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Fluorine in PDB 5efq: Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride

Enzymatic activity of Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride

All present enzymatic activity of Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride:
2.7.11.22; 2.7.11.23;

Protein crystallography data

The structure of Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride, PDB code: 5efq was solved by D.Hoenig, A.K.Greifenberg, K.Anand, M.Geyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.19 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.780, 81.820, 93.140, 74.08, 84.26, 76.89
R / Rfree (%) 19.4 / 24.7

Other elements in 5efq:

The structure of Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride (pdb code 5efq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride, PDB code: 5efq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5efq

Go back to Fluorine Binding Sites List in 5efq
Fluorine binding site 1 out of 6 in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride


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 Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:49.4
occ:1.00
 F1 A:AF31102 0.0 49.4 1.0
AL A:AF31102 1.6 0.7 1.0
MG A:MG1103 2.1 49.4 1.0
OD2 A:ASP855 2.7 46.0 1.0
O3B A:ADP1101 2.8 61.7 1.0
F3 A:AF31102 2.8 95.0 1.0
F2 A:AF31102 2.9 80.9 1.0
O A:HOH1207 2.9 49.9 1.0
ND2 A:ASN842 2.9 46.8 1.0
OD1 A:ASN842 3.0 46.1 1.0
OD2 A:ASP837 3.3 55.0 1.0
CG A:ASN842 3.4 50.5 1.0
CE A:LYS839 3.4 61.6 1.0
MG A:MG1104 3.5 68.1 1.0
CG A:ASP855 3.9 48.1 1.0
NZ A:LYS839 4.0 65.6 1.0
PB A:ADP1101 4.0 56.5 1.0
O2A A:ADP1101 4.2 44.6 1.0
CG A:ASP837 4.3 54.7 1.0
O2B A:ADP1101 4.3 85.2 1.0
O A:HOH1204 4.3 61.7 1.0
OG A:SER841 4.3 52.4 1.0
OD1 A:ASP837 4.6 49.6 1.0
CD A:LYS839 4.7 54.9 1.0
CB A:ASP855 4.7 44.2 1.0
OD1 A:ASP855 4.8 48.4 1.0
CB A:ASN842 4.9 46.6 1.0
O A:HOH1223 4.9 73.3 1.0
O3A A:ADP1101 4.9 96.2 1.0
CG A:LYS839 5.0 51.0 1.0

Fluorine binding site 2 out of 6 in 5efq

Go back to Fluorine Binding Sites List in 5efq
Fluorine binding site 2 out of 6 in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride


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 Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:80.9
occ:1.00
 F2 A:AF31102 0.0 80.9 1.0
AL A:AF31102 1.7 0.7 1.0
OD2 A:ASP837 2.3 55.0 1.0
F3 A:AF31102 2.8 95.0 1.0
F1 A:AF31102 2.9 49.4 1.0
CG A:ASP837 3.2 54.7 1.0
MG A:MG1104 3.2 68.1 1.0
OD1 A:ASP837 3.5 49.6 1.0
O A:HOH1204 3.6 61.7 1.0
OD2 A:ASP855 4.1 46.0 1.0
O A:HOH1271 4.1 0.3 1.0
NZ A:LYS839 4.1 65.6 1.0
CE A:LYS839 4.1 61.6 1.0
CB A:ASP837 4.6 48.1 1.0
ND2 A:ASN842 4.6 46.8 1.0
MG A:MG1103 4.7 49.4 1.0
CD1 A:LEU858 4.7 79.4 1.0
O3B A:ADP1101 4.8 61.7 1.0

Fluorine binding site 3 out of 6 in 5efq

Go back to Fluorine Binding Sites List in 5efq
Fluorine binding site 3 out of 6 in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride


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 Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:95.0
occ:1.00
 F3 A:AF31102 0.0 95.0 1.0
AL A:AF31102 1.6 0.7 1.0
F1 A:AF31102 2.8 49.4 1.0
F2 A:AF31102 2.8 80.9 1.0
O3B A:ADP1101 3.4 61.7 1.0
O A:HOH1223 3.7 73.3 1.0
MG A:MG1104 3.7 68.1 1.0
PB A:ADP1101 4.0 56.5 1.0
O2B A:ADP1101 4.1 85.2 1.0
MG A:MG1103 4.2 49.4 1.0
O A:HOH1207 4.3 49.9 1.0
O1B A:ADP1101 4.3 60.9 1.0
NZ A:LYS839 4.4 65.6 1.0
OD2 A:ASP855 4.6 46.0 1.0
OD2 A:ASP837 4.8 55.0 1.0
CE A:LYS839 4.8 61.6 1.0
OG1 A:THR715 5.0 74.7 1.0

