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Magnesium in PDB 4nst: Crystal Structure of Human CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride

Enzymatic activity of Crystal Structure of Human CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride

All present enzymatic activity of Crystal Structure of Human CDK12/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 CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride, PDB code: 4nst was solved by C.A.Boesken, L.Farnung, K.Anand, M.Geyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.71 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.720, 78.850, 91.490, 104.04, 85.76, 101.46
R / Rfree (%) 19.5 / 24

Other elements in 4nst:

The structure of Crystal Structure of Human CDK12/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 CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride (pdb code 4nst). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Human CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride, PDB code: 4nst:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4nst

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Magnesium binding site 1 out of 7 in the Crystal Structure of Human CDK12/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 CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:27.9
occ:1.00
 OD2 A:ASP877 1.9 36.1 1.0
O A:HOH1263 2.1 30.1 1.0
O3B A:ADP1101 2.1 29.1 1.0
OD1 A:ASN864 2.2 24.8 1.0
F1 A:AF31102 2.2 41.9 1.0
O1A A:ADP1101 2.3 27.9 1.0
CG A:ASP877 3.0 20.9 1.0
CG A:ASN864 3.1 30.4 1.0
AL A:AF31102 3.2 89.1 1.0
PB A:ADP1101 3.4 35.5 1.0
ND2 A:ASN864 3.4 20.7 1.0
PA A:ADP1101 3.5 31.3 1.0
CB A:ASP877 3.6 21.1 1.0
MG A:MG1104 3.6 51.9 1.0
O3A A:ADP1101 3.8 26.4 1.0
OD1 A:ASP877 3.9 33.2 1.0
F3 A:AF31102 4.0 97.5 1.0
O2B A:ADP1101 4.0 45.7 1.0
OG A:SER863 4.1 38.9 1.0
F2 A:AF31102 4.3 68.7 1.0
CB A:ASN864 4.4 25.0 1.0
O2A A:ADP1101 4.5 27.8 1.0
O5' A:ADP1101 4.5 59.8 1.0
C5' A:ADP1101 4.5 65.0 1.0
O1B A:ADP1101 4.5 37.1 1.0
OD2 A:ASP859 4.7 35.1 1.0
O A:SER863 4.7 27.6 1.0
O3' A:ADP1101 4.7 60.6 1.0
CE A:LYS861 4.8 36.5 1.0
CA A:ASN864 4.8 25.4 1.0
O A:HOH1216 4.9 54.8 1.0
C A:SER863 4.9 31.2 1.0
C3' A:ADP1101 5.0 56.1 1.0
O A:HOH1201 5.0 34.3 1.0

Magnesium binding site 2 out of 7 in 4nst

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Magnesium binding site 2 out of 7 in the Crystal Structure of Human CDK12/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 CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:51.9
occ:1.00
 O2B A:ADP1101 2.1 45.7 1.0
F2 A:AF31102 2.4 68.7 1.0
OD2 A:ASP877 2.6 36.1 1.0
OD1 A:ASP877 2.7 33.2 1.0
O A:HOH1201 2.8 34.3 1.0
AL A:AF31102 2.9 89.1 1.0
CG A:ASP877 3.0 20.9 1.0
O3B A:ADP1101 3.0 29.1 1.0
PB A:ADP1101 3.1 35.5 1.0
O A:HOH1262 3.5 45.0 1.0
F1 A:AF31102 3.6 41.9 1.0
MG A:MG1103 3.6 27.9 1.0
F3 A:AF31102 3.8 97.5 1.0
OG1 A:THR737 3.8 49.5 1.0
OD2 A:ASP859 4.0 35.1 1.0
O3A A:ADP1101 4.0 26.4 1.0
O1B A:ADP1101 4.2 37.1 1.0
CB A:ASP877 4.5 21.1 1.0
O1A A:ADP1101 4.7 27.9 1.0
PA A:ADP1101 4.9 31.3 1.0
CA A:GLY879 5.0 36.4 1.0

Magnesium binding site 3 out of 7 in 4nst

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Magnesium binding site 3 out of 7 in the Crystal Structure of Human CDK12/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 CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:70.3
occ:1.00
 ND1 A:HIS999 3.3 48.8 1.0
CB A:SER1017 3.8 40.3 1.0
O A:HOH1297 4.0 48.8 1.0
CG A:HIS999 4.2 35.0 1.0
CB A:HIS999 4.2 32.7 1.0
CE1 A:HIS999 4.2 49.4 1.0
CD1 A:LEU996 4.4 28.7 1.0
CA A:SER1017 4.4 44.6 1.0
CA A:LEU996 4.5 36.5 1.0
O A:GLN1013 4.6 52.0 1.0
N A:LEU996 4.8 41.9 1.0
O A:ASP995 5.0 42.2 1.0
SG A:CYS1009 5.0 48.6 1.0
O A:HOH1233 5.0 47.0 1.0

