Magnesium in PDB 8r9b: A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp

The structure of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp, PDB code: 8r9b was solved by M.Mukherjee, A.Cleasby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.14 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.14, 180.285, 76.335, 90, 117.85, 90
R / Rfree (%)	19.2 / 24.3

The binding sites of Magnesium atom in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp (pdb code 8r9b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp, PDB code: 8r9b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:48.5 occ:1.00 O1A A:ANP401 2.3 49.8 1.0 O1B A:ANP401 2.3 39.2 1.0 O A:HOH584 2.4 47.3 1.0 OD1 A:ASN142 2.5 36.0 1.0 OD2 A:ASP155 2.6 54.9 1.0 PA A:ANP401 3.0 46.9 1.0 HNB1 A:ANP401 3.1 41.8 1.0 ND2 A:ASN141 3.1 46.2 1.0 PB A:ANP401 3.1 40.8 1.0 O3A A:ANP401 3.3 48.6 1.0 N3B A:ANP401 3.4 39.5 1.0 O2A A:ANP401 3.5 49.8 1.0 CG A:ASP155 3.6 59.4 1.0 CG A:ASN142 3.7 34.2 1.0 O A:HOH533 3.7 40.3 1.0 CB A:ASP155 3.9 58.2 1.0 O A:ASN141 4.0 34.7 1.0 O A:HOH531 4.2 43.6 1.0 NZ A:LYS41 4.3 50.8 1.0 CG A:ASN141 4.3 46.8 1.0 ND2 A:ASN142 4.3 30.0 1.0 H8 A:ANP401 4.5 45.1 1.0 H5'2 A:ANP401 4.5 54.7 1.0 O5' A:ANP401 4.5 54.5 1.0 O2B A:ANP401 4.6 50.2 1.0 C A:ASN141 4.7 35.1 1.0 OD1 A:ASP155 4.7 58.8 1.0 CA A:ASN142 4.8 31.3 1.0 CB A:ASN142 4.8 32.7 1.0 PG A:ANP401 4.9 49.1 1.0 OD1 A:ASN141 5.0 51.3 1.0 O A:HOH595 5.0 51.7 1.0 N A:ASN142 5.0 29.8 1.0

Magnesium binding site 2 out of 3 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:57.2 occ:1.00 OD1 B:ASN142 2.1 38.7 1.0 O1A B:ANP402 2.3 69.0 1.0 O1B B:ANP402 2.5 44.5 1.0 OD2 B:ASP155 2.6 47.4 1.0 HNB1 B:ANP402 3.2 50.8 1.0 CG B:ASN142 3.3 35.6 1.0 CG B:ASP155 3.5 55.4 1.0 PB B:ANP402 3.5 51.1 1.0 OD1 B:ASN141 3.5 53.9 1.0 PA B:ANP402 3.6 58.6 1.0 CB B:ASP155 3.6 55.4 1.0 O B:HOH517 3.7 37.9 1.0 O B:ASN141 3.7 39.4 1.0 N3B B:ANP402 3.7 49.9 1.0 O3A B:ANP402 3.8 56.9 1.0 ND2 B:ASN142 4.1 33.9 1.0 CA B:ASN142 4.2 35.1 1.0 C B:ASN141 4.3 42.4 1.0 CB B:ASN142 4.3 39.1 1.0 NZ B:LYS41 4.5 55.0 1.0 N B:ASN142 4.5 36.5 1.0 O5' B:ANP402 4.6 62.9 1.0 O2A B:ANP402 4.6 59.4 1.0 H8 B:ANP402 4.6 44.8 1.0 OD1 B:ASP155 4.7 57.0 1.0 CG B:ASN141 4.7 55.6 1.0 O2B B:ANP402 4.9 42.9 1.0 CA B:ASP155 5.0 58.0 1.0

Magnesium binding site 3 out of 3 in the A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Soakable Crystal Form of Human CDK7 in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:64.1 occ:1.00 O1A D:ANP402 2.4 52.9 1.0 OD1 D:ASN142 2.7 44.5 1.0 OD2 D:ASP155 2.9 74.7 1.0 O D:ASN141 3.3 47.8 1.0 O D:HOH556 3.3 56.3 1.0 H3' D:ANP402 3.5 66.7 1.0 PA D:ANP402 3.6 59.5 1.0 CG D:ASN142 3.9 41.1 1.0 O5' D:ANP402 3.9 62.7 1.0 OD1 D:ASN141 3.9 44.6 1.0 H8 D:ANP402 3.9 50.7 1.0 C D:ASN141 4.1 40.1 1.0 CG D:ASP155 4.1 76.1 1.0 O2A D:ANP402 4.1 75.3 1.0 O2G D:ANP402 4.2 87.7 1.0 CA D:ASN142 4.3 37.4 1.0 O1G D:ANP402 4.4 64.2 1.0 N D:ASN142 4.5 34.5 1.0 CG D:ASN141 4.5 39.9 1.0 C3' D:ANP402 4.6 60.3 1.0 C8 D:ANP402 4.6 51.9 1.0 CB D:ASN142 4.7 34.5 1.0 HO3' D:ANP402 4.7 64.0 0.0 OD1 D:ASP155 4.8 60.9 1.0 H2' D:ANP402 4.8 59.7 1.0 PG D:ANP402 4.8 83.2 1.0 CB D:ASN141 4.9 40.9 1.0 CD2 D:LEU144 4.9 36.0 1.0 ND2 D:ASN142 4.9 39.8 1.0

M.Mukherjee, P.Day, D.Laverty, J.A.Bueren-Calabuig, A.Woodhead, C.Griffiths-Jones, S.Hiscock, C.East, S.Boyd, M.O'reilly. Protein Engineering Enables A Soakable Crystal Form of Human CDK7 Primed For High-Throughput Crystallography and Structure-Based Drug Design To Be Published.