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

Enzymatic activity of 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;

Protein crystallography data

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

Bromine Binding Sites:

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 7om3

Go back to Bromine Binding Sites List in 7om3
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 7om3

Go back to Bromine Binding Sites List in 7om3
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

Reference:

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
Page generated: Thu Jul 11 04:16:07 2024

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