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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: Tue Dec 15 11:03:17 2020

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