Fluorine in PDB 6t00: Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues

Protein crystallography data

The structure of Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues, PDB code: 6t00 was solved by T.Zhou, O.Mayans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.79 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 54.940, 54.940, 57.710, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues (pdb code 6t00). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues, PDB code: 6t00:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 6t00

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Fluorine binding site 1 out of 7 in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues


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 Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9

b:64.4
occ:1.00
 F A:PFF9 0.0 64.4 1.0
CZ A:PFF9 1.3 56.9 1.0
CE2 A:PFF9 2.4 50.6 1.0
CE1 A:PFF9 2.4 52.4 1.0
C A:GLY14 3.1 49.3 1.0
CB A:PFF30 3.2 43.1 1.0
CA A:GLY14 3.2 50.2 1.0
O A:GLY14 3.3 52.1 1.0
CA A:PFF30 3.5 43.8 1.0
N A:PFF15 3.6 48.6 1.0
CD2 A:PFF9 3.6 51.6 1.0
CD1 A:PFF9 3.6 43.9 1.0
CD1 A:ILE33 3.7 42.0 1.0
N A:PFF30 3.8 40.8 1.0
CA A:PFF15 4.1 50.0 1.0
CG A:PFF9 4.1 46.7 1.0
CA A:THR40 4.2 49.2 1.0
O A:LYS39 4.3 49.8 1.0
N A:GLY14 4.5 52.1 1.0
CG A:PFF30 4.5 48.2 1.0
N A:LEU41 4.6 61.0 1.0
C A:HIS29 4.6 47.3 1.0
C A:THR40 4.7 59.4 1.0
C A:PFF15 4.8 53.4 1.0
O A:ASN10 4.8 50.6 1.0
CD2 A:PFF30 4.8 48.9 1.0
OG1 A:THR40 4.9 59.6 1.0
C A:LYS39 4.9 53.0 1.0
N A:THR40 4.9 51.6 1.0
C A:PFF30 5.0 48.5 1.0

Fluorine binding site 2 out of 7 in 6t00

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Fluorine binding site 2 out of 7 in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F15

b:79.5
occ:1.00
 F A:PFF15 0.0 79.5 1.0
CZ A:PFF15 1.4 68.6 1.0
CE1 A:PFF15 2.4 60.6 1.0
CE2 A:PFF15 2.4 70.0 1.0
CD1 A:PFF15 3.7 49.2 1.0
CD2 A:PFF15 3.7 53.8 1.0
CG A:PFF15 4.2 49.7 1.0
CG A:LYS13 4.4 64.7 1.0
CB A:LYS13 4.5 65.0 1.0
ND2 A:ASN10 4.7 78.2 1.0
NZ A:LYS13 4.8 0.0 1.0

Fluorine binding site 3 out of 7 in 6t00

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Fluorine binding site 3 out of 7 in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues


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 Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F17

b:67.8
occ:1.00
 F A:PFF17 0.0 67.8 1.0
CZ A:PFF17 1.3 60.7 1.0
CE1 A:PFF17 2.4 64.2 1.0
CE2 A:PFF17 2.4 58.7 1.0
CD1 A:PFF17 3.6 68.5 1.0
CD2 A:PFF17 3.6 61.5 1.0
CD1 A:PFF27 4.0 53.8 1.0
CB A:PFF27 4.0 48.1 1.0
CG A:PFF17 4.1 62.0 1.0
CG A:PFF27 4.5 53.6 1.0
O A:HOH216 4.6 81.7 1.0
CA A:PFF27 4.6 49.1 1.0
CE1 A:PFF27 5.0 48.9 1.0

Fluorine binding site 4 out of 7 in 6t00

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Fluorine binding site 4 out of 7 in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues


