Bromine in PDB 7om3: Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template

All present enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template:
2.7.7.7;

The structure of Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template, PDB code: 7om3 was solved by K.Betz, H.M.Kropp, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.45 / 1.92
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.356, 142.936, 65.582, 90, 90, 90
R / Rfree (%)	18.3 / 23.4

The binding sites of Bromine atom in the Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template (pdb code 7om3). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template, PDB code: 7om3:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Br905 b:97.7 occ:1.00 HZ2 A:LYS659 2.7 88.1 1.0 HG22 A:VAL655 3.3 58.1 1.0 HD2 A:PRO656 3.3 69.5 1.0 HD2 A:LYS659 3.4 62.7 1.0 HG13 A:VAL655 3.5 59.4 1.0 HD13 A:ILE618 3.6 58.1 1.0 NZ A:LYS659 3.6 73.4 1.0 HA A:VAL655 3.8 65.0 1.0 HD2 A:LYS649 3.8 98.2 1.0 HD11 A:ILE618 3.9 58.1 1.0 HZ2 A:LYS649 3.9 113.9 1.0 HZ3 A:LYS659 3.9 88.1 1.0 HD3 A:PRO656 4.0 69.5 1.0 CD A:PRO656 4.1 57.9 1.0 HZ1 A:LYS659 4.1 88.1 1.0 CD1 A:ILE618 4.1 48.4 1.0 CD A:LYS659 4.2 52.3 1.0 CG2 A:VAL655 4.2 48.5 1.0 OE2 A:GLU621 4.3 55.6 1.0 CE A:LYS659 4.3 60.6 1.0 CG1 A:VAL655 4.4 49.5 1.0 HD3 A:LYS659 4.4 62.7 1.0 HE3 A:LYS659 4.5 72.7 1.0 HD12 A:ILE618 4.5 58.1 1.0 HG21 A:VAL655 4.6 58.1 1.0 CA A:VAL655 4.6 54.2 1.0 CB A:VAL655 4.6 57.3 1.0 CD A:LYS649 4.7 81.8 1.0 HG11 A:VAL655 4.7 59.4 1.0 NZ A:LYS649 4.7 94.9 1.0 HG23 A:VAL655 4.8 58.1 1.0 HD3 A:LYS649 4.8 98.2 1.0 HG3 A:PRO656 4.9 66.3 1.0 CG A:PRO656 4.9 55.3 1.0 HG2 A:PRO656 5.0 66.3 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Kod Dna Polymerase in A Binary Complex with Hypoxanthine Containing Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Br906 b:93.6 occ:1.00 HZ1 A:LYS487 2.5 76.4 1.0 HZ1 A:LYS464 2.6 95.0 1.0 O A:HOH1309 2.8 51.5 1.0 HH22 A:ARG460 2.9 53.0 1.0 O A:HOH1008 3.1 55.6 1.0 HH12 A:ARG460 3.3 49.4 1.0 NZ A:LYS487 3.3 63.6 1.0 NZ A:LYS464 3.5 79.1 1.0 HZ3 A:LYS487 3.6 76.4 1.0 HZ2 A:LYS487 3.7 76.4 1.0 HZ3 A:LYS464 3.7 95.0 1.0 NH2 A:ARG460 3.7 44.2 1.0 HZ2 A:LYS464 3.8 95.0 1.0 NH1 A:ARG460 4.0 41.2 1.0 HE3 A:LYS487 4.1 66.3 1.0 HH21 A:ARG460 4.3 53.0 1.0 CE A:LYS487 4.3 55.2 1.0 CZ A:ARG460 4.4 38.1 1.0 HE3 A:LYS464 4.5 81.8 1.0 CE A:LYS464 4.5 68.1 1.0 HD2 A:LYS487 4.6 50.7 1.0 HE2 A:LYS464 4.7 81.8 1.0 HH11 A:ARG460 4.8 49.4 1.0

H.M.Kropp, S.Ludmann, K.Diederichs, K.Betz, A.Marx. Structural Basis For the Recognition of Deaminated Nucleobases By An Archaeal Dna Polymerase. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 34486208
DOI: 10.1002/CBIC.202100306