Atomistry » Sodium » PDB 5gu8-5hl0 » 5hhi
Atomistry »
  Sodium »
    PDB 5gu8-5hl0 »
      5hhi »

Sodium in PDB 5hhi: Structure of Human Dna Polymerase Beta Host-Guest Complexed with Cbz- Platinated N7-G

Enzymatic activity of Structure of Human Dna Polymerase Beta Host-Guest Complexed with Cbz- Platinated N7-G

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

Protein crystallography data

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

Resolution Low / High (Å) 18.26 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.372, 80.119, 54.674, 90.00, 108.94, 90.00
R / Rfree (%) 22.2 / 27.9

Other elements in 5hhi:

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complexed with Cbz- Platinated N7-G also contains other interesting chemical elements:

Platinum (Pt) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Host-Guest Complexed with Cbz- Platinated N7-G (pdb code 5hhi). 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 Cbz- Platinated N7-G, PDB code: 5hhi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5hhi

Go back to Sodium Binding Sites List in 5hhi
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Host-Guest Complexed with Cbz- Platinated N7-G


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 Cbz- Platinated N7-G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:34.8
occ:1.00
O A:THR101 2.3 34.6 1.0
OP1 P:DT9 2.4 30.1 1.0
O A:VAL103 2.6 29.9 1.0
O P:HOH206 2.6 40.7 1.0
O A:ILE106 2.7 33.5 1.0
C A:THR101 3.4 29.4 1.0
P P:DT9 3.4 26.1 1.0
C A:VAL103 3.4 31.3 1.0
O A:HOH509 3.4 38.6 1.0
OP2 P:DT9 3.6 32.4 1.0
C A:ILE106 3.6 32.2 1.0
CA A:SER104 3.8 28.4 1.0
N A:ILE106 3.8 30.9 1.0
N A:SER104 4.0 37.7 1.0
N A:GLY105 4.0 31.9 1.0
CA A:THR101 4.1 33.1 1.0
N A:VAL103 4.1 23.1 1.0
C A:ARG102 4.2 32.0 1.0
CA A:ILE106 4.3 34.3 1.0
C A:SER104 4.3 32.7 1.0
O3' P:DC8 4.4 29.3 1.0
N A:ARG102 4.4 26.8 1.0
CA A:VAL103 4.4 31.0 1.0
CA A:ARG102 4.5 35.9 1.0
N A:GLY107 4.6 33.1 1.0
O5' P:DT9 4.6 34.7 1.0
CB A:THR101 4.6 34.8 1.0
CB A:ILE106 4.7 35.5 1.0
O A:ARG102 4.7 34.2 1.0
C A:GLY105 4.8 27.1 1.0
CA A:GLY107 4.9 35.0 1.0
CA A:GLY105 4.9 31.0 1.0

Sodium binding site 2 out of 2 in 5hhi

Go back to Sodium Binding Sites List in 5hhi
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Host-Guest Complexed with Cbz- Platinated N7-G


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 Cbz- Platinated N7-G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:62.5
occ:1.00
OP1 D:DC3 2.5 48.3 1.0
O A:VAL65 2.5 47.7 1.0
O A:LYS60 2.6 48.5 1.0
O D:HOH201 3.0 57.4 1.0
P D:DC3 3.4 40.3 1.0
OP2 D:DC3 3.4 48.1 1.0
O A:LEU62 3.6 50.9 1.0
C A:VAL65 3.8 47.2 1.0
C A:LYS60 3.8 49.5 1.0
CG A:LYS60 4.1 49.9 1.0
O5' D:DC3 4.4 34.5 1.0
CA A:GLY66 4.5 40.9 1.0
C A:LEU62 4.5 44.5 1.0
CA A:LYS60 4.5 54.2 1.0
N A:GLY66 4.6 46.6 1.0
N A:VAL65 4.6 47.0 1.0
C A:LYS61 4.6 48.8 1.0
O3' D:DT2 4.7 46.3 1.0
O A:LYS61 4.7 52.2 1.0
CA A:VAL65 4.7 48.8 1.0
N A:LYS61 4.8 50.0 1.0
CA A:LYS61 4.9 49.1 1.0
CB A:LYS60 4.9 52.3 1.0
N A:LEU62 4.9 53.1 1.0
N A:GLY64 4.9 48.4 1.0
CA A:PRO63 5.0 34.5 1.0

Reference:

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
Page generated: Thu Oct 29 05:28:47 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy