Fluorine Binding Sites List in 2zbd
Fluorine binding site 2 out of 4 in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:55.3
occ:1.00
 F2 A:ALF998 0.0 55.3 1.0
AL A:ALF998 1.8 57.0 1.0
F4 A:ALF998 2.5 55.3 1.0
F3 A:ALF998 2.5 56.2 1.0
OD1 A:ASP351 2.5 58.7 1.0
O A:HOH1038 2.5 65.2 1.0
ND2 A:ASN706 2.6 57.0 1.0
O3B A:ADP1002 2.9 48.9 1.0
MG A:MG1001 3.2 49.4 1.0
OD1 A:ASN706 3.3 54.2 1.0
CG A:ASN706 3.3 56.5 1.0
MG A:MG997 3.3 0.5 1.0
CG A:ASP351 3.5 59.9 1.0
F1 A:ALF998 3.6 57.1 1.0
NZ A:LYS684 3.6 60.0 1.0
O3A A:ADP1002 3.8 53.1 1.0
O A:HOH1046 3.8 73.3 1.0
PB A:ADP1002 3.8 52.4 1.0
O1A A:ADP1002 3.9 52.8 1.0
OD2 A:ASP351 4.0 59.4 1.0
O A:HOH1041 4.1 55.8 1.0
OD1 A:ASP707 4.1 55.3 1.0
O1B A:ADP1002 4.2 50.0 1.0
PA A:ADP1002 4.3 53.3 1.0
OD2 A:ASP707 4.4 53.0 1.0
CB A:ASP351 4.6 60.8 1.0
CG A:ASP707 4.7 56.4 1.0
CE A:LYS684 4.7 61.2 1.0
O2A A:ADP1002 4.8 52.6 1.0
CB A:ASN706 4.8 57.0 1.0
O A:HOH1051 4.8 83.9 1.0
OD1 A:ASP703 4.8 62.7 1.0

Fluorine binding site 3 out of 4 in 2zbd

Go back to Fluorine Binding Sites List in 2zbd
Fluorine binding site 3 out of 4 in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:56.2
occ:1.00
 F3 A:ALF998 0.0 56.2 1.0
AL A:ALF998 1.8 57.0 1.0
F2 A:ALF998 2.5 55.3 1.0
F1 A:ALF998 2.5 57.1 1.0
OD1 A:ASP351 2.7 58.7 1.0
O3B A:ADP1002 2.7 48.9 1.0
NZ A:LYS684 2.8 60.0 1.0
N A:GLY626 2.8 57.9 1.0
CA A:THR625 3.0 58.8 1.0
OG1 A:THR625 3.1 58.7 1.0
C A:THR625 3.3 58.3 1.0
O3A A:ADP1002 3.5 53.1 1.0
CB A:THR625 3.6 59.1 1.0
F4 A:ALF998 3.6 55.3 1.0
CE A:LYS684 3.6 61.2 1.0
ND2 A:ASN706 3.6 57.0 1.0
O A:ILE624 3.8 60.2 1.0
PB A:ADP1002 3.8 52.4 1.0
CG A:ASP351 3.9 59.9 1.0
CA A:GLY626 4.0 57.6 1.0
N A:THR625 4.1 59.9 1.0
C A:ILE624 4.3 60.7 1.0
O A:HOH1051 4.4 83.9 1.0
O A:THR625 4.5 58.4 1.0
CB A:ASP351 4.6 60.8 1.0
O2B A:ADP1002 4.6 51.5 1.0
PA A:ADP1002 4.7 53.3 1.0
N A:LYS352 4.7 60.5 1.0
O A:HOH1038 4.7 65.2 1.0
O2A A:ADP1002 4.8 52.6 1.0
N A:ASP627 4.8 57.2 1.0
OD2 A:ASP351 4.8 59.4 1.0
CG A:ASN706 4.9 56.5 1.0
O1B A:ADP1002 4.9 50.0 1.0
CA A:ASP351 4.9 61.4 1.0
C A:GLY626 4.9 57.2 1.0
OD1 A:ASP707 5.0 55.3 1.0

Fluorine binding site 4 out of 4 in 2zbd

Go back to Fluorine Binding Sites List in 2zbd
Fluorine binding site 4 out of 4 in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:55.3
occ:1.00
 F4 A:ALF998 0.0 55.3 1.0
AL A:ALF998 1.8 57.0 1.0
MG A:MG1001 2.0 49.4 1.0
F2 A:ALF998 2.5 55.3 1.0
OD1 A:ASP351 2.5 58.7 1.0
O3B A:ADP1002 2.6 48.9 1.0
F1 A:ALF998 2.6 57.1 1.0
O A:THR353 2.9 62.5 1.0
CB A:THR353 2.9 61.4 1.0
OD2 A:ASP351 2.9 59.4 1.0
O A:HOH1041 3.0 55.8 1.0
N A:THR353 3.0 61.1 1.0
CG A:ASP351 3.1 59.9 1.0
OG1 A:THR353 3.1 61.2 1.0
O A:HOH1038 3.1 65.2 1.0
CA A:THR353 3.2 61.7 1.0
MG A:MG997 3.2 0.5 1.0
C A:THR353 3.4 62.5 1.0
F3 A:ALF998 3.6 56.2 1.0
PB A:ADP1002 3.8 52.4 1.0
O1B A:ADP1002 4.0 50.0 1.0
OD1 A:ASP703 4.0 62.7 1.0
C A:LYS352 4.1 60.8 1.0
CG2 A:THR353 4.3 60.7 1.0
N A:LYS352 4.3 60.5 1.0
CB A:ASP351 4.5 60.8 1.0
OD2 A:ASP703 4.7 63.5 1.0
CA A:LYS352 4.7 60.7 1.0
O3A A:ADP1002 4.7 53.1 1.0
N A:GLY354 4.8 63.4 1.0
OG1 A:THR625 4.8 58.7 1.0
CG A:ASP703 4.8 62.9 1.0
O A:LYS352 4.9 60.6 1.0
O2B A:ADP1002 5.0 51.5 1.0

Reference:

C.Toyoshima, H.Nomura, T.Tsuda. Lumenal Gating Mechanism Revealed in Calcium Pump Crystal Structures with Phosphate Analogues Nature V. 432 361 2004.
ISSN: ISSN 0028-0836
PubMed: 15448704
DOI: 10.1038/NATURE02981
Page generated: Wed Jul 31 16:59:05 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy