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Magnesium 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:

Fluorine (F) 6 atoms
Aluminium (Al) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human CDK13/Cyclin K in Complex with Adp-Aluminum Fluoride, PDB code: 5efq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5efq

Go back to Magnesium Binding Sites List in 5efq
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg1103

b:49.4
occ:1.00
 O3B A:ADP1101 1.8 61.7 1.0
OD1 A:ASN842 2.0 46.1 1.0
OD2 A:ASP855 2.0 46.0 1.0
O2A A:ADP1101 2.1 44.6 1.0
F1 A:AF31102 2.1 49.4 1.0
O A:HOH1207 2.2 49.9 1.0
CG A:ASP855 2.9 48.1 1.0
CG A:ASN842 2.9 50.5 1.0
PB A:ADP1101 3.0 56.5 1.0
PA A:ADP1101 3.2 46.0 1.0
ND2 A:ASN842 3.3 46.8 1.0
O3A A:ADP1101 3.3 96.2 1.0
CB A:ASP855 3.3 44.2 1.0
AL A:AF31102 3.4 0.7 1.0
O2B A:ADP1101 3.6 85.2 1.0
MG A:MG1104 3.7 68.1 1.0
OD1 A:ASP855 3.9 48.4 1.0
F3 A:AF31102 4.2 95.0 1.0
O1B A:ADP1101 4.2 60.9 1.0
O1A A:ADP1101 4.2 42.4 1.0
O5' A:ADP1101 4.3 52.6 1.0
CB A:ASN842 4.3 46.6 1.0
C5' A:ADP1101 4.4 47.6 1.0
OG A:SER841 4.6 52.4 1.0
F2 A:AF31102 4.7 80.9 1.0
OD2 A:ASP837 4.7 55.0 1.0
CA A:ASN842 4.7 44.5 1.0
O A:HOH1204 4.7 61.7 1.0
O A:HOH1223 4.8 73.3 1.0
CA A:ASP855 4.8 40.9 1.0
O3' A:ADP1101 4.8 51.0 1.0
O A:SER841 4.9 50.1 1.0
C3' A:ADP1101 5.0 49.2 1.0

Magnesium binding site 2 out of 4 in 5efq

Go back to Magnesium Binding Sites List in 5efq
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg1104

b:68.1
occ:1.00
 O2B A:ADP1101 2.3 85.2 1.0
OD2 A:ASP855 2.4 46.0 1.0
O A:HOH1204 2.6 61.7 1.0
OD1 A:ASP855 2.8 48.4 1.0
AL A:AF31102 2.9 0.7 1.0
CG A:ASP855 2.9 48.1 1.0
F2 A:AF31102 3.2 80.9 1.0
PB A:ADP1101 3.3 56.5 1.0
O A:HOH1271 3.4 0.3 1.0
O3B A:ADP1101 3.4 61.7 1.0
F1 A:AF31102 3.5 49.4 1.0
O A:HOH1218 3.7 84.9 1.0
OD2 A:ASP837 3.7 55.0 1.0
MG A:MG1103 3.7 49.4 1.0
F3 A:AF31102 3.7 95.0 1.0
OG1 A:THR715 3.9 74.7 1.0
O3A A:ADP1101 4.1 96.2 1.0
CD1 A:LEU858 4.4 79.4 1.0
O1B A:ADP1101 4.4 60.9 1.0
CB A:ASP855 4.4 44.2 1.0
O A:ASP855 4.6 37.4 1.0
O A:HOH1224 4.9 57.1 1.0
CG A:ASP837 4.9 54.7 1.0
O2A A:ADP1101 5.0 44.6 1.0

Magnesium binding site 3 out of 4 in 5efq

Go back to Magnesium Binding Sites List in 5efq
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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
C:Mg1103

b:44.6
occ:1.00
 O1B C:ADP1101 1.5 58.8 1.0
OD2 C:ASP855 2.0 49.1 1.0
O C:HOH1203 2.0 62.1 1.0
OD1 C:ASN842 2.1 40.9 1.0
O1A C:ADP1101 2.1 48.9 1.0
F2 C:AF31102 2.2 50.6 1.0
PB C:ADP1101 2.9 57.9 1.0
CG C:ASP855 3.0 48.6 1.0
CG C:ASN842 3.0 49.1 1.0
PA C:ADP1101 3.2 43.4 1.0
O3A C:ADP1101 3.3 0.7 1.0
ND2 C:ASN842 3.4 38.5 1.0
AL C:AF31102 3.4 0.6 1.0
CB C:ASP855 3.5 34.2 1.0
MG C:MG1104 3.8 75.2 1.0
O2B C:ADP1101 3.9 84.7 1.0
O3B C:ADP1101 4.0 53.6 1.0
OD1 C:ASP855 4.0 42.1 1.0
F3 C:AF31102 4.1 0.5 1.0
O5' C:ADP1101 4.2 46.3 1.0
O C:HOH1247 4.3 91.0 1.0
O2A C:ADP1101 4.3 51.7 1.0
C5' C:ADP1101 4.4 43.0 1.0
CB C:ASN842 4.4 41.0 1.0
OG C:SER841 4.5 53.2 1.0
F1 C:AF31102 4.6 95.1 1.0
CA C:ASN842 4.8 39.3 1.0
OD2 C:ASP837 4.8 64.6 1.0
O3' C:ADP1101 4.8 56.5 1.0
O C:SER841 4.9 48.3 1.0
CA C:ASP855 4.9 39.5 1.0

Magnesium binding site 4 out of 4 in 5efq

Go back to Magnesium Binding Sites List in 5efq
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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:Mg1104

b:75.2
occ:1.00
 O2B C:ADP1101 2.4 84.7 1.0
OD2 C:ASP855 2.6 49.1 1.0
O C:HOH1269 2.6 99.2 1.0
OD1 C:ASP855 3.0 42.1 1.0
AL C:AF31102 3.0 0.6 1.0
O C:HOH1221 3.1 47.8 1.0
F1 C:AF31102 3.1 95.1 1.0
CG C:ASP855 3.2 48.6 1.0
O1B C:ADP1101 3.2 58.8 1.0
PB C:ADP1101 3.2 57.9 1.0
F3 C:AF31102 3.5 0.5 1.0
F2 C:AF31102 3.7 50.6 1.0
MG C:MG1103 3.8 44.6 1.0
OG1 C:THR715 3.8 74.1 1.0
O3A C:ADP1101 4.0 0.7 1.0
OD2 C:ASP837 4.1 64.6 1.0
O C:HOH1241 4.3 49.4 1.0
O3B C:ADP1101 4.4 53.6 1.0
CB C:ASP855 4.7 34.2 1.0
CD1 C:LEU858 4.7 75.4 1.0
O C:ASP855 4.9 42.9 1.0
O1A C:ADP1101 4.9 48.9 1.0
PA C:ADP1101 5.0 43.4 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: Sun Sep 29 03:41:04 2024

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