Magnesium binding site 4 out of 7 in 4nst

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Magnesium binding site 4 out of 7 in the Crystal Structure of Human CDK12/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 CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:32.6
occ:1.00
 OD1 C:ASN864 2.1 26.7 1.0
O3B C:ADP1101 2.2 28.7 1.0
O C:HOH1268 2.2 26.4 1.0
O1A C:ADP1101 2.3 25.1 1.0
OD2 C:ASP877 2.4 39.5 1.0
F2 C:AF31102 2.7 45.4 1.0
CG C:ASN864 3.0 29.9 1.0
CG C:ASP877 3.1 26.5 1.0
ND2 C:ASN864 3.3 22.5 1.0
CB C:ASP877 3.4 29.1 1.0
PA C:ADP1101 3.4 30.2 1.0
PB C:ADP1101 3.5 36.8 1.0
AL C:AF31102 3.5 0.4 1.0
O3A C:ADP1101 3.7 28.2 1.0
MG C:MG1104 3.9 56.8 1.0
F1 C:AF31102 4.1 86.7 1.0
OG C:SER863 4.1 42.2 1.0
OD1 C:ASP877 4.2 29.5 1.0
O2B C:ADP1101 4.3 40.7 1.0
CB C:ASN864 4.3 23.9 1.0
O3' C:ADP1101 4.3 36.1 1.0
C5' C:ADP1101 4.4 42.4 1.0
O5' C:ADP1101 4.4 40.2 1.0
O2A C:ADP1101 4.4 27.7 1.0
O1B C:ADP1101 4.6 40.1 1.0
O C:HOH1258 4.7 57.2 1.0
F3 C:AF31102 4.7 69.8 1.0
CA C:ASN864 4.7 27.8 1.0
O C:SER863 4.7 32.1 1.0
CA C:ASP877 4.8 30.4 1.0
CE C:LYS861 4.9 41.2 1.0
O C:HOH1254 4.9 59.0 1.0
C C:SER863 4.9 37.2 1.0
O C:HOH1259 5.0 41.5 1.0
OD2 C:ASP859 5.0 37.4 1.0

Magnesium binding site 5 out of 7 in 4nst

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Magnesium binding site 5 out of 7 in the Crystal Structure of Human CDK12/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 5 of Crystal Structure of Human CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1104

b:56.8
occ:1.00
 F1 C:AF31102 2.2 86.7 1.0
OD2 C:ASP877 2.2 39.5 1.0
O2B C:ADP1101 2.4 40.7 1.0
OD1 C:ASP877 2.7 29.5 1.0
CG C:ASP877 2.8 26.5 1.0
O C:HOH1259 3.0 41.5 1.0
AL C:AF31102 3.1 0.4 1.0
O3B C:ADP1101 3.3 28.7 1.0
PB C:ADP1101 3.3 36.8 1.0
O C:HOH1287 3.4 44.1 1.0
OG1 C:THR737 3.8 46.6 1.0
MG C:MG1103 3.9 32.6 1.0
F3 C:AF31102 3.9 69.8 1.0
O3A C:ADP1101 4.0 28.2 1.0
F2 C:AF31102 4.2 45.4 1.0
CB C:ASP877 4.3 29.1 1.0
OD2 C:ASP859 4.4 37.4 1.0
CA C:GLY879 4.5 34.4 1.0
O1B C:ADP1101 4.6 40.1 1.0
O1A C:ADP1101 4.8 25.1 1.0
N C:GLY879 4.8 33.3 1.0
PA C:ADP1101 4.8 30.2 1.0

Magnesium binding site 6 out of 7 in 4nst

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Magnesium binding site 6 out of 7 in the Crystal Structure of Human CDK12/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 6 of Crystal Structure of Human CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:49.7
occ:1.00
 O D:LEU41 3.4 30.3 1.0
O D:GLN37 3.5 24.9 1.0
O D:HOH417 3.8 51.2 1.0
OE1 D:GLN37 3.9 55.8 1.0
O D:HOH425 4.1 43.0 1.0
C D:GLY40 4.1 33.8 1.0
C D:LEU41 4.1 26.3 1.0
CA D:GLN37 4.1 22.2 1.0
C D:GLN37 4.2 19.8 1.0
CB D:GLN37 4.2 26.3 1.0
O D:GLY40 4.3 33.5 1.0
CA D:ASP42 4.3 33.0 1.0
CA D:GLY40 4.3 24.1 1.0
O D:HOH493 4.3 30.0 1.0
N D:LEU41 4.5 30.2 1.0
CD D:PRO43 4.6 32.7 1.0
CD D:GLN37 4.6 74.7 1.0
N D:ASP42 4.6 33.3 1.0
N D:GLY40 5.0 24.6 1.0

Magnesium binding site 7 out of 7 in 4nst

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Magnesium binding site 7 out of 7 in the Crystal Structure of Human CDK12/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 7 of Crystal Structure of Human CDK12/Cyclin K in Complex with Adp-Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:74.7
occ:1.00
 OE2 D:GLU204 3.6 33.0 1.0
OE1 D:GLU204 3.8 34.2 1.0
OE2 D:GLU202 3.8 56.0 1.0
CG D:GLU202 3.9 30.1 1.0
CD D:GLU204 4.0 35.0 1.0
CB D:GLU202 4.3 25.1 1.0
CD D:GLU202 4.4 62.9 1.0

Reference:

C.A.Bosken, L.Farnung, C.Hintermair, M.Merzel Schachter, K.Vogel-Bachmayr, D.Blazek, K.Anand, R.P.Fisher, D.Eick, M.Geyer. The Structure and Substrate Specificity of Human CDK12/Cyclin K. Nat Commun V. 5 3505 2014.
ISSN: ESSN 2041-1723
PubMed: 24662513
DOI: 10.1038/NCOMMS4505
Page generated: Mon Aug 19 23:44:44 2024

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