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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: Mon Jul 14 15:04:52 2025

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