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 Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F27

b:59.1
occ:1.00
 F A:PFF27 0.0 59.1 1.0
CZ A:PFF27 1.4 56.1 1.0
CE1 A:PFF27 2.4 48.9 1.0
CE2 A:PFF27 2.4 49.4 1.0
CB A:PFF15 3.5 48.2 1.0
CD2 A:HIS29 3.5 51.1 1.0
CD1 A:PFF27 3.6 53.8 1.0
CB A:HIS29 3.6 48.3 1.0
CD2 A:PFF27 3.7 51.9 1.0
CG A:HIS29 3.9 51.4 1.0
CG A:PFF15 4.0 49.7 1.0
CA A:HIS29 4.1 44.6 1.0
CG A:PFF27 4.1 53.6 1.0
CD2 A:PFF15 4.3 53.8 1.0
O A:VAL28 4.5 50.0 1.0
N A:HIS29 4.5 38.5 1.0
O A:HOH215 4.6 73.1 1.0
C A:VAL28 4.7 52.8 1.0
NE2 A:HIS29 4.8 53.6 1.0
CD1 A:PFF15 4.8 49.2 1.0
CA A:PFF15 4.8 50.0 1.0

Fluorine binding site 5 out of 7 in 6t00

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Fluorine binding site 5 out of 7 in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F30

b:69.8
occ:1.00
 F A:PFF30 0.0 69.8 1.0
CZ A:PFF30 1.3 62.3 1.0
CE1 A:PFF30 2.4 54.6 1.0
CE2 A:PFF30 2.4 57.9 1.0
CD1 A:PFF30 3.6 46.8 1.0
CD2 A:PFF30 3.6 48.9 1.0
O3 A:GOL102 3.9 84.0 1.0
CG A:PFF30 4.1 48.2 1.0
CE1 A:HIS29 4.1 57.6 1.0
NE2 A:HIS29 4.5 53.6 1.0
C3 A:GOL102 4.9 90.2 1.0

Fluorine binding site 6 out of 7 in 6t00

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Fluorine binding site 6 out of 7 in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F38

b:83.3
occ:1.00
 F A:PFF38 0.0 83.3 1.0
CZ A:PFF38 1.3 69.5 1.0
CE1 A:PFF38 2.4 72.7 1.0
CE2 A:PFF38 2.4 65.5 1.0
CD2 A:PFF38 3.6 58.8 1.0
CD1 A:PFF38 3.6 68.4 1.0
CG A:PFF38 4.1 61.0 1.0
C1 A:NHE101 4.6 98.6 1.0
O A:SER11 4.7 58.0 1.0
C2 A:NHE101 4.9 0.9 1.0

Fluorine binding site 7 out of 7 in 6t00

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Fluorine binding site 7 out of 7 in the Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Cold Shock Protein B (Csp-B) Containing 4-F-Phe Modified Residues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F49

b:66.4
occ:1.00
 F A:PFF49 0.0 66.4 1.0
CZ A:PFF49 1.3 62.3 1.0
CE2 A:PFF49 2.4 60.9 1.0
CE1 A:PFF49 2.4 52.0 1.0
CG1 A:VAL20 3.4 83.7 1.0
CB A:VAL20 3.4 83.3 1.0
CD2 A:PFF49 3.6 58.6 1.0
CD1 A:PFF49 3.6 49.9 1.0
CG2 A:VAL20 3.7 88.5 1.0
CG2 A:ILE18 3.9 41.4 1.0
CG2 A:VAL26 4.1 48.1 1.0
CG A:PFF49 4.2 51.8 1.0
CB A:LEU2 4.2 50.6 1.0
CD1 A:LEU2 4.2 61.9 1.0
O A:GLU3 4.6 72.8 1.0
CB A:VAL26 4.6 48.6 1.0
CB A:ILE18 4.8 48.3 1.0
CG A:LEU2 4.8 53.0 1.0
CA A:VAL20 4.9 76.0 1.0
CA A:GLY4 4.9 55.6 1.0
CG1 A:ILE51 4.9 53.9 1.0
CD1 A:ILE51 4.9 49.2 1.0
C A:GLU3 5.0 66.9 1.0

Reference:

H.Welte, T.Zhou, X.Mihajlenko, O.Mayans, M.Kovermann. What Does Fluorine Do to A Protein? Thermodynamic, and Highly-Resolved Structural Insights Into Fluorine-Labelled Variants of the Cold Shock Protein. Sci Rep V. 10 2640 2020.
ISSN: ESSN 2045-2322
PubMed: 32060391
DOI: 10.1038/S41598-020-59446-W
Page generated: Sun Dec 13 13:12:49 2020

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