Sodium in PDB 5hhh: Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination

All present enzymatic activity of Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination, PDB code: 5hhh was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.64 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.334, 84.595, 55.523, 90.00, 107.49, 90.00
R / Rfree (%)	21.3 / 26.5

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination (pdb code 5hhh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination, PDB code: 5hhh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:29.1 occ:1.00 OP1 P:DT9 2.3 27.8 1.0 O A:THR101 2.3 29.9 1.0 O A:ILE106 2.4 27.7 1.0 O A:HOH551 2.4 28.3 1.0 O A:VAL103 2.4 22.1 1.0 O P:HOH103 2.5 25.6 1.0 P P:DT9 3.2 30.2 1.0 OP2 P:DT9 3.4 26.9 1.0 C A:THR101 3.4 28.7 1.0 C A:ILE106 3.4 30.4 1.0 C A:VAL103 3.4 28.4 1.0 O A:HOH534 3.5 29.6 1.0 N A:ILE106 3.7 30.0 1.0 CA A:SER104 4.0 26.5 1.0 N A:GLY105 4.0 29.3 1.0 CA A:THR101 4.0 24.2 1.0 N A:SER104 4.0 30.4 1.0 CA A:ILE106 4.0 26.0 1.0 N A:VAL103 4.1 26.1 1.0 O3' P:DC8 4.2 31.1 1.0 C A:ARG102 4.3 27.3 1.0 C A:SER104 4.3 28.4 1.0 N A:GLY107 4.3 28.7 1.0 N A:ARG102 4.4 31.2 1.0 CA A:VAL103 4.4 26.9 1.0 CB A:ILE106 4.5 25.5 1.0 O5' P:DT9 4.5 29.2 1.0 C A:GLY105 4.6 27.6 1.0 CB A:THR101 4.6 25.6 1.0 CA A:ARG102 4.6 27.0 1.0 CA A:GLY107 4.7 27.8 1.0 O A:ARG102 4.8 30.6 1.0 CA A:GLY105 4.8 27.1 1.0 O A:HOH528 4.9 27.4 1.0 O A:LEU100 4.9 29.6 1.0

Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta Host-Guest Complexed with the Control G For N7-Cbz-Platination within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:46.0 occ:1.00 O A:LYS60 2.4 39.7 1.0 OP1 D:DC3 2.4 41.5 1.0 O A:VAL65 2.5 40.5 1.0 O A:HOH512 2.7 38.5 1.0 O A:LEU62 2.7 40.4 1.0 P D:DC3 3.5 41.7 1.0 C A:LYS60 3.6 40.5 1.0 C A:VAL65 3.6 37.3 1.0 OP2 D:DC3 3.7 38.6 1.0 C A:LEU62 3.8 40.0 1.0 O A:LYS61 4.1 40.0 1.0 C A:LYS61 4.1 40.5 1.0 N A:VAL65 4.1 30.7 1.0 N A:LEU62 4.3 40.7 1.0 CA A:LYS60 4.4 43.0 1.0 CA A:VAL65 4.4 35.4 1.0 N A:GLY64 4.4 39.4 1.0 CA A:PRO63 4.4 32.8 1.0 CG A:LYS60 4.5 42.6 1.0 N A:PRO63 4.5 37.1 1.0 N A:LYS61 4.5 37.1 1.0 O3' D:DT2 4.6 38.4 1.0 CA A:LYS61 4.6 41.6 1.0 N A:GLY66 4.6 39.9 1.0 O5' D:DC3 4.7 44.4 1.0 CA A:LEU62 4.7 37.7 1.0 CA A:GLY66 4.8 35.5 1.0 CB A:VAL65 4.8 37.0 1.0 C A:PRO63 4.9 39.2 1.0 NZ A:LYS60 5.0 52.8 1.0

Y.Cheun, M.C.Koag, Y.W.Naguib, H.Ouzon-Shubeita, Z.Cui, D.Pakotiprapha, S.Lee. Synthesis, Structure, and Biological Evaluation of A Platinum-Carbazole Conjugate. Chem Biol Drug Des V. 91 116 2018.
ISSN: ESSN 1747-0285
PubMed: 28649747
DOI: 10.1111/CBDD.13062