Fluorine binding site 4 out of 6 in 5efq

Go back to Fluorine Binding Sites List in 5efq
Fluorine binding site 4 out of 6 in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride


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 Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1102

b:95.1
occ:1.00
 F1 C:AF31102 0.0 95.1 1.0
AL C:AF31102 1.6 0.6 1.0
OD2 C:ASP837 2.4 64.6 1.0
F3 C:AF31102 2.8 0.5 1.0
F2 C:AF31102 2.8 50.6 1.0
MG C:MG1104 3.1 75.2 1.0
CG C:ASP837 3.4 63.2 1.0
O C:HOH1221 3.7 47.8 1.0
OD1 C:ASP837 3.8 54.7 1.0
OD2 C:ASP855 4.1 49.1 1.0
NZ C:LYS839 4.3 70.2 1.0
CE C:LYS839 4.4 61.3 1.0
O1B C:ADP1101 4.6 58.8 1.0
CD1 C:LEU858 4.6 75.4 1.0
MG C:MG1103 4.6 44.6 1.0
O C:HOH1269 4.6 99.2 1.0
CB C:ASP837 4.7 48.8 1.0
ND2 C:ASN842 4.7 38.5 1.0
O2B C:ADP1101 5.0 84.7 1.0

Fluorine binding site 5 out of 6 in 5efq

Go back to Fluorine Binding Sites List in 5efq
Fluorine binding site 5 out of 6 in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride


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 Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1102

b:50.6
occ:1.00
 F2 C:AF31102 0.0 50.6 1.0
AL C:AF31102 1.6 0.6 1.0
MG C:MG1103 2.2 44.6 1.0
O1B C:ADP1101 2.8 58.8 1.0
O C:HOH1203 2.8 62.1 1.0
F3 C:AF31102 2.8 0.5 1.0
F1 C:AF31102 2.8 95.1 1.0
OD2 C:ASP855 2.9 49.1 1.0
ND2 C:ASN842 3.0 38.5 1.0
OD1 C:ASN842 3.1 40.9 1.0
CE C:LYS839 3.3 61.3 1.0
OD2 C:ASP837 3.3 64.6 1.0
CG C:ASN842 3.4 49.1 1.0
MG C:MG1104 3.7 75.2 1.0
NZ C:LYS839 3.8 70.2 1.0
CG C:ASP855 4.1 48.6 1.0
PB C:ADP1101 4.1 57.9 1.0
CG C:ASP837 4.3 63.2 1.0
O C:HOH1247 4.3 91.0 1.0
OG C:SER841 4.4 53.2 1.0
O1A C:ADP1101 4.4 48.9 1.0
CD C:LYS839 4.6 52.6 1.0
O2B C:ADP1101 4.6 84.7 1.0
OD1 C:ASP837 4.6 54.7 1.0
O C:HOH1221 4.7 47.8 1.0
CB C:ASP855 4.9 34.2 1.0
OD1 C:ASP855 4.9 42.1 1.0
O3B C:ADP1101 4.9 53.6 1.0
CG C:LYS839 4.9 46.7 1.0
CB C:ASN842 4.9 41.0 1.0

Fluorine binding site 6 out of 6 in 5efq

Go back to Fluorine Binding Sites List in 5efq
Fluorine binding site 6 out of 6 in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride


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 Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1102

b:0.5
occ:1.00
 F3 C:AF31102 0.0 0.5 1.0
AL C:AF31102 1.6 0.6 1.0
F2 C:AF31102 2.8 50.6 1.0
F1 C:AF31102 2.8 95.1 1.0
O1B C:ADP1101 3.3 58.8 1.0
O C:HOH1247 3.3 91.0 1.0
MG C:MG1104 3.5 75.2 1.0
O2B C:ADP1101 3.8 84.7 1.0
PB C:ADP1101 3.8 57.9 1.0
O C:HOH1202 3.9 61.4 1.0
O3B C:ADP1101 4.0 53.6 1.0
O C:HOH1203 4.0 62.1 1.0
MG C:MG1103 4.1 44.6 1.0
OD2 C:ASP855 4.5 49.1 1.0
OG1 C:THR715 4.6 74.1 1.0
NZ C:LYS839 4.6 70.2 1.0
OD2 C:ASP837 4.9 64.6 1.0

Reference:

A.K.Greifenberg, D.Honig, K.Pilarova, R.Duster, K.Bartholomeeusen, C.A.Bosken, K.Anand, D.Blazek, M.Geyer. Structural and Functional Analysis of the CDK13/Cyclin K Complex. Cell Rep V. 14 320 2016.
ISSN: ESSN 2211-1247
PubMed: 26748711
DOI: 10.1016/J.CELREP.2015.12.025
Page generated: Thu Aug 1 09:02:44 2